From LHU004 at e.ntu.edu.sg Sun Mar 4 05:34:33 2018 From: LHU004 at e.ntu.edu.sg (#HU LEI#) Date: Sun, 4 Mar 2018 13:34:33 +0000 Subject: [CIG-SEISMO] Why SPECFEM2D can't deal with adjoint simulation with all boundaries set free? In-Reply-To: References: , Message-ID: Hi, Prof.Komatitsch and who it may concern, After typing the commands which you suggested and trying another run with all boundaries set free, I found that the error message in the screen-shot below is all that I got. I exported the simulation log into a file which is attached in this email and named as 'running_log'. Also I attached the files in 'EXAMPLES/LuoYang_fluid_solid_kernel' that I used for the simulation. >From this file, I found that the forward modeling is good while the adjoint simulation stopped at time step = 1000, which indicates that the adjoint simulation did run for a period, but met a problem somewhere during its process. I strongly suggest that you may run this 'EXAMPLES/LuoYang_fluid_solid_kernel' case on your own laptop with your own case files in your SPECFEM2D and change STACEY to FREE to see if you also met this problem, just in case that I might have made mistakes with some setting, if you haven't done that. Thanks and warm regards, Ray [cid:02571d22-c227-463d-838c-bb48b6688463] ________________________________ From: Dimitri Komatitsch Sent: Friday, March 2, 2018 6:38 AM To: #HU LEI# Subject: Re: Why SPECFEM2D can't deal with adjoint simulation with all boundaries set free? Dear Ray, Thanks for your message. Free boundaries on all the sides of a model are rarely used in geophysics, thus it is probably a minor bug just coming from the fact that such a configuration has never been tested by anybody else. Probably easy to fix. Could you type this: ./configure --enable-debug make clean make all and try the run again, and let us know if you get any useful error message at run time? Also, could you please send your message below to the mailing list? (cig-seismo at geodynamics.org). Someone may know the answer. Thanks, Best regards, Dimitri. On 03/01/2018 08:34 AM, #HU LEI# wrote: > Hi, Prof.Komatitsch, > > > I am a PHD student from NANYANG TECHONOLOGICAL UNIVERSITY. I found that, > in the case of 'EXAMPLES/Luoyang_fluid_solid_kernal', SPECFEM2D can't > run properly if I change only all the four boundary conditions from > Stacey ABC to free. > > And I am curious about why. the images indicating the setting and error > is indicated below. > > Hope to hear from you soon. > > > Thanks and regards, > > > Ray > > > > -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr Dimitri Komatitsch komatitsch.free.fr CNRS Research Director (Directeur de Recherche CNRS) Laboratory of Mechanics and Acoustics, CNRS/University of Aix-Marseille, France (je suis français, vous pouvez m ... -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pastedImage.png Type: image/png Size: 90923 bytes Desc: pastedImage.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: running_log Type: application/octet-stream Size: 78546 bytes Desc: running_log URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: LuoYang_fluid_solid_kernel_free_boundaries.tar.gz Type: application/gzip Size: 11537 bytes Desc: LuoYang_fluid_solid_kernel_free_boundaries.tar.gz URL: From LHU004 at e.ntu.edu.sg Sun Mar 4 18:20:03 2018 From: LHU004 at e.ntu.edu.sg (#HU LEI#) Date: Mon, 5 Mar 2018 02:20:03 +0000 Subject: [CIG-SEISMO] Why SPECFEM2D can't deal with adjoint simulation with all boundaries set free? In-Reply-To: References: , Message-ID: Hi, Prof.Komatitsch and whom it may concern, After typing the commands which you suggested and trying another run with all boundaries set free, I found that the error message in the screen-shot below is all that I got. I exported the simulation log into a file which is attached in this email and named as 'running_log'. From this file, I found that the forward modeling is good while the adjoint simulation stopped at time step = 1000, which indicates that the adjoint simulation did run for a period, but met a problem somewhere during its process. I strongly suggest that you may first run this 'EXAMPLES/LuoYang_fluid_solid_kernel' case on your own laptop by setting 'STACEY_ABSORBING_CONDITIONS = .false.' in your SPECFEM2D to see if you also meet this problem, just in case that I might have made mistakes with some setting. Warm regards, Ray [https://outlook.office.com/owa/service.svc/s/GetFileAttachment?id=AAMkADY1YTk5NTlmLTk4ZWEtNGVmYS04YzkwLTZlZTYyYmFjMzEwZABGAAAAAACLRP8oPOz8RZpU%2B40JfAOoBwBoaJqhvzRZSrqLvSbQOhMFAAAAAAEJAABoaJqhvzRZSrqLvSbQOhMFAAGT81WhAAABEgAQAKMGNZSb1GdLkhaVgejOryw%3D&X-OWA-CANARY=iaIYowiveUSiP8GwwwCYEkDcdT4-gtUYGyS1_AahLX2kSpotOoSVpeV9Ww8aknfXNw5QyU5-BNA.&isImagePreview=True] ________________________________ From: Dimitri Komatitsch Sent: Friday, March 2, 2018 6:38 AM To: #HU LEI# Subject: Re: Why SPECFEM2D can't deal with adjoint simulation with all boundaries set free? Dear Ray, Thanks for your message. Free boundaries on all the sides of a model are rarely used in geophysics, thus it is probably a minor bug just coming from the fact that such a configuration has never been tested by anybody else. Probably easy to fix. Could you type this: ./configure --enable-debug make clean make all and try the run again, and let us know if you get any useful error message at run time? Also, could you please send your message below to the mailing list? (cig-seismo at geodynamics.org). Someone may know the answer. Thanks, Best regards, Dimitri. On 03/01/2018 08:34 AM, #HU LEI# wrote: > Hi, Prof.Komatitsch, > > > I am a PHD student from NANYANG TECHONOLOGICAL UNIVERSITY. I found that, > in the case of 'EXAMPLES/Luoyang_fluid_solid_kernal', SPECFEM2D can't > run properly if I change only all the four boundary conditions from > Stacey ABC to free. > > And I am curious about why. the images indicating the setting and error > is indicated below. > > Hope to hear from you soon. > > > Thanks and regards, > > > Ray > > > > -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr Dimitri Komatitsch komatitsch.free.fr CNRS Research Director (Directeur de Recherche CNRS) Laboratory of Mechanics and Acoustics, CNRS/University of Aix-Marseille, France (je suis français, vous pouvez m ... -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: running_log Type: application/octet-stream Size: 78546 bytes Desc: running_log URL: From aflinders at usgs.gov Tue Mar 6 09:55:13 2018 From: aflinders at usgs.gov (Flinders, Ashton) Date: Tue, 6 Mar 2018 09:55:13 -0800 Subject: [CIG-SEISMO] RTM specfm3d Message-ID: Anyone know if there is a published paper out there using specfm3d for RTM? thanks! -ashton -- Ashton F. Flinders, Ph.D U.S. Geological Survey 345 Middlefield Road Menlo Park, CA 94025 (650) 329-5050 -------------- next part -------------- An HTML attachment was scrubbed... URL: From komatitsch at lma.cnrs-mrs.fr Wed Mar 7 12:03:22 2018 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Wed, 7 Mar 2018 21:03:22 +0100 Subject: [CIG-SEISMO] RTM specfm3d In-Reply-To: References: Message-ID: <648f5780-6428-0f23-848b-8b2f11633de9@lma.cnrs-mrs.fr> Yes :-) @Article{DoYiVaTr10, Title = {On the connection between artifact filtering in reverse-time migration and adjoint tomography}, Author = {H. Douma and D. Yingst and I. Vasconcelos and J. Tromp}, Journal = Geophysics, Year = {2010}, Number = {6}, Pages = {S219-S223}, Volume = {75}} Best regards, Dimitri. On 03/06/2018 06:55 PM, Flinders, Ashton wrote: > Anyone know if there is a published paper out there using specfm3d for RTM? > > thanks! > -ashton > > -- > Ashton F. Flinders, Ph.D > U.S. Geological Survey > 345 Middlefield Road > Menlo Park, CA 94025 > (650) 329-5050 > > > > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr From alexis.bottero at gmail.com Fri Mar 9 06:06:54 2018 From: alexis.bottero at gmail.com (Alexis Bottero) Date: Fri, 9 Mar 2018 15:06:54 +0100 Subject: [CIG-SEISMO] Unresolved issues in specfem2d Message-ID: Hello everybody, I just commited a new folder called unresolvedBugs in specfem2d/EXAMPLES in order to gather all unresolved issues. The examples there are supposed to be simple, working, not containing useless features and have a minimum computational cost. I think that it can be useful for the community. For the moment I have added five cases that I have detected during my PhD. 1. bugPMLs_1 : Strong spurious reflections from the PMLs in some particular cases. 2. bugPMLs_2 : This bug (the worse by far) occurs in simulations with many time steps (>100000) and viscoelastic media with PMLs. Even if the PMLs are not in contact with the viscoelastic part! 3. bugPMLs_3 : Small bug when using PMLs with the internal mesher in some particular configurations. 4. bugSource : Strange (small) unphysical dispersion in acoustic domains. 5. bugViscoelasticity : This shows a gradual, very slow explosion in viscoelastic media. This issue is probably not a "bug" strictly speaking but may arise from the inconsistency of memory variables between two adjacent elements. The real problem occurs when considering also acoustic media in the same run. In that case the instability occurs faster. Do not hesitate to take a look at these examples and add yours! Thank you very much! Cheers Alexis Bottero, PhD student Tel: +0033 6 95 17 00 97 Waves and imaging Laboratoire de Mécanique et d'Acoustique de Marseille -------------- next part -------------- An HTML attachment was scrubbed... URL: From komatitsch at lma.cnrs-mrs.fr Fri Mar 9 08:56:20 2018 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Fri, 9 Mar 2018 17:56:20 +0100 Subject: [CIG-SEISMO] Unresolved issues in specfem2d In-Reply-To: References: Message-ID: <187a8c0f-e9a6-6c6e-a4e4-0b89c5771cb9@lma.cnrs-mrs.fr> Hi Alexis, Hi all, Thanks a lot. Very useful! I will have a look at 4 and 5. (in two or three weeks) 4 could be classical Hourglass-like modes (see http://www.uni-magdeburg.de/ifme/zeitschrift_tm/2014_Heft2/01_Schmicker_et_al.pdf), i.e. not a bug but a property of finite element methods. Bernhard Schuberth had noticed that in 2003 already (in the 3D code). 5 could be related to the viscoelastic memory variables being in L^2 rather than H^1, if so, same thing, not a bug but a "feature". Zhinan, could your student have a look at 1, 2 and 3? Thanks! Best wishes, Dimitri. On 03/09/2018 03:06 PM, Alexis Bottero wrote: > Hello everybody, > I just commited a new folder called unresolvedBugs in specfem2d/EXAMPLES > in order to gather all unresolved issues. The examples there are > supposed to be simple, working, not containing useless features and have > a minimum computational cost. > I think that it can be useful for the community. > > For the moment I have added five cases that I have detected during my PhD. > > 1. bugPMLs_1 : Strong spurious reflections from the PMLs in some > particular cases. > > 2. bugPMLs_2 : This bug (the worse by far) occurs in simulations with > many time steps (>100000) and viscoelastic media with PMLs. Even if the > PMLs are not in contact with the viscoelastic part! > > 3. bugPMLs_3 : Small bug when using PMLs with the internal mesher in > some particular configurations. > > 4. bugSource : Strange (small) unphysical dispersion in acoustic domains. > > 5. bugViscoelasticity : This shows a gradual, very slow explosion in > viscoelastic media. This issue is probably not a "bug" strictly speaking > but may arise from the inconsistency of memory variables between two > adjacent elements. The real problem occurs when considering also > acoustic media in the same run. In that case the instability occurs faster. > > Do not hesitate to take a look at these examples and add yours! > > Thank you very much! > > Cheers > > Alexis Bottero, PhD student > Tel: +0033 6 95 17 00 97 > Waves and imaging > Laboratoire de Mécanique et d'Acoustique de Marseille > > > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr From tjesser at ucdavis.edu Wed Mar 14 14:43:14 2018 From: tjesser at ucdavis.edu (Tyler Esser) Date: Wed, 14 Mar 2018 14:43:14 -0700 Subject: [CIG-SEISMO] Using Github Protected Branches Message-ID: This conversation was originally started with the SPECFEM Admins Github team. There were requests from other people to join the discussion so we decided to post it to the mailing list. Tyler Esser ---------- Forwarded message ---------- From: Tyler Esser Date: Fri, Mar 9, 2018 at 1:05 PM Subject: [geodynamics/specfem-admins] Using Github's protected branches (#1) To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com> Cc: Tyler Esser , Your activity < your_activity at noreply.github.com> Hi SPECFEM admins, CIG recently had a discussion with a CIG project dev about protecting branches from certain actions and discovered that Github has a protected branch feature. The option seems to be a good general practice and so I wanted to ask what you thought about turning it on for SPECFEM master branches. Github documentation for the feature is here: https://help.github.com/articles/about-protected-branches/ Mostly we were interested in preventing accidental deletion or altering git history with force pushing, but there are other options that may be worth using. See the attached picture. [image: protectedbranches] The Github team interface seemed the best way to contact you when dealing with Github administration issues. Please let me know if you would have preferred a different method. Tyler Esser — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub , or mute the thread . ---------- Forwarded message ---------- From: daniel peter Date: Fri, Mar 9, 2018 at 11:20 PM Subject: Re: [geodynamics/specfem-admins] Using Github's protected branches (#1) To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com> Cc: Tyler Esser , Author Hi Tyler, probably David has a better answer, since he put most of this already in place. I think we already protect the master branch in all SPECFEM repos. no pull requests are allowed on master by users. only admins are allowed to push/merge commits to it. so the most important safeguards from above are already in place. as it seems to work pretty well so far for us, i don't see much need for further restrictions. best wishes, daniel — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or mute the thread . ---------- Forwarded message ---------- From: Tyler Esser Date: Mon, Mar 12, 2018 at 5:18 PM Subject: Re: [geodynamics/specfem-admins] Using Github's protected branches (#1) To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com> Cc: Tyler Esser , Your activity < your_activity at noreply.github.com> When you say the master branch is already protected, are you referring to Github branch protection or are you referring to the Github teams SPECFEM Admins and SPECFEM Devs being exclusive? As far as I can tell, the people in those teams have permission to push, merge, force push, and/or delete any branch in the SPECFEM repos. If I understand you correctly, that's fine because everyone in those teams is already trusted. Is that correct? Tyler — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub , or mute the thread . ---------- Forwarded message ---------- From: daniel peter Date: Tue, Mar 13, 2018 at 1:46 AM Subject: Re: [geodynamics/specfem-admins] Using Github's protected branches (#1) To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com> Cc: Tyler Esser , Author the master branch is protected by buildbot, which David set up. every pull request goes through buildbot which will close it automatically if the request is towards the master branch. and yes, only those team admins are allowed to push, merge, etc. on the master/devel branch which is fine, as they probably know what they're doing :) -daniel — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or mute the thread . ---------- Forwarded message ---------- From: Tyler Esser Date: Wed, Mar 14, 2018 at 12:09 PM Subject: Re: [geodynamics/specfem-admins] Using Github's protected branches (#1) To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com> Cc: Tyler Esser , Your activity < your_activity at noreply.github.com> There's been a few requests to join this discussion. Do you mind if I copy this thread to the cig-seismo mailing list? Tyler — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub , or mute the thread . ---------- Forwarded message ---------- From: daniel peter Date: Wed, Mar 14, 2018 at 1:49 PM Subject: Re: [geodynamics/specfem-admins] Using Github's protected branches (#1) To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com> Cc: Tyler Esser , Author sure, let's see some more opinions :) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or mute the thread . -------------- next part -------------- An HTML attachment was scrubbed... URL: From rene.gassmoeller at mailbox.org Wed Mar 14 15:42:43 2018 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Wed, 14 Mar 2018 15:42:43 -0700 Subject: [CIG-SEISMO] Using Github Protected Branches In-Reply-To: References: Message-ID: <08db03b1-1770-2fb5-cf18-7163c7cac5c9@mailbox.org> Hi all, let me join in on this as one of the maintainers of the ASPECT mantle convection code. We had the branch protection on Github enabled for our master branch for several years now (in addition to the automatic tester that tests pull requests). There are two scenarios in which this can be helpful: One of your project's developers (no admin, otherwise you are out of luck in any case) account is hacked. They have write access to the repository, but can not change their rights on github. Without a protected master branch they can force-push to that branch or more dangerously reset it and delete the complete project history. You would then need to restore it from a local copy somewhere (hopefully you have one). They can of course still merge bogus pull requests (unless you add the required status checks protection), but all of that can be reverted. The other scenario does not even need evil intentions. Let's assume you are in a hurry to fix a bug and you do this on the master branch (you should be on a feature branch, but the next seminar is in 5 minutes and you can create the branch later). You do not finish the fix, but want to save the history so you push to your personal github repo for now to create the pull request later. 'git push origin master'. Unfortunately you did this on the cluster where you cloned the repository and you cloned from the main repository instead of your own, so you mess up the master branch. You walk away and your repo is in an unusable state until you return or somebody notices. Every user who updated in the meantime gets an unusable version, and worse, they will get a conflict unless you fix up the master branch with a new commit (instead of reset it) and keep the messed up commit in there. Now I admit these cases need bad luck, but that can happen to anyone (even experienced admins). While we had no attempts to delete our master branch yet, people did accidentally upload branches to the main repository without realizing and having the branch protection on just gives us some extra peace of mind. Of course that is the decision of every project, but I personally feel a protected master branch should be included in the set of best practices. Cheers, Rene On 03/14/2018 02:43 PM, Tyler Esser wrote: > This conversation was originally started with the SPECFEM Admins > Github team. There were requests from other people to join the > discussion so we decided to post it to the mailing list. > > > Tyler Esser > > > ---------- Forwarded message ---------- > From: *Tyler Esser* > > Date: Fri, Mar 9, 2018 at 1:05 PM > Subject: [geodynamics/specfem-admins] Using Github's protected > branches (#1) > To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com > > > Cc: Tyler Esser >, > Your activity > > > > Hi SPECFEM admins, > > CIG recently had a discussion with a CIG project dev about protecting > branches from certain actions and discovered that Github has a > protected branch feature. The option seems to be a good general > practice and so I wanted to ask what you thought about turning it on > for SPECFEM master branches. Github documentation for the feature is > here: https://help.github.com/articles/about-protected-branches/ > > > Mostly we were interested in preventing accidental deletion or > altering git history with force pushing, but there are other options > that may be worth using. See the attached picture. > > protectedbranches > > > The Github team interface seemed the best way to contact you when > dealing with Github administration issues. Please let me know if you > would have preferred a different method. > > Tyler Esser > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > . > > > > ---------- Forwarded message ---------- > From: *daniel peter* > > Date: Fri, Mar 9, 2018 at 11:20 PM > Subject: Re: [geodynamics/specfem-admins] Using Github's protected > branches (#1) > To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com > > > Cc: Tyler Esser >, > Author > > > > Hi Tyler, > > probably David has a better answer, since he put most of this already > in place. I think we already protect the master branch in all SPECFEM > repos. no pull requests are allowed on master by users. only admins > are allowed to push/merge commits to it. so the most important > safeguards from above are already in place. > > as it seems to work pretty well so far for us, i don't see much need > for further restrictions. > > best wishes, > daniel > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > . > > > > ---------- Forwarded message ---------- > From: *Tyler Esser* > > Date: Mon, Mar 12, 2018 at 5:18 PM > Subject: Re: [geodynamics/specfem-admins] Using Github's protected > branches (#1) > To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com > > > Cc: Tyler Esser >, > Your activity > > > > When you say the master branch is already protected, are you referring > to Github branch protection or are you referring to the Github teams > SPECFEM Admins > and > SPECFEM Devs > > being exclusive? > > As far as I can tell, the people in those teams have permission to > push, merge, force push, and/or delete any branch in the SPECFEM > repos. If I understand you correctly, that's fine because everyone in > those teams is already trusted. Is that correct? > > Tyler > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > . > > > > ---------- Forwarded message ---------- > From: *daniel peter* > > Date: Tue, Mar 13, 2018 at 1:46 AM > Subject: Re: [geodynamics/specfem-admins] Using Github's protected > branches (#1) > To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com > > > Cc: Tyler Esser >, > Author > > > > the master branch is protected by buildbot, which David set up. every > pull request goes through buildbot which will close it automatically > if the request is towards the master branch. > > and yes, only those team admins are allowed to push, merge, etc. on > the master/devel branch which is fine, as they probably know what > they're doing :) > > -daniel > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > . > > > > ---------- Forwarded message ---------- > From: *Tyler Esser* > > Date: Wed, Mar 14, 2018 at 12:09 PM > Subject: Re: [geodynamics/specfem-admins] Using Github's protected > branches (#1) > To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com > > > Cc: Tyler Esser >, > Your activity > > > > There's been a few requests to join this discussion. Do you mind if I > copy this thread to the cig-seismo mailing list? > > Tyler > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > . > > > > ---------- Forwarded message ---------- > From: *daniel peter* > > Date: Wed, Mar 14, 2018 at 1:49 PM > Subject: Re: [geodynamics/specfem-admins] Using Github's protected > branches (#1) > To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com > > > Cc: Tyler Esser >, > Author > > > > sure, let's see some more opinions :) > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > . > > > > > > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo -- Rene Gassmoeller http://www.math.colostate.edu/~gassmoel/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tjesser at ucdavis.edu Wed Mar 14 16:08:55 2018 From: tjesser at ucdavis.edu (Tyler Esser) Date: Wed, 14 Mar 2018 16:08:55 -0700 Subject: [CIG-SEISMO] Using Github Protected Branches In-Reply-To: <08db03b1-1770-2fb5-cf18-7163c7cac5c9@mailbox.org> References: <08db03b1-1770-2fb5-cf18-7163c7cac5c9@mailbox.org> Message-ID: Talking with Louise and Lorraine, it seems that CIG's position is that anything that protects against accidents or compromised accounts is seen as best practices. Rene mentioned that having an admin make a mistake means you're out of luck, but protected branches do have the option to enforce their settings even on admins. Have the Aspect devs discussed flipping that switch and applying the limitations to admins as well? Tyler On Wed, Mar 14, 2018 at 3:42 PM, Rene Gassmoeller < rene.gassmoeller at mailbox.org> wrote: > Hi all, > > let me join in on this as one of the maintainers of the ASPECT mantle > convection code. We had the branch protection on Github enabled for our > master branch for several years now (in addition to the automatic tester > that tests pull requests). There are two scenarios in which this can be > helpful: > > One of your project's developers (no admin, otherwise you are out of luck > in any case) account is hacked. They have write access to the repository, > but can not change their rights on github. Without a protected master > branch they can force-push to that branch or more dangerously reset it and > delete the complete project history. You would then need to restore it from > a local copy somewhere (hopefully you have one). They can of course still > merge bogus pull requests (unless you add the required status checks > protection), but all of that can be reverted. > > The other scenario does not even need evil intentions. Let's assume you > are in a hurry to fix a bug and you do this on the master branch (you > should be on a feature branch, but the next seminar is in 5 minutes and you > can create the branch later). You do not finish the fix, but want to save > the history so you push to your personal github repo for now to create the > pull request later. 'git push origin master'. Unfortunately you did this on > the cluster where you cloned the repository and you cloned from the main > repository instead of your own, so you mess up the master branch. You walk > away and your repo is in an unusable state until you return or somebody > notices. Every user who updated in the meantime gets an unusable version, > and worse, they will get a conflict unless you fix up the master branch > with a new commit (instead of reset it) and keep the messed up commit in > there. > > Now I admit these cases need bad luck, but that can happen to anyone (even > experienced admins). While we had no attempts to delete our master branch > yet, people did accidentally upload branches to the main repository without > realizing and having the branch protection on just gives us some extra > peace of mind. Of course that is the decision of every project, but I > personally feel a protected master branch should be included in the set of > best practices. > > Cheers, > > Rene > > On 03/14/2018 02:43 PM, Tyler Esser wrote: > > This conversation was originally started with the SPECFEM Admins Github > team. There were requests from other people to join the discussion so we > decided to post it to the mailing list. > > > Tyler Esser > > > ---------- Forwarded message ---------- > From: Tyler Esser > Date: Fri, Mar 9, 2018 at 1:05 PM > Subject: [geodynamics/specfem-admins] Using Github's protected branches > (#1) > To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com> > Cc: Tyler Esser , Your activity < > your_activity at noreply.github.com> > > > Hi SPECFEM admins, > > CIG recently had a discussion with a CIG project dev about protecting > branches from certain actions and discovered that Github has a protected > branch feature. The option seems to be a good general practice and so I > wanted to ask what you thought about turning it on for SPECFEM master > branches. Github documentation for the feature is here: > https://help.github.com/articles/about-protected-branches/ > > Mostly we were interested in preventing accidental deletion or altering > git history with force pushing, but there are other options that may be > worth using. See the attached picture. > > [image: protectedbranches] > > > The Github team interface seemed the best way to contact you when dealing > with Github administration issues. Please let me know if you would have > preferred a different method. > > Tyler Esser > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > > . > > > ---------- Forwarded message ---------- > From: daniel peter > Date: Fri, Mar 9, 2018 at 11:20 PM > Subject: Re: [geodynamics/specfem-admins] Using Github's protected > branches (#1) > To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com> > Cc: Tyler Esser , Author > > > Hi Tyler, > > probably David has a better answer, since he put most of this already in > place. I think we already protect the master branch in all SPECFEM repos. > no pull requests are allowed on master by users. only admins are allowed to > push/merge commits to it. so the most important safeguards from above are > already in place. > > as it seems to work pretty well so far for us, i don't see much need for > further restrictions. > > best wishes, > daniel > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > > . > > > ---------- Forwarded message ---------- > From: Tyler Esser > Date: Mon, Mar 12, 2018 at 5:18 PM > Subject: Re: [geodynamics/specfem-admins] Using Github's protected > branches (#1) > To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com> > Cc: Tyler Esser , Your activity < > your_activity at noreply.github.com> > > > When you say the master branch is already protected, are you referring to > Github branch protection or are you referring to the Github teams SPECFEM > Admins > and SPECFEM Devs > > being exclusive? > > As far as I can tell, the people in those teams have permission to push, > merge, force push, and/or delete any branch in the SPECFEM repos. If I > understand you correctly, that's fine because everyone in those teams is > already trusted. Is that correct? > > Tyler > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > > . > > > ---------- Forwarded message ---------- > From: daniel peter > Date: Tue, Mar 13, 2018 at 1:46 AM > Subject: Re: [geodynamics/specfem-admins] Using Github's protected > branches (#1) > To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com> > Cc: Tyler Esser , Author > > > the master branch is protected by buildbot, which David set up. every pull > request goes through buildbot which will close it automatically if the > request is towards the master branch. > > and yes, only those team admins are allowed to push, merge, etc. on the > master/devel branch which is fine, as they probably know what they're doing > :) > > -daniel > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > > . > > > ---------- Forwarded message ---------- > From: Tyler Esser > Date: Wed, Mar 14, 2018 at 12:09 PM > Subject: Re: [geodynamics/specfem-admins] Using Github's protected > branches (#1) > To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com> > Cc: Tyler Esser , Your activity < > your_activity at noreply.github.com> > > > There's been a few requests to join this discussion. Do you mind if I copy > this thread to the cig-seismo mailing list? > > Tyler > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > > . > > > ---------- Forwarded message ---------- > From: daniel peter > Date: Wed, Mar 14, 2018 at 1:49 PM > Subject: Re: [geodynamics/specfem-admins] Using Github's protected > branches (#1) > To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com> > Cc: Tyler Esser , Author > > > sure, let's see some more opinions :) > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > > . > > > > > _______________________________________________ > CIG-SEISMO mailing listCIG-SEISMO at geodynamics.orghttp://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > > > -- > Rene Gassmoellerhttp://www.math.colostate.edu/~gassmoel/ > > > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > -------------- next part -------------- An HTML attachment was scrubbed... URL: From komatitsch at lma.cnrs-mrs.fr Wed Mar 14 16:11:50 2018 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Thu, 15 Mar 2018 00:11:50 +0100 Subject: [CIG-SEISMO] Using Github Protected Branches In-Reply-To: <08db03b1-1770-2fb5-cf18-7163c7cac5c9@mailbox.org> References: <08db03b1-1770-2fb5-cf18-7163c7cac5c9@mailbox.org> Message-ID: <30e76d8c-750a-65c3-05e2-5cd586abc7dd@lma.cnrs-mrs.fr> Hi all, Thanks for the discussion. I went to https://help.github.com/articles/about-protected-branches but it is not clear to me how one then makes changes in the protected branch (for instance to release a new version of the code by merging "devel" into "master", which we do a few times a year). If that can still be done very easily (if so, how?), then why not; if that becomes complex, then it is likely too complex, at least for SPECFEM. Thanks, Best regards, Dimitri. On 03/14/2018 11:42 PM, Rene Gassmoeller wrote: > Hi all, > > let me join in on this as one of the maintainers of the ASPECT mantle > convection code. We had the branch protection on Github enabled for our > master branch for several years now (in addition to the automatic tester > that tests pull requests). There are two scenarios in which this can be > helpful: > > One of your project's developers (no admin, otherwise you are out of > luck in any case) account is hacked. They have write access to the > repository, but can not change their rights on github. Without a > protected master branch they can force-push to that branch or more > dangerously reset it and delete the complete project history. You would > then need to restore it from a local copy somewhere (hopefully you have > one). They can of course still merge bogus pull requests (unless you add > the required status checks protection), but all of that can be reverted. > > The other scenario does not even need evil intentions. Let's assume you > are in a hurry to fix a bug and you do this on the master branch (you > should be on a feature branch, but the next seminar is in 5 minutes and > you can create the branch later). You do not finish the fix, but want to > save the history so you push to your personal github repo for now to > create the pull request later. 'git push origin master'. Unfortunately > you did this on the cluster where you cloned the repository and you > cloned from the main repository instead of your own, so you mess up the > master branch. You walk away and your repo is in an unusable state until > you return or somebody notices. Every user who updated in the meantime > gets an unusable version, and worse, they will get a conflict unless you > fix up the master branch with a new commit (instead of reset it) and > keep the messed up commit in there. > > Now I admit these cases need bad luck, but that can happen to anyone > (even experienced admins). While we had no attempts to delete our master > branch yet, people did accidentally upload branches to the main > repository without realizing and having the branch protection on just > gives us some extra peace of mind. Of course that is the decision of > every project, but I personally feel a protected master branch should be > included in the set of best practices. > > Cheers, > > Rene > > > On 03/14/2018 02:43 PM, Tyler Esser wrote: >> This conversation was originally started with the SPECFEM Admins >> Github team. There were requests from other people to join the >> discussion so we decided to post it to the mailing list. >> >> >> Tyler Esser >> >> >> ---------- Forwarded message ---------- >> From: *Tyler Esser* > > >> Date: Fri, Mar 9, 2018 at 1:05 PM >> Subject: [geodynamics/specfem-admins] Using Github's protected >> branches (#1) >> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >> > >> Cc: Tyler Esser >, >> Your activity > > >> >> >> Hi SPECFEM admins, >> >> CIG recently had a discussion with a CIG project dev about protecting >> branches from certain actions and discovered that Github has a >> protected branch feature. The option seems to be a good general >> practice and so I wanted to ask what you thought about turning it on >> for SPECFEM master branches. Github documentation for the feature is >> here: https://help.github.com/articles/about-protected-branches/ >> >> >> Mostly we were interested in preventing accidental deletion or >> altering git history with force pushing, but there are other options >> that may be worth using. See the attached picture. >> >> protectedbranches >> >> >> The Github team interface seemed the best way to contact you when >> dealing with Github administration issues. Please let me know if you >> would have preferred a different method. >> >> Tyler Esser >> >> — >> You are receiving this because you are subscribed to this thread. >> Reply to this email directly, view it on GitHub >> , >> or mute the thread >> . >> >> >> >> ---------- Forwarded message ---------- >> From: *daniel peter* > > >> Date: Fri, Mar 9, 2018 at 11:20 PM >> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >> branches (#1) >> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >> > >> Cc: Tyler Esser >, >> Author > >> >> >> Hi Tyler, >> >> probably David has a better answer, since he put most of this already >> in place. I think we already protect the master branch in all SPECFEM >> repos. no pull requests are allowed on master by users. only admins >> are allowed to push/merge commits to it. so the most important >> safeguards from above are already in place. >> >> as it seems to work pretty well so far for us, i don't see much need >> for further restrictions. >> >> best wishes, >> daniel >> >> — >> You are receiving this because you authored the thread. >> Reply to this email directly, view it on GitHub >> , >> or mute the thread >> . >> >> >> >> ---------- Forwarded message ---------- >> From: *Tyler Esser* > > >> Date: Mon, Mar 12, 2018 at 5:18 PM >> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >> branches (#1) >> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >> > >> Cc: Tyler Esser >, >> Your activity > > >> >> >> When you say the master branch is already protected, are you referring >> to Github branch protection or are you referring to the Github teams >> SPECFEM Admins >> and >> SPECFEM Devs >> >> being exclusive? >> >> As far as I can tell, the people in those teams have permission to >> push, merge, force push, and/or delete any branch in the SPECFEM >> repos. If I understand you correctly, that's fine because everyone in >> those teams is already trusted. Is that correct? >> >> Tyler >> >> — >> You are receiving this because you are subscribed to this thread. >> Reply to this email directly, view it on GitHub >> , >> or mute the thread >> . >> >> >> >> ---------- Forwarded message ---------- >> From: *daniel peter* > > >> Date: Tue, Mar 13, 2018 at 1:46 AM >> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >> branches (#1) >> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >> > >> Cc: Tyler Esser >, >> Author > >> >> >> the master branch is protected by buildbot, which David set up. every >> pull request goes through buildbot which will close it automatically >> if the request is towards the master branch. >> >> and yes, only those team admins are allowed to push, merge, etc. on >> the master/devel branch which is fine, as they probably know what >> they're doing :) >> >> -daniel >> >> — >> You are receiving this because you authored the thread. >> Reply to this email directly, view it on GitHub >> , >> or mute the thread >> . >> >> >> >> ---------- Forwarded message ---------- >> From: *Tyler Esser* > > >> Date: Wed, Mar 14, 2018 at 12:09 PM >> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >> branches (#1) >> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >> > >> Cc: Tyler Esser >, >> Your activity > > >> >> >> There's been a few requests to join this discussion. Do you mind if I >> copy this thread to the cig-seismo mailing list? >> >> Tyler >> >> — >> You are receiving this because you are subscribed to this thread. >> Reply to this email directly, view it on GitHub >> , >> or mute the thread >> . >> >> >> >> ---------- Forwarded message ---------- >> From: *daniel peter* > > >> Date: Wed, Mar 14, 2018 at 1:49 PM >> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >> branches (#1) >> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >> > >> Cc: Tyler Esser >, >> Author > >> >> >> sure, let's see some more opinions :) >> >> — >> You are receiving this because you authored the thread. >> Reply to this email directly, view it on GitHub >> , >> or mute the thread >> . >> >> >> >> >> >> _______________________________________________ >> CIG-SEISMO mailing list >> CIG-SEISMO at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > > -- > Rene Gassmoeller > http://www.math.colostate.edu/~gassmoel/ > > > > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr From rene.gassmoeller at mailbox.org Wed Mar 14 16:13:47 2018 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Wed, 14 Mar 2018 16:13:47 -0700 Subject: [CIG-SEISMO] Using Github Protected Branches In-Reply-To: References: <08db03b1-1770-2fb5-cf18-7163c7cac5c9@mailbox.org> Message-ID: <212721be-12f5-7a5f-0c2c-1044e48a636a@mailbox.org> Oh, I was not clear about that. The options are enabled for admins as well (no force push, no deletions of the master branch), but if you are an admin you can remove the protected branch feature on github, so if you are hacked then you are out of luck. It protects me as an admin from my own mistakes (which inevitably happen), but it can not save me if somebody compromises my account. I should also mention that the protected branch feature only keeps you from doing things that you would / should never want to do anyway. It just prevents accidents. Best, Rene On 03/14/2018 04:08 PM, Tyler Esser wrote: > Talking with Louise and Lorraine, it seems that CIG's position is that > anything that protects against accidents or compromised accounts is > seen as best practices. Rene mentioned that having an admin make a > mistake means you're out of luck, but protected branches do have the > option to enforce their settings even on admins. Have the Aspect devs > discussed flipping that switch and applying the limitations to admins > as well? > > > Tyler > > On Wed, Mar 14, 2018 at 3:42 PM, Rene Gassmoeller > > > wrote: > > Hi all, > > let me join in on this as one of the maintainers of the ASPECT > mantle convection code. We had the branch protection on Github > enabled for our master branch for several years now (in addition > to the automatic tester that tests pull requests). There are two > scenarios in which this can be helpful: > > One of your project's developers (no admin, otherwise you are out > of luck in any case) account is hacked. They have write access to > the repository, but can not change their rights on github. Without > a protected master branch they can force-push to that branch or > more dangerously reset it and delete the complete project history. > You would then need to restore it from a local copy somewhere > (hopefully you have one). They can of course still merge bogus > pull requests (unless you add the required status checks > protection), but all of that can be reverted. > > The other scenario does not even need evil intentions. Let's > assume you are in a hurry to fix a bug and you do this on the > master branch (you should be on a feature branch, but the next > seminar is in 5 minutes and you can create the branch later). You > do not finish the fix, but want to save the history so you push to > your personal github repo for now to create the pull request > later. 'git push origin master'. Unfortunately you did this on the > cluster where you cloned the repository and you cloned from the > main repository instead of your own, so you mess up the master > branch. You walk away and your repo is in an unusable state until > you return or somebody notices. Every user who updated in the > meantime gets an unusable version, and worse, they will get a > conflict unless you fix up the master branch with a new commit > (instead of reset it) and keep the messed up commit in there. > > Now I admit these cases need bad luck, but that can happen to > anyone (even experienced admins). While we had no attempts to > delete our master branch yet, people did accidentally upload > branches to the main repository without realizing and having the > branch protection on just gives us some extra peace of mind. Of > course that is the decision of every project, but I personally > feel a protected master branch should be included in the set of > best practices. > > Cheers, > > Rene > > > On 03/14/2018 02:43 PM, Tyler Esser wrote: >> This conversation was originally started with the SPECFEM Admins >> Github team. There were requests from other people to join the >> discussion so we decided to post it to the mailing list. >> >> >> Tyler Esser >> >> >> ---------- Forwarded message ---------- >> From: *Tyler Esser* > > >> Date: Fri, Mar 9, 2018 at 1:05 PM >> Subject: [geodynamics/specfem-admins] Using Github's protected >> branches (#1) >> To: geodynamics/specfem-admins <"SPECFEM >> Admins"@noreply.github.com > >> Cc: Tyler Esser > >, Your activity >> > > >> >> >> Hi SPECFEM admins, >> >> CIG recently had a discussion with a CIG project dev about >> protecting branches from certain actions and discovered that >> Github has a protected branch feature. The option seems to be a >> good general practice and so I wanted to ask what you thought >> about turning it on for SPECFEM master branches. Github >> documentation for the feature is here: >> https://help.github.com/articles/about-protected-branches/ >> >> >> Mostly we were interested in preventing accidental deletion or >> altering git history with force pushing, but there are other >> options that may be worth using. See the attached picture. >> >> protectedbranches >> >> >> The Github team interface seemed the best way to contact you when >> dealing with Github administration issues. Please let me know if >> you would have preferred a different method. >> >> Tyler Esser >> >> — >> You are receiving this because you are subscribed to this thread. >> Reply to this email directly, view it on GitHub >> , >> or mute the thread >> . >> >> >> >> ---------- Forwarded message ---------- >> From: *daniel peter* > > >> Date: Fri, Mar 9, 2018 at 11:20 PM >> Subject: Re: [geodynamics/specfem-admins] Using Github's >> protected branches (#1) >> To: geodynamics/specfem-admins <"SPECFEM >> Admins"@noreply.github.com > >> Cc: Tyler Esser > >, Author > > >> >> >> Hi Tyler, >> >> probably David has a better answer, since he put most of this >> already in place. I think we already protect the master branch in >> all SPECFEM repos. no pull requests are allowed on master by >> users. only admins are allowed to push/merge commits to it. so >> the most important safeguards from above are already in place. >> >> as it seems to work pretty well so far for us, i don't see much >> need for further restrictions. >> >> best wishes, >> daniel >> >> — >> You are receiving this because you authored the thread. >> Reply to this email directly, view it on GitHub >> , >> or mute the thread >> . >> >> >> >> ---------- Forwarded message ---------- >> From: *Tyler Esser* > > >> Date: Mon, Mar 12, 2018 at 5:18 PM >> Subject: Re: [geodynamics/specfem-admins] Using Github's >> protected branches (#1) >> To: geodynamics/specfem-admins <"SPECFEM >> Admins"@noreply.github.com > >> Cc: Tyler Esser > >, Your activity >> > > >> >> >> When you say the master branch is already protected, are you >> referring to Github branch protection or are you referring to the >> Github teams SPECFEM Admins >> >> and SPECFEM Devs >> >> being exclusive? >> >> As far as I can tell, the people in those teams have permission >> to push, merge, force push, and/or delete any branch in the >> SPECFEM repos. If I understand you correctly, that's fine because >> everyone in those teams is already trusted. Is that correct? >> >> Tyler >> >> — >> You are receiving this because you are subscribed to this thread. >> Reply to this email directly, view it on GitHub >> , >> or mute the thread >> . >> >> >> >> ---------- Forwarded message ---------- >> From: *daniel peter* > > >> Date: Tue, Mar 13, 2018 at 1:46 AM >> Subject: Re: [geodynamics/specfem-admins] Using Github's >> protected branches (#1) >> To: geodynamics/specfem-admins <"SPECFEM >> Admins"@noreply.github.com > >> Cc: Tyler Esser > >, Author > > >> >> >> the master branch is protected by buildbot, which David set up. >> every pull request goes through buildbot which will close it >> automatically if the request is towards the master branch. >> >> and yes, only those team admins are allowed to push, merge, etc. >> on the master/devel branch which is fine, as they probably know >> what they're doing :) >> >> -daniel >> >> — >> You are receiving this because you authored the thread. >> Reply to this email directly, view it on GitHub >> , >> or mute the thread >> . >> >> >> >> ---------- Forwarded message ---------- >> From: *Tyler Esser* > > >> Date: Wed, Mar 14, 2018 at 12:09 PM >> Subject: Re: [geodynamics/specfem-admins] Using Github's >> protected branches (#1) >> To: geodynamics/specfem-admins <"SPECFEM >> Admins"@noreply.github.com > >> Cc: Tyler Esser > >, Your activity >> > > >> >> >> There's been a few requests to join this discussion. Do you mind >> if I copy this thread to the cig-seismo mailing list? >> >> Tyler >> >> — >> You are receiving this because you are subscribed to this thread. >> Reply to this email directly, view it on GitHub >> , >> or mute the thread >> . >> >> >> >> ---------- Forwarded message ---------- >> From: *daniel peter* > > >> Date: Wed, Mar 14, 2018 at 1:49 PM >> Subject: Re: [geodynamics/specfem-admins] Using Github's >> protected branches (#1) >> To: geodynamics/specfem-admins <"SPECFEM >> Admins"@noreply.github.com > >> Cc: Tyler Esser > >, Author > > >> >> >> sure, let's see some more opinions :) >> >> — >> You are receiving this because you authored the thread. >> Reply to this email directly, view it on GitHub >> , >> or mute the thread >> . >> >> >> >> >> >> _______________________________________________ >> CIG-SEISMO mailing list >> CIG-SEISMO at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >> > > -- > Rene Gassmoeller > http://www.math.colostate.edu/~gassmoel/ > > > > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > > > > > > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo -- Rene Gassmoeller http://www.math.colostate.edu/~gassmoel/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jed at jedbrown.org Wed Mar 14 16:15:42 2018 From: jed at jedbrown.org (Jed Brown) Date: Wed, 14 Mar 2018 17:15:42 -0600 Subject: [CIG-SEISMO] Using Github Protected Branches In-Reply-To: <30e76d8c-750a-65c3-05e2-5cd586abc7dd@lma.cnrs-mrs.fr> References: <08db03b1-1770-2fb5-cf18-7163c7cac5c9@mailbox.org> <30e76d8c-750a-65c3-05e2-5cd586abc7dd@lma.cnrs-mrs.fr> Message-ID: <87efkm2qqp.fsf@jedbrown.org> Merging in that mode is a fast-forward so protection doesn't block it (for anyone authorized to push to the branch). Dimitri Komatitsch writes: > Hi all, > > Thanks for the discussion. > > I went to https://help.github.com/articles/about-protected-branches but > it is not clear to me how one then makes changes in the protected branch > (for instance to release a new version of the code by merging "devel" > into "master", which we do a few times a year). If that can still be > done very easily (if so, how?), then why not; if that becomes complex, > then it is likely too complex, at least for SPECFEM. > > Thanks, > Best regards, > Dimitri. > > On 03/14/2018 11:42 PM, Rene Gassmoeller wrote: >> Hi all, >> >> let me join in on this as one of the maintainers of the ASPECT mantle >> convection code. We had the branch protection on Github enabled for our >> master branch for several years now (in addition to the automatic tester >> that tests pull requests). There are two scenarios in which this can be >> helpful: >> >> One of your project's developers (no admin, otherwise you are out of >> luck in any case) account is hacked. They have write access to the >> repository, but can not change their rights on github. Without a >> protected master branch they can force-push to that branch or more >> dangerously reset it and delete the complete project history. You would >> then need to restore it from a local copy somewhere (hopefully you have >> one). They can of course still merge bogus pull requests (unless you add >> the required status checks protection), but all of that can be reverted. >> >> The other scenario does not even need evil intentions. Let's assume you >> are in a hurry to fix a bug and you do this on the master branch (you >> should be on a feature branch, but the next seminar is in 5 minutes and >> you can create the branch later). You do not finish the fix, but want to >> save the history so you push to your personal github repo for now to >> create the pull request later. 'git push origin master'. Unfortunately >> you did this on the cluster where you cloned the repository and you >> cloned from the main repository instead of your own, so you mess up the >> master branch. You walk away and your repo is in an unusable state until >> you return or somebody notices. Every user who updated in the meantime >> gets an unusable version, and worse, they will get a conflict unless you >> fix up the master branch with a new commit (instead of reset it) and >> keep the messed up commit in there. >> >> Now I admit these cases need bad luck, but that can happen to anyone >> (even experienced admins). While we had no attempts to delete our master >> branch yet, people did accidentally upload branches to the main >> repository without realizing and having the branch protection on just >> gives us some extra peace of mind. Of course that is the decision of >> every project, but I personally feel a protected master branch should be >> included in the set of best practices. >> >> Cheers, >> >> Rene >> >> >> On 03/14/2018 02:43 PM, Tyler Esser wrote: >>> This conversation was originally started with the SPECFEM Admins >>> Github team. There were requests from other people to join the >>> discussion so we decided to post it to the mailing list. >>> >>> >>> Tyler Esser >>> >>> >>> ---------- Forwarded message ---------- >>> From: *Tyler Esser* >> > >>> Date: Fri, Mar 9, 2018 at 1:05 PM >>> Subject: [geodynamics/specfem-admins] Using Github's protected >>> branches (#1) >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>> > >>> Cc: Tyler Esser >, >>> Your activity >> > >>> >>> >>> Hi SPECFEM admins, >>> >>> CIG recently had a discussion with a CIG project dev about protecting >>> branches from certain actions and discovered that Github has a >>> protected branch feature. The option seems to be a good general >>> practice and so I wanted to ask what you thought about turning it on >>> for SPECFEM master branches. Github documentation for the feature is >>> here: https://help.github.com/articles/about-protected-branches/ >>> >>> >>> Mostly we were interested in preventing accidental deletion or >>> altering git history with force pushing, but there are other options >>> that may be worth using. See the attached picture. >>> >>> protectedbranches >>> >>> >>> The Github team interface seemed the best way to contact you when >>> dealing with Github administration issues. Please let me know if you >>> would have preferred a different method. >>> >>> Tyler Esser >>> >>> — >>> You are receiving this because you are subscribed to this thread. >>> Reply to this email directly, view it on GitHub >>> , >>> or mute the thread >>> . >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: *daniel peter* >> > >>> Date: Fri, Mar 9, 2018 at 11:20 PM >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>> branches (#1) >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>> > >>> Cc: Tyler Esser >, >>> Author > >>> >>> >>> Hi Tyler, >>> >>> probably David has a better answer, since he put most of this already >>> in place. I think we already protect the master branch in all SPECFEM >>> repos. no pull requests are allowed on master by users. only admins >>> are allowed to push/merge commits to it. so the most important >>> safeguards from above are already in place. >>> >>> as it seems to work pretty well so far for us, i don't see much need >>> for further restrictions. >>> >>> best wishes, >>> daniel >>> >>> — >>> You are receiving this because you authored the thread. >>> Reply to this email directly, view it on GitHub >>> , >>> or mute the thread >>> . >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: *Tyler Esser* >> > >>> Date: Mon, Mar 12, 2018 at 5:18 PM >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>> branches (#1) >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>> > >>> Cc: Tyler Esser >, >>> Your activity >> > >>> >>> >>> When you say the master branch is already protected, are you referring >>> to Github branch protection or are you referring to the Github teams >>> SPECFEM Admins >>> and >>> SPECFEM Devs >>> >>> being exclusive? >>> >>> As far as I can tell, the people in those teams have permission to >>> push, merge, force push, and/or delete any branch in the SPECFEM >>> repos. If I understand you correctly, that's fine because everyone in >>> those teams is already trusted. Is that correct? >>> >>> Tyler >>> >>> — >>> You are receiving this because you are subscribed to this thread. >>> Reply to this email directly, view it on GitHub >>> , >>> or mute the thread >>> . >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: *daniel peter* >> > >>> Date: Tue, Mar 13, 2018 at 1:46 AM >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>> branches (#1) >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>> > >>> Cc: Tyler Esser >, >>> Author > >>> >>> >>> the master branch is protected by buildbot, which David set up. every >>> pull request goes through buildbot which will close it automatically >>> if the request is towards the master branch. >>> >>> and yes, only those team admins are allowed to push, merge, etc. on >>> the master/devel branch which is fine, as they probably know what >>> they're doing :) >>> >>> -daniel >>> >>> — >>> You are receiving this because you authored the thread. >>> Reply to this email directly, view it on GitHub >>> , >>> or mute the thread >>> . >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: *Tyler Esser* >> > >>> Date: Wed, Mar 14, 2018 at 12:09 PM >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>> branches (#1) >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>> > >>> Cc: Tyler Esser >, >>> Your activity >> > >>> >>> >>> There's been a few requests to join this discussion. Do you mind if I >>> copy this thread to the cig-seismo mailing list? >>> >>> Tyler >>> >>> — >>> You are receiving this because you are subscribed to this thread. >>> Reply to this email directly, view it on GitHub >>> , >>> or mute the thread >>> . >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: *daniel peter* >> > >>> Date: Wed, Mar 14, 2018 at 1:49 PM >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>> branches (#1) >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>> > >>> Cc: Tyler Esser >, >>> Author > >>> >>> >>> sure, let's see some more opinions :) >>> >>> — >>> You are receiving this because you authored the thread. >>> Reply to this email directly, view it on GitHub >>> , >>> or mute the thread >>> . >>> >>> >>> >>> >>> >>> _______________________________________________ >>> CIG-SEISMO mailing list >>> CIG-SEISMO at geodynamics.org >>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >> >> -- >> Rene Gassmoeller >> http://www.math.colostate.edu/~gassmoel/ >> >> >> >> _______________________________________________ >> CIG-SEISMO mailing list >> CIG-SEISMO at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >> > > -- > Dimitri Komatitsch, CNRS Research Director (DR CNRS) > Laboratory of Mechanics and Acoustics, Marseille, France > http://komatitsch.free.fr > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo From luet at Princeton.EDU Thu Mar 15 08:28:02 2018 From: luet at Princeton.EDU (David J. Luet) Date: Thu, 15 Mar 2018 15:28:02 +0000 Subject: [CIG-SEISMO] Using Github Protected Branches In-Reply-To: <87efkm2qqp.fsf@jedbrown.org> References: <08db03b1-1770-2fb5-cf18-7163c7cac5c9@mailbox.org> <30e76d8c-750a-65c3-05e2-5cd586abc7dd@lma.cnrs-mrs.fr> <87efkm2qqp.fsf@jedbrown.org> Message-ID: It looks like we can protect the branch master without affecting our workflow. For the most part, we have system in place to prevent people from modifying master, but we don't have a system to prevent a member of the "SPECFEM Admins" or "SPECFEM Developers" team to force push to the master branch. But all the branch protection does is protect us from one of the admins doing "git push --force" after trying, and failing, a regular, fast-forward "git push". Unless we want to remove the ability of the admins to push to the master branch, which would require a change in our workflow. The bottom line is that I think there is no harm in protecting master. It also makes sense to protect the branch devel against force-pushes. But buildbot rejects those anyway, but again not from the admins. David On 3/14/18, 7:27 PM, "CIG-SEISMO on behalf of Jed Brown" wrote: Merging in that mode is a fast-forward so protection doesn't block it (for anyone authorized to push to the branch). Dimitri Komatitsch writes: > Hi all, > > Thanks for the discussion. > > I went to https://help.github.com/articles/about-protected-branches but > it is not clear to me how one then makes changes in the protected branch > (for instance to release a new version of the code by merging "devel" > into "master", which we do a few times a year). If that can still be > done very easily (if so, how?), then why not; if that becomes complex, > then it is likely too complex, at least for SPECFEM. > > Thanks, > Best regards, > Dimitri. > > On 03/14/2018 11:42 PM, Rene Gassmoeller wrote: >> Hi all, >> >> let me join in on this as one of the maintainers of the ASPECT mantle >> convection code. We had the branch protection on Github enabled for our >> master branch for several years now (in addition to the automatic tester >> that tests pull requests). There are two scenarios in which this can be >> helpful: >> >> One of your project's developers (no admin, otherwise you are out of >> luck in any case) account is hacked. They have write access to the >> repository, but can not change their rights on github. Without a >> protected master branch they can force-push to that branch or more >> dangerously reset it and delete the complete project history. You would >> then need to restore it from a local copy somewhere (hopefully you have >> one). They can of course still merge bogus pull requests (unless you add >> the required status checks protection), but all of that can be reverted. >> >> The other scenario does not even need evil intentions. Let's assume you >> are in a hurry to fix a bug and you do this on the master branch (you >> should be on a feature branch, but the next seminar is in 5 minutes and >> you can create the branch later). You do not finish the fix, but want to >> save the history so you push to your personal github repo for now to >> create the pull request later. 'git push origin master'. Unfortunately >> you did this on the cluster where you cloned the repository and you >> cloned from the main repository instead of your own, so you mess up the >> master branch. You walk away and your repo is in an unusable state until >> you return or somebody notices. Every user who updated in the meantime >> gets an unusable version, and worse, they will get a conflict unless you >> fix up the master branch with a new commit (instead of reset it) and >> keep the messed up commit in there. >> >> Now I admit these cases need bad luck, but that can happen to anyone >> (even experienced admins). While we had no attempts to delete our master >> branch yet, people did accidentally upload branches to the main >> repository without realizing and having the branch protection on just >> gives us some extra peace of mind. Of course that is the decision of >> every project, but I personally feel a protected master branch should be >> included in the set of best practices. >> >> Cheers, >> >> Rene >> >> >> On 03/14/2018 02:43 PM, Tyler Esser wrote: >>> This conversation was originally started with the SPECFEM Admins >>> Github team. There were requests from other people to join the >>> discussion so we decided to post it to the mailing list. >>> >>> >>> Tyler Esser >>> >>> >>> ---------- Forwarded message ---------- >>> From: *Tyler Esser* >> > >>> Date: Fri, Mar 9, 2018 at 1:05 PM >>> Subject: [geodynamics/specfem-admins] Using Github's protected >>> branches (#1) >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>> > >>> Cc: Tyler Esser >, >>> Your activity >> > >>> >>> >>> Hi SPECFEM admins, >>> >>> CIG recently had a discussion with a CIG project dev about protecting >>> branches from certain actions and discovered that Github has a >>> protected branch feature. The option seems to be a good general >>> practice and so I wanted to ask what you thought about turning it on >>> for SPECFEM master branches. Github documentation for the feature is >>> here: https://help.github.com/articles/about-protected-branches/ >>> >>> >>> Mostly we were interested in preventing accidental deletion or >>> altering git history with force pushing, but there are other options >>> that may be worth using. See the attached picture. >>> >>> protectedbranches >>> >>> >>> The Github team interface seemed the best way to contact you when >>> dealing with Github administration issues. Please let me know if you >>> would have preferred a different method. >>> >>> Tyler Esser >>> >>> — >>> You are receiving this because you are subscribed to this thread. >>> Reply to this email directly, view it on GitHub >>> , >>> or mute the thread >>> . >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: *daniel peter* >> > >>> Date: Fri, Mar 9, 2018 at 11:20 PM >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>> branches (#1) >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>> > >>> Cc: Tyler Esser >, >>> Author > >>> >>> >>> Hi Tyler, >>> >>> probably David has a better answer, since he put most of this already >>> in place. I think we already protect the master branch in all SPECFEM >>> repos. no pull requests are allowed on master by users. only admins >>> are allowed to push/merge commits to it. so the most important >>> safeguards from above are already in place. >>> >>> as it seems to work pretty well so far for us, i don't see much need >>> for further restrictions. >>> >>> best wishes, >>> daniel >>> >>> — >>> You are receiving this because you authored the thread. >>> Reply to this email directly, view it on GitHub >>> , >>> or mute the thread >>> . >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: *Tyler Esser* >> > >>> Date: Mon, Mar 12, 2018 at 5:18 PM >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>> branches (#1) >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>> > >>> Cc: Tyler Esser >, >>> Your activity >> > >>> >>> >>> When you say the master branch is already protected, are you referring >>> to Github branch protection or are you referring to the Github teams >>> SPECFEM Admins >>> and >>> SPECFEM Devs >>> >>> being exclusive? >>> >>> As far as I can tell, the people in those teams have permission to >>> push, merge, force push, and/or delete any branch in the SPECFEM >>> repos. If I understand you correctly, that's fine because everyone in >>> those teams is already trusted. Is that correct? >>> >>> Tyler >>> >>> — >>> You are receiving this because you are subscribed to this thread. >>> Reply to this email directly, view it on GitHub >>> , >>> or mute the thread >>> . >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: *daniel peter* >> > >>> Date: Tue, Mar 13, 2018 at 1:46 AM >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>> branches (#1) >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>> > >>> Cc: Tyler Esser >, >>> Author > >>> >>> >>> the master branch is protected by buildbot, which David set up. every >>> pull request goes through buildbot which will close it automatically >>> if the request is towards the master branch. >>> >>> and yes, only those team admins are allowed to push, merge, etc. on >>> the master/devel branch which is fine, as they probably know what >>> they're doing :) >>> >>> -daniel >>> >>> — >>> You are receiving this because you authored the thread. >>> Reply to this email directly, view it on GitHub >>> , >>> or mute the thread >>> . >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: *Tyler Esser* >> > >>> Date: Wed, Mar 14, 2018 at 12:09 PM >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>> branches (#1) >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>> > >>> Cc: Tyler Esser >, >>> Your activity >> > >>> >>> >>> There's been a few requests to join this discussion. Do you mind if I >>> copy this thread to the cig-seismo mailing list? >>> >>> Tyler >>> >>> — >>> You are receiving this because you are subscribed to this thread. >>> Reply to this email directly, view it on GitHub >>> , >>> or mute the thread >>> . >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: *daniel peter* >> > >>> Date: Wed, Mar 14, 2018 at 1:49 PM >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>> branches (#1) >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>> > >>> Cc: Tyler Esser >, >>> Author > >>> >>> >>> sure, let's see some more opinions :) >>> >>> — >>> You are receiving this because you authored the thread. >>> Reply to this email directly, view it on GitHub >>> , >>> or mute the thread >>> . >>> >>> >>> >>> >>> >>> _______________________________________________ >>> CIG-SEISMO mailing list >>> CIG-SEISMO at geodynamics.org >>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >> >> -- >> Rene Gassmoeller >> http://www.math.colostate.edu/~gassmoel/ >> >> >> >> _______________________________________________ >> CIG-SEISMO mailing list >> CIG-SEISMO at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >> > > -- > Dimitri Komatitsch, CNRS Research Director (DR CNRS) > Laboratory of Mechanics and Acoustics, Marseille, France > http://komatitsch.free.fr > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo _______________________________________________ CIG-SEISMO mailing list CIG-SEISMO at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo From komatitsch at lma.cnrs-mrs.fr Thu Mar 15 09:47:28 2018 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Thu, 15 Mar 2018 17:47:28 +0100 Subject: [CIG-SEISMO] Using Github Protected Branches In-Reply-To: <87efkm2qqp.fsf@jedbrown.org> References: <08db03b1-1770-2fb5-cf18-7163c7cac5c9@mailbox.org> <30e76d8c-750a-65c3-05e2-5cd586abc7dd@lma.cnrs-mrs.fr> <87efkm2qqp.fsf@jedbrown.org> Message-ID: <607c3c39-06ea-9645-cc94-0c24b19b7223@lma.cnrs-mrs.fr> Thanks! Perfect. If so, let us do it I guess :-) To all: it is easy to unprotect the branch later if needed, thus we can safely try. It looks like a nice feature, and good practice. I remember that around 2014 or so I made a mistake and deleted the master branch (I deleted geodynamics/specfem3d instead of deleting komatitsch/specfem3d). A protected branch would have avoided that. Fortunately Jed had a local backup and managed to restore it... Even though the GitHub web interface says (in red bold font) "Are you sure about what you are doing", I clicked on Yes because I was tired... thanks Best regards, Dimitri. On 03/15/2018 12:15 AM, Jed Brown wrote: > Merging in that mode is a fast-forward so protection doesn't block it > (for anyone authorized to push to the branch). > > Dimitri Komatitsch writes: > >> Hi all, >> >> Thanks for the discussion. >> >> I went to https://help.github.com/articles/about-protected-branches but >> it is not clear to me how one then makes changes in the protected branch >> (for instance to release a new version of the code by merging "devel" >> into "master", which we do a few times a year). If that can still be >> done very easily (if so, how?), then why not; if that becomes complex, >> then it is likely too complex, at least for SPECFEM. >> >> Thanks, >> Best regards, >> Dimitri. >> >> On 03/14/2018 11:42 PM, Rene Gassmoeller wrote: >>> Hi all, >>> >>> let me join in on this as one of the maintainers of the ASPECT mantle >>> convection code. We had the branch protection on Github enabled for our >>> master branch for several years now (in addition to the automatic tester >>> that tests pull requests). There are two scenarios in which this can be >>> helpful: >>> >>> One of your project's developers (no admin, otherwise you are out of >>> luck in any case) account is hacked. They have write access to the >>> repository, but can not change their rights on github. Without a >>> protected master branch they can force-push to that branch or more >>> dangerously reset it and delete the complete project history. You would >>> then need to restore it from a local copy somewhere (hopefully you have >>> one). They can of course still merge bogus pull requests (unless you add >>> the required status checks protection), but all of that can be reverted. >>> >>> The other scenario does not even need evil intentions. Let's assume you >>> are in a hurry to fix a bug and you do this on the master branch (you >>> should be on a feature branch, but the next seminar is in 5 minutes and >>> you can create the branch later). You do not finish the fix, but want to >>> save the history so you push to your personal github repo for now to >>> create the pull request later. 'git push origin master'. Unfortunately >>> you did this on the cluster where you cloned the repository and you >>> cloned from the main repository instead of your own, so you mess up the >>> master branch. You walk away and your repo is in an unusable state until >>> you return or somebody notices. Every user who updated in the meantime >>> gets an unusable version, and worse, they will get a conflict unless you >>> fix up the master branch with a new commit (instead of reset it) and >>> keep the messed up commit in there. >>> >>> Now I admit these cases need bad luck, but that can happen to anyone >>> (even experienced admins). While we had no attempts to delete our master >>> branch yet, people did accidentally upload branches to the main >>> repository without realizing and having the branch protection on just >>> gives us some extra peace of mind. Of course that is the decision of >>> every project, but I personally feel a protected master branch should be >>> included in the set of best practices. >>> >>> Cheers, >>> >>> Rene >>> >>> >>> On 03/14/2018 02:43 PM, Tyler Esser wrote: >>>> This conversation was originally started with the SPECFEM Admins >>>> Github team. There were requests from other people to join the >>>> discussion so we decided to post it to the mailing list. >>>> >>>> >>>> Tyler Esser >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: *Tyler Esser* >>> > >>>> Date: Fri, Mar 9, 2018 at 1:05 PM >>>> Subject: [geodynamics/specfem-admins] Using Github's protected >>>> branches (#1) >>>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>>> > >>>> Cc: Tyler Esser >, >>>> Your activity >>> > >>>> >>>> >>>> Hi SPECFEM admins, >>>> >>>> CIG recently had a discussion with a CIG project dev about protecting >>>> branches from certain actions and discovered that Github has a >>>> protected branch feature. The option seems to be a good general >>>> practice and so I wanted to ask what you thought about turning it on >>>> for SPECFEM master branches. Github documentation for the feature is >>>> here: https://help.github.com/articles/about-protected-branches/ >>>> >>>> >>>> Mostly we were interested in preventing accidental deletion or >>>> altering git history with force pushing, but there are other options >>>> that may be worth using. See the attached picture. >>>> >>>> protectedbranches >>>> >>>> >>>> The Github team interface seemed the best way to contact you when >>>> dealing with Github administration issues. Please let me know if you >>>> would have preferred a different method. >>>> >>>> Tyler Esser >>>> >>>> — >>>> You are receiving this because you are subscribed to this thread. >>>> Reply to this email directly, view it on GitHub >>>> , >>>> or mute the thread >>>> . >>>> >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: *daniel peter* >>> > >>>> Date: Fri, Mar 9, 2018 at 11:20 PM >>>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>>> branches (#1) >>>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>>> > >>>> Cc: Tyler Esser >, >>>> Author > >>>> >>>> >>>> Hi Tyler, >>>> >>>> probably David has a better answer, since he put most of this already >>>> in place. I think we already protect the master branch in all SPECFEM >>>> repos. no pull requests are allowed on master by users. only admins >>>> are allowed to push/merge commits to it. so the most important >>>> safeguards from above are already in place. >>>> >>>> as it seems to work pretty well so far for us, i don't see much need >>>> for further restrictions. >>>> >>>> best wishes, >>>> daniel >>>> >>>> — >>>> You are receiving this because you authored the thread. >>>> Reply to this email directly, view it on GitHub >>>> , >>>> or mute the thread >>>> . >>>> >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: *Tyler Esser* >>> > >>>> Date: Mon, Mar 12, 2018 at 5:18 PM >>>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>>> branches (#1) >>>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>>> > >>>> Cc: Tyler Esser >, >>>> Your activity >>> > >>>> >>>> >>>> When you say the master branch is already protected, are you referring >>>> to Github branch protection or are you referring to the Github teams >>>> SPECFEM Admins >>>> and >>>> SPECFEM Devs >>>> >>>> being exclusive? >>>> >>>> As far as I can tell, the people in those teams have permission to >>>> push, merge, force push, and/or delete any branch in the SPECFEM >>>> repos. If I understand you correctly, that's fine because everyone in >>>> those teams is already trusted. Is that correct? >>>> >>>> Tyler >>>> >>>> — >>>> You are receiving this because you are subscribed to this thread. >>>> Reply to this email directly, view it on GitHub >>>> , >>>> or mute the thread >>>> . >>>> >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: *daniel peter* >>> > >>>> Date: Tue, Mar 13, 2018 at 1:46 AM >>>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>>> branches (#1) >>>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>>> > >>>> Cc: Tyler Esser >, >>>> Author > >>>> >>>> >>>> the master branch is protected by buildbot, which David set up. every >>>> pull request goes through buildbot which will close it automatically >>>> if the request is towards the master branch. >>>> >>>> and yes, only those team admins are allowed to push, merge, etc. on >>>> the master/devel branch which is fine, as they probably know what >>>> they're doing :) >>>> >>>> -daniel >>>> >>>> — >>>> You are receiving this because you authored the thread. >>>> Reply to this email directly, view it on GitHub >>>> , >>>> or mute the thread >>>> . >>>> >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: *Tyler Esser* >>> > >>>> Date: Wed, Mar 14, 2018 at 12:09 PM >>>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>>> branches (#1) >>>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>>> > >>>> Cc: Tyler Esser >, >>>> Your activity >>> > >>>> >>>> >>>> There's been a few requests to join this discussion. Do you mind if I >>>> copy this thread to the cig-seismo mailing list? >>>> >>>> Tyler >>>> >>>> — >>>> You are receiving this because you are subscribed to this thread. >>>> Reply to this email directly, view it on GitHub >>>> , >>>> or mute the thread >>>> . >>>> >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: *daniel peter* >>> > >>>> Date: Wed, Mar 14, 2018 at 1:49 PM >>>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >>>> branches (#1) >>>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >>>> > >>>> Cc: Tyler Esser >, >>>> Author > >>>> >>>> >>>> sure, let's see some more opinions :) >>>> >>>> — >>>> You are receiving this because you authored the thread. >>>> Reply to this email directly, view it on GitHub >>>> , >>>> or mute the thread >>>> . >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> CIG-SEISMO mailing list >>>> CIG-SEISMO at geodynamics.org >>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >>> >>> -- >>> Rene Gassmoeller >>> http://www.math.colostate.edu/~gassmoel/ >>> >>> >>> >>> _______________________________________________ >>> CIG-SEISMO mailing list >>> CIG-SEISMO at geodynamics.org >>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >>> >> >> -- >> Dimitri Komatitsch, CNRS Research Director (DR CNRS) >> Laboratory of Mechanics and Acoustics, Marseille, France >> http://komatitsch.free.fr >> _______________________________________________ >> CIG-SEISMO mailing list >> CIG-SEISMO at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr From komatitsch at lma.cnrs-mrs.fr Thu Mar 15 09:52:38 2018 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Thu, 15 Mar 2018 17:52:38 +0100 Subject: [CIG-SEISMO] Using Github Protected Branches In-Reply-To: References: <08db03b1-1770-2fb5-cf18-7163c7cac5c9@mailbox.org> <30e76d8c-750a-65c3-05e2-5cd586abc7dd@lma.cnrs-mrs.fr> <87efkm2qqp.fsf@jedbrown.org> Message-ID: <256b783a-853a-bea2-b92c-f03f6182b54c@lma.cnrs-mrs.fr> Hi David, Hi all, Thanks! Very useful. Let us do it then I guess, if everybody agrees. Thanks, Best regards, Dimitri. On 03/15/2018 04:28 PM, David J. Luet wrote: > It looks like we can protect the branch master without affecting our workflow. For the most part, we have system in place to prevent people from modifying master, but we don't have a system to prevent a member of the "SPECFEM Admins" or "SPECFEM Developers" team to force push to the master branch. But all the branch protection does is protect us from one of the admins doing "git push --force" after trying, and failing, a regular, fast-forward "git push". Unless we want to remove the ability of the admins to push to the master branch, which would require a change in our workflow. > > The bottom line is that I think there is no harm in protecting master. It also makes sense to protect the branch devel against force-pushes. But buildbot rejects those anyway, but again not from the admins. > > David > > > On 3/14/18, 7:27 PM, "CIG-SEISMO on behalf of Jed Brown" wrote: > > Merging in that mode is a fast-forward so protection doesn't block it > (for anyone authorized to push to the branch). > > Dimitri Komatitsch writes: > > > Hi all, > > > > Thanks for the discussion. > > > > I went to https://help.github.com/articles/about-protected-branches but > > it is not clear to me how one then makes changes in the protected branch > > (for instance to release a new version of the code by merging "devel" > > into "master", which we do a few times a year). If that can still be > > done very easily (if so, how?), then why not; if that becomes complex, > > then it is likely too complex, at least for SPECFEM. > > > > Thanks, > > Best regards, > > Dimitri. > > > > On 03/14/2018 11:42 PM, Rene Gassmoeller wrote: > >> Hi all, > >> > >> let me join in on this as one of the maintainers of the ASPECT mantle > >> convection code. We had the branch protection on Github enabled for our > >> master branch for several years now (in addition to the automatic tester > >> that tests pull requests). There are two scenarios in which this can be > >> helpful: > >> > >> One of your project's developers (no admin, otherwise you are out of > >> luck in any case) account is hacked. They have write access to the > >> repository, but can not change their rights on github. Without a > >> protected master branch they can force-push to that branch or more > >> dangerously reset it and delete the complete project history. You would > >> then need to restore it from a local copy somewhere (hopefully you have > >> one). They can of course still merge bogus pull requests (unless you add > >> the required status checks protection), but all of that can be reverted. > >> > >> The other scenario does not even need evil intentions. Let's assume you > >> are in a hurry to fix a bug and you do this on the master branch (you > >> should be on a feature branch, but the next seminar is in 5 minutes and > >> you can create the branch later). You do not finish the fix, but want to > >> save the history so you push to your personal github repo for now to > >> create the pull request later. 'git push origin master'. Unfortunately > >> you did this on the cluster where you cloned the repository and you > >> cloned from the main repository instead of your own, so you mess up the > >> master branch. You walk away and your repo is in an unusable state until > >> you return or somebody notices. Every user who updated in the meantime > >> gets an unusable version, and worse, they will get a conflict unless you > >> fix up the master branch with a new commit (instead of reset it) and > >> keep the messed up commit in there. > >> > >> Now I admit these cases need bad luck, but that can happen to anyone > >> (even experienced admins). While we had no attempts to delete our master > >> branch yet, people did accidentally upload branches to the main > >> repository without realizing and having the branch protection on just > >> gives us some extra peace of mind. Of course that is the decision of > >> every project, but I personally feel a protected master branch should be > >> included in the set of best practices. > >> > >> Cheers, > >> > >> Rene > >> > >> > >> On 03/14/2018 02:43 PM, Tyler Esser wrote: > >>> This conversation was originally started with the SPECFEM Admins > >>> Github team. There were requests from other people to join the > >>> discussion so we decided to post it to the mailing list. > >>> > >>> > >>> Tyler Esser > >>> > >>> > >>> ---------- Forwarded message ---------- > >>> From: *Tyler Esser* >>> > > >>> Date: Fri, Mar 9, 2018 at 1:05 PM > >>> Subject: [geodynamics/specfem-admins] Using Github's protected > >>> branches (#1) > >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com > >>> > > >>> Cc: Tyler Esser >, > >>> Your activity >>> > > >>> > >>> > >>> Hi SPECFEM admins, > >>> > >>> CIG recently had a discussion with a CIG project dev about protecting > >>> branches from certain actions and discovered that Github has a > >>> protected branch feature. The option seems to be a good general > >>> practice and so I wanted to ask what you thought about turning it on > >>> for SPECFEM master branches. Github documentation for the feature is > >>> here: https://help.github.com/articles/about-protected-branches/ > >>> > >>> > >>> Mostly we were interested in preventing accidental deletion or > >>> altering git history with force pushing, but there are other options > >>> that may be worth using. See the attached picture. > >>> > >>> protectedbranches > >>> > >>> > >>> The Github team interface seemed the best way to contact you when > >>> dealing with Github administration issues. Please let me know if you > >>> would have preferred a different method. > >>> > >>> Tyler Esser > >>> > >>> — > >>> You are receiving this because you are subscribed to this thread. > >>> Reply to this email directly, view it on GitHub > >>> , > >>> or mute the thread > >>> . > >>> > >>> > >>> > >>> ---------- Forwarded message ---------- > >>> From: *daniel peter* >>> > > >>> Date: Fri, Mar 9, 2018 at 11:20 PM > >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected > >>> branches (#1) > >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com > >>> > > >>> Cc: Tyler Esser >, > >>> Author > > >>> > >>> > >>> Hi Tyler, > >>> > >>> probably David has a better answer, since he put most of this already > >>> in place. I think we already protect the master branch in all SPECFEM > >>> repos. no pull requests are allowed on master by users. only admins > >>> are allowed to push/merge commits to it. so the most important > >>> safeguards from above are already in place. > >>> > >>> as it seems to work pretty well so far for us, i don't see much need > >>> for further restrictions. > >>> > >>> best wishes, > >>> daniel > >>> > >>> — > >>> You are receiving this because you authored the thread. > >>> Reply to this email directly, view it on GitHub > >>> , > >>> or mute the thread > >>> . > >>> > >>> > >>> > >>> ---------- Forwarded message ---------- > >>> From: *Tyler Esser* >>> > > >>> Date: Mon, Mar 12, 2018 at 5:18 PM > >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected > >>> branches (#1) > >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com > >>> > > >>> Cc: Tyler Esser >, > >>> Your activity >>> > > >>> > >>> > >>> When you say the master branch is already protected, are you referring > >>> to Github branch protection or are you referring to the Github teams > >>> SPECFEM Admins > >>> and > >>> SPECFEM Devs > >>> > >>> being exclusive? > >>> > >>> As far as I can tell, the people in those teams have permission to > >>> push, merge, force push, and/or delete any branch in the SPECFEM > >>> repos. If I understand you correctly, that's fine because everyone in > >>> those teams is already trusted. Is that correct? > >>> > >>> Tyler > >>> > >>> — > >>> You are receiving this because you are subscribed to this thread. > >>> Reply to this email directly, view it on GitHub > >>> , > >>> or mute the thread > >>> . > >>> > >>> > >>> > >>> ---------- Forwarded message ---------- > >>> From: *daniel peter* >>> > > >>> Date: Tue, Mar 13, 2018 at 1:46 AM > >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected > >>> branches (#1) > >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com > >>> > > >>> Cc: Tyler Esser >, > >>> Author > > >>> > >>> > >>> the master branch is protected by buildbot, which David set up. every > >>> pull request goes through buildbot which will close it automatically > >>> if the request is towards the master branch. > >>> > >>> and yes, only those team admins are allowed to push, merge, etc. on > >>> the master/devel branch which is fine, as they probably know what > >>> they're doing :) > >>> > >>> -daniel > >>> > >>> — > >>> You are receiving this because you authored the thread. > >>> Reply to this email directly, view it on GitHub > >>> , > >>> or mute the thread > >>> . > >>> > >>> > >>> > >>> ---------- Forwarded message ---------- > >>> From: *Tyler Esser* >>> > > >>> Date: Wed, Mar 14, 2018 at 12:09 PM > >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected > >>> branches (#1) > >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com > >>> > > >>> Cc: Tyler Esser >, > >>> Your activity >>> > > >>> > >>> > >>> There's been a few requests to join this discussion. Do you mind if I > >>> copy this thread to the cig-seismo mailing list? > >>> > >>> Tyler > >>> > >>> — > >>> You are receiving this because you are subscribed to this thread. > >>> Reply to this email directly, view it on GitHub > >>> , > >>> or mute the thread > >>> . > >>> > >>> > >>> > >>> ---------- Forwarded message ---------- > >>> From: *daniel peter* >>> > > >>> Date: Wed, Mar 14, 2018 at 1:49 PM > >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected > >>> branches (#1) > >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com > >>> > > >>> Cc: Tyler Esser >, > >>> Author > > >>> > >>> > >>> sure, let's see some more opinions :) > >>> > >>> — > >>> You are receiving this because you authored the thread. > >>> Reply to this email directly, view it on GitHub > >>> , > >>> or mute the thread > >>> . > >>> > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> CIG-SEISMO mailing list > >>> CIG-SEISMO at geodynamics.org > >>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > >> > >> -- > >> Rene Gassmoeller > >> http://www.math.colostate.edu/~gassmoel/ > >> > >> > >> > >> _______________________________________________ > >> CIG-SEISMO mailing list > >> CIG-SEISMO at geodynamics.org > >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > >> > > > > -- > > Dimitri Komatitsch, CNRS Research Director (DR CNRS) > > Laboratory of Mechanics and Acoustics, Marseille, France > > http://komatitsch.free.fr > > _______________________________________________ > > CIG-SEISMO mailing list > > CIG-SEISMO at geodynamics.org > > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr From ljhwang at ucdavis.edu Thu Mar 15 10:35:58 2018 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Thu, 15 Mar 2018 10:35:58 -0700 Subject: [CIG-SEISMO] Using Github Protected Branches In-Reply-To: <256b783a-853a-bea2-b92c-f03f6182b54c@lma.cnrs-mrs.fr> References: <08db03b1-1770-2fb5-cf18-7163c7cac5c9@mailbox.org> <30e76d8c-750a-65c3-05e2-5cd586abc7dd@lma.cnrs-mrs.fr> <87efkm2qqp.fsf@jedbrown.org> <256b783a-853a-bea2-b92c-f03f6182b54c@lma.cnrs-mrs.fr> Message-ID: Great! We do mirror the repo but it is best that we play it safe. thanks everyone for the discussion. Best, -Lorraine ***************************** Lorraine Hwang, Ph.D. Associate Director, CIG 530.752.3656 > On Mar 15, 2018, at 9:52 AM, Dimitri Komatitsch wrote: > > > Hi David, Hi all, > > Thanks! Very useful. Let us do it then I guess, if everybody agrees. > > Thanks, > Best regards, > Dimitri. > > On 03/15/2018 04:28 PM, David J. Luet wrote: >> It looks like we can protect the branch master without affecting our workflow. For the most part, we have system in place to prevent people from modifying master, but we don't have a system to prevent a member of the "SPECFEM Admins" or "SPECFEM Developers" team to force push to the master branch. But all the branch protection does is protect us from one of the admins doing "git push --force" after trying, and failing, a regular, fast-forward "git push". Unless we want to remove the ability of the admins to push to the master branch, which would require a change in our workflow. >> The bottom line is that I think there is no harm in protecting master. It also makes sense to protect the branch devel against force-pushes. But buildbot rejects those anyway, but again not from the admins. >> David >> On 3/14/18, 7:27 PM, "CIG-SEISMO on behalf of Jed Brown" wrote: >> Merging in that mode is a fast-forward so protection doesn't block it >> (for anyone authorized to push to the branch). >> Dimitri Komatitsch writes: >> > Hi all, >> > >> > Thanks for the discussion. >> > >> > I went to https://help.github.com/articles/about-protected-branches but >> > it is not clear to me how one then makes changes in the protected branch >> > (for instance to release a new version of the code by merging "devel" >> > into "master", which we do a few times a year). If that can still be >> > done very easily (if so, how?), then why not; if that becomes complex, >> > then it is likely too complex, at least for SPECFEM. >> > >> > Thanks, >> > Best regards, >> > Dimitri. >> > >> > On 03/14/2018 11:42 PM, Rene Gassmoeller wrote: >> >> Hi all, >> >> >> >> let me join in on this as one of the maintainers of the ASPECT mantle >> >> convection code. We had the branch protection on Github enabled for our >> >> master branch for several years now (in addition to the automatic tester >> >> that tests pull requests). There are two scenarios in which this can be >> >> helpful: >> >> >> >> One of your project's developers (no admin, otherwise you are out of >> >> luck in any case) account is hacked. They have write access to the >> >> repository, but can not change their rights on github. Without a >> >> protected master branch they can force-push to that branch or more >> >> dangerously reset it and delete the complete project history. You would >> >> then need to restore it from a local copy somewhere (hopefully you have >> >> one). They can of course still merge bogus pull requests (unless you add >> >> the required status checks protection), but all of that can be reverted. >> >> >> >> The other scenario does not even need evil intentions. Let's assume you >> >> are in a hurry to fix a bug and you do this on the master branch (you >> >> should be on a feature branch, but the next seminar is in 5 minutes and >> >> you can create the branch later). You do not finish the fix, but want to >> >> save the history so you push to your personal github repo for now to >> >> create the pull request later. 'git push origin master'. Unfortunately >> >> you did this on the cluster where you cloned the repository and you >> >> cloned from the main repository instead of your own, so you mess up the >> >> master branch. You walk away and your repo is in an unusable state until >> >> you return or somebody notices. Every user who updated in the meantime >> >> gets an unusable version, and worse, they will get a conflict unless you >> >> fix up the master branch with a new commit (instead of reset it) and >> >> keep the messed up commit in there. >> >> >> >> Now I admit these cases need bad luck, but that can happen to anyone >> >> (even experienced admins). While we had no attempts to delete our master >> >> branch yet, people did accidentally upload branches to the main >> >> repository without realizing and having the branch protection on just >> >> gives us some extra peace of mind. Of course that is the decision of >> >> every project, but I personally feel a protected master branch should be >> >> included in the set of best practices. >> >> >> >> Cheers, >> >> >> >> Rene >> >> >> >> >> >> On 03/14/2018 02:43 PM, Tyler Esser wrote: >> >>> This conversation was originally started with the SPECFEM Admins >> >>> Github team. There were requests from other people to join the >> >>> discussion so we decided to post it to the mailing list. >> >>> >> >>> >> >>> Tyler Esser >> >>> >> >>> >> >>> ---------- Forwarded message ---------- >> >>> From: *Tyler Esser* > >>> > >> >>> Date: Fri, Mar 9, 2018 at 1:05 PM >> >>> Subject: [geodynamics/specfem-admins] Using Github's protected >> >>> branches (#1) >> >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >> >>> > >> >>> Cc: Tyler Esser >, >> >>> Your activity > >>> > >> >>> >> >>> >> >>> Hi SPECFEM admins, >> >>> >> >>> CIG recently had a discussion with a CIG project dev about protecting >> >>> branches from certain actions and discovered that Github has a >> >>> protected branch feature. The option seems to be a good general >> >>> practice and so I wanted to ask what you thought about turning it on >> >>> for SPECFEM master branches. Github documentation for the feature is >> >>> here: https://help.github.com/articles/about-protected-branches/ >> >>> >> >>> >> >>> Mostly we were interested in preventing accidental deletion or >> >>> altering git history with force pushing, but there are other options >> >>> that may be worth using. See the attached picture. >> >>> >> >>> protectedbranches >> >>> >> >>> >> >>> The Github team interface seemed the best way to contact you when >> >>> dealing with Github administration issues. Please let me know if you >> >>> would have preferred a different method. >> >>> >> >>> Tyler Esser >> >>> >> >>> — >> >>> You are receiving this because you are subscribed to this thread. >> >>> Reply to this email directly, view it on GitHub >> >>> , >> >>> or mute the thread >> >>> . >> >>> >> >>> >> >>> >> >>> ---------- Forwarded message ---------- >> >>> From: *daniel peter* > >>> > >> >>> Date: Fri, Mar 9, 2018 at 11:20 PM >> >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >> >>> branches (#1) >> >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >> >>> > >> >>> Cc: Tyler Esser >, >> >>> Author > >> >>> >> >>> >> >>> Hi Tyler, >> >>> >> >>> probably David has a better answer, since he put most of this already >> >>> in place. I think we already protect the master branch in all SPECFEM >> >>> repos. no pull requests are allowed on master by users. only admins >> >>> are allowed to push/merge commits to it. so the most important >> >>> safeguards from above are already in place. >> >>> >> >>> as it seems to work pretty well so far for us, i don't see much need >> >>> for further restrictions. >> >>> >> >>> best wishes, >> >>> daniel >> >>> >> >>> — >> >>> You are receiving this because you authored the thread. >> >>> Reply to this email directly, view it on GitHub >> >>> , >> >>> or mute the thread >> >>> . >> >>> >> >>> >> >>> >> >>> ---------- Forwarded message ---------- >> >>> From: *Tyler Esser* > >>> > >> >>> Date: Mon, Mar 12, 2018 at 5:18 PM >> >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >> >>> branches (#1) >> >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >> >>> > >> >>> Cc: Tyler Esser >, >> >>> Your activity > >>> > >> >>> >> >>> >> >>> When you say the master branch is already protected, are you referring >> >>> to Github branch protection or are you referring to the Github teams >> >>> SPECFEM Admins >> >>> and >> >>> SPECFEM Devs >> >>> >> >>> being exclusive? >> >>> >> >>> As far as I can tell, the people in those teams have permission to >> >>> push, merge, force push, and/or delete any branch in the SPECFEM >> >>> repos. If I understand you correctly, that's fine because everyone in >> >>> those teams is already trusted. Is that correct? >> >>> >> >>> Tyler >> >>> >> >>> — >> >>> You are receiving this because you are subscribed to this thread. >> >>> Reply to this email directly, view it on GitHub >> >>> , >> >>> or mute the thread >> >>> . >> >>> >> >>> >> >>> >> >>> ---------- Forwarded message ---------- >> >>> From: *daniel peter* > >>> > >> >>> Date: Tue, Mar 13, 2018 at 1:46 AM >> >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >> >>> branches (#1) >> >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >> >>> > >> >>> Cc: Tyler Esser >, >> >>> Author > >> >>> >> >>> >> >>> the master branch is protected by buildbot, which David set up. every >> >>> pull request goes through buildbot which will close it automatically >> >>> if the request is towards the master branch. >> >>> >> >>> and yes, only those team admins are allowed to push, merge, etc. on >> >>> the master/devel branch which is fine, as they probably know what >> >>> they're doing :) >> >>> >> >>> -daniel >> >>> >> >>> — >> >>> You are receiving this because you authored the thread. >> >>> Reply to this email directly, view it on GitHub >> >>> , >> >>> or mute the thread >> >>> . >> >>> >> >>> >> >>> >> >>> ---------- Forwarded message ---------- >> >>> From: *Tyler Esser* > >>> > >> >>> Date: Wed, Mar 14, 2018 at 12:09 PM >> >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >> >>> branches (#1) >> >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >> >>> > >> >>> Cc: Tyler Esser >, >> >>> Your activity > >>> > >> >>> >> >>> >> >>> There's been a few requests to join this discussion. Do you mind if I >> >>> copy this thread to the cig-seismo mailing list? >> >>> >> >>> Tyler >> >>> >> >>> — >> >>> You are receiving this because you are subscribed to this thread. >> >>> Reply to this email directly, view it on GitHub >> >>> , >> >>> or mute the thread >> >>> . >> >>> >> >>> >> >>> >> >>> ---------- Forwarded message ---------- >> >>> From: *daniel peter* > >>> > >> >>> Date: Wed, Mar 14, 2018 at 1:49 PM >> >>> Subject: Re: [geodynamics/specfem-admins] Using Github's protected >> >>> branches (#1) >> >>> To: geodynamics/specfem-admins <"SPECFEM Admins"@noreply.github.com >> >>> > >> >>> Cc: Tyler Esser >, >> >>> Author > >> >>> >> >>> >> >>> sure, let's see some more opinions :) >> >>> >> >>> — >> >>> You are receiving this because you authored the thread. >> >>> Reply to this email directly, view it on GitHub >> >>> , >> >>> or mute the thread >> >>> . >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> _______________________________________________ >> >>> CIG-SEISMO mailing list >> >>> CIG-SEISMO at geodynamics.org >> >>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >> >> >> >> -- >> >> Rene Gassmoeller >> >> http://www.math.colostate.edu/~gassmoel/ >> >> >> >> >> >> >> >> _______________________________________________ >> >> CIG-SEISMO mailing list >> >> CIG-SEISMO at geodynamics.org >> >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >> >> >> > >> > -- >> > Dimitri Komatitsch, CNRS Research Director (DR CNRS) >> > Laboratory of Mechanics and Acoustics, Marseille, France >> > http://komatitsch.free.fr >> > _______________________________________________ >> > CIG-SEISMO mailing list >> > CIG-SEISMO at geodynamics.org >> > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >> _______________________________________________ >> CIG-SEISMO mailing list >> CIG-SEISMO at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > > -- > Dimitri Komatitsch, CNRS Research Director (DR CNRS) > Laboratory of Mechanics and Acoustics, Marseille, France > http://komatitsch.free.fr > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo -------------- next part -------------- An HTML attachment was scrubbed... URL: From tonyndokalemma at gmail.com Tue Mar 27 03:11:30 2018 From: tonyndokalemma at gmail.com (Emmanuel Anthony) Date: Tue, 27 Mar 2018 15:41:30 +0530 Subject: [CIG-SEISMO] Full waveform inversion assistance Message-ID: I write to seek for you assistance concerning my thesis. I am working on "Full Waveform Inversion of Earthquakes in Decan Province India". I have downloaded and install the SPECFEM3D Cartesian. I discovered that Full waveform inversion has been implemented. Please can you help me to understand how I can implement full waveform inversion with SPECFEM3D Cartesian? Thanks. Best Regards, Emmanuel Anthony, *CSIR-TWAS Ph.D Research Scholar,* *Academy of Scientific & Innovative Research (AcSIR),* *National Geophysical Research Institute (NGRI),* *Hyderabad,* *India.* *+918639278953* -------------- next part -------------- An HTML attachment was scrubbed... URL: From tonyndokalemma at gmail.com Tue Mar 27 21:42:55 2018 From: tonyndokalemma at gmail.com (Emmanuel Anthony) Date: Wed, 28 Mar 2018 10:12:55 +0530 Subject: [CIG-SEISMO] Help on Full Waveform Inversion Examples files Message-ID: Dear Sir/Madam, I write to seek for you assistance concerning my thesis. I am working on "Full Waveform Inversion of Earthquake in Decan Province India" I have gone through SPECFEM3D Cartesian and discovered I can used the software for waveform inversion. Please can I get the example file/folder for the inverse problem because it is not available in the example directory of the software. Thanks. Best Regards, Emmanuel Anthony, *CSIR-TWAS Ph.D Research Scholar,* *Academy of Scientific & Innovative Research (AcSIR),* *National Geophysical Research Institute (NGRI),* *Hyderabad,* *India.* *+918639278953* -------------- next part -------------- An HTML attachment was scrubbed... URL: From dirkphilip.vanherwaarden at erdw.ethz.ch Tue Mar 27 22:47:30 2018 From: dirkphilip.vanherwaarden at erdw.ethz.ch (van Herwaarden Dirk Philippus) Date: Wed, 28 Mar 2018 05:47:30 +0000 Subject: [CIG-SEISMO] Help on Full Waveform Inversion Examples files In-Reply-To: References: Message-ID: <332DF730760CA24989E9E3A12C9A8C6535904B5F@MBX116.d.ethz.ch> Hello, Sorry, I have never used Specfem Cartesian for a full waveform inversion. I have no experience with this. Best wishes, Dirk-Philip ________________________________ From: CIG-SEISMO [cig-seismo-bounces at geodynamics.org] on behalf of Emmanuel Anthony [tonyndokalemma at gmail.com] Sent: Wednesday, March 28, 2018 6:42 AM To: cig-seismo at geodynamics.org Subject: [CIG-SEISMO] Help on Full Waveform Inversion Examples files Dear Sir/Madam, I write to seek for you assistance concerning my thesis. I am working on "Full Waveform Inversion of Earthquake in Decan Province India" I have gone through SPECFEM3D Cartesian and discovered I can used the software for waveform inversion. Please can I get the example file/folder for the inverse problem because it is not available in the example directory of the software. Thanks. Best Regards, Emmanuel Anthony, CSIR-TWAS Ph.D Research Scholar, Academy of Scientific & Innovative Research (AcSIR), National Geophysical Research Institute (NGRI), Hyderabad, India. +918639278953 -------------- next part -------------- An HTML attachment was scrubbed... URL: From kriukova at mail.ru Wed Mar 28 01:56:03 2018 From: kriukova at mail.ru (=?UTF-8?B?0J7Qu9GM0LPQsCDQo9GB0L7Qu9GM0YbQtdCy0LA=?=) Date: Wed, 28 Mar 2018 11:56:03 +0300 Subject: [CIG-SEISMO] =?utf-8?q?error_specfem3D=5Fglobe_7=2E0_with_cuda5?= Message-ID: <1522227363.403330202@f420.i.mail.ru> Dear colleagues. I have a problem with running of specfem3D_globe 7.0 with cuda5. I send you texts of my error, file names gpu_device_info.txt and result of utility check_cuda_device.cu. Could you explain me how to correct error. Thank you.   My error is   Error testing memory allocation on device failed Error rank 1: cudaMalloc failed: unknown error   ERROR: CUDA runtime error: cudaMalloc failed     Error: cudaMemGetInfo fails, unknown error ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:   Process name: [[6221,1],0] Exit code: 1 ---------------------------   This is information from OUTPUT_FILES/gpu_device_info.txt   Device Name = Tesla X2070 memory: totalGlobalMem (in MB): 5375.437500 totalGlobalMem (in GB): 5.249451 totalConstMem (in bytes): 65536 Maximum 1D texture size (in bytes): 65536 sharedMemPerBlock (in bytes): 49152 regsPerBlock (in bytes): 32768 blocks: Maximum number of threads per block: 1024 Maximum size of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 65535 features: Compute capability of the device = 2.0 multiProcessorCount: 14 canMapHostMemory: TRUE deviceOverlap: TRUE concurrentKernels: TRUE   This is a result of check_cuda_device.cu (mpi case). process 1 found number of CUDA devices = 2   process 0 found number of CUDA devices = 2     GPU device for rank: 0   Device Name = Tesla X2070 memory: totalGlobalMem (in MB): 5375.437500 totalGlobalMem (in GB): 5.249451 sharedMemPerBlock (in bytes): 49152 blocks: Maximum number of threads per block: 1024 Maximum size of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 65535 features: Compute capability of the device = 2.0 multiProcessorCount: 14 canMapHostMemory: TRUE deviceOverlap: TRUE     GPU device for rank: 1   Device Name = Tesla X2070 memory: totalGlobalMem (in MB): 5375.437500 totalGlobalMem (in GB): 5.249451 sharedMemPerBlock (in bytes): 49152 blocks: Maximum number of threads per block: 1024 Maximum size of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 65535 features: Compute capability of the device = 2.0 multiProcessorCount: 14 canMapHostMemory: TRUE deviceOverlap: TRUE   0: GPU memory usage: used = 59.343750 MB, free = 5316.093750 MB, total = 5375.437500 MB     1: GPU memory usage: used = 59.343750 MB, free = 5316.093750 MB, total = 5375.437500 MB   number of total devices: 2   number of total devices: 2   -------------- next part -------------- An HTML attachment was scrubbed... URL: From INCHINP at my.erau.edu Wed Mar 28 07:58:19 2018 From: INCHINP at my.erau.edu (Inchin, Pavel) Date: Wed, 28 Mar 2018 14:58:19 +0000 Subject: [CIG-SEISMO] Specfem3d_Globe Movie problem Message-ID: <582758FB-944A-430B-8DFC-1BB2314D5AB8@my.erau.edu> Good day, I have a problem with running of SPECFEM3D Globe on a cluster. When I run it with MOVIE_SURFACE = .false. and MOVIE_VOLUME=.false., the simulation runs without problems. But if I want to output movie, xspecfem3D gives error: forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source xspecfem3D 00000000006376E4 Unknown Unknown Unknown libpthread-2.17.s 00002AAAAC1C95E0 Unknown Unknown Unknown xspecfem3D 00000000005CF907 Unknown Unknown Unknown xspecfem3D 00000000004F0E18 Unknown Unknown Unknown xspecfem3D 00000000004EF900 Unknown Unknown Unknown xspecfem3D 0000000000507C23 Unknown Unknown Unknown xspecfem3D 00000000005CA25D Unknown Unknown Unknown xspecfem3D 00000000004044DE Unknown Unknown Unknown libc-2.17.so 00002AAAAC6F9C05 __libc_start_main Unknown Unknown xspecfem3D 00000000004043E9 Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source xspecfem3D 00000000006376E4 Unknown Unknown Unknown libpthread-2.17.s 00002AAAAC1C95E0 Unknown Unknown Unknown xspecfem3D 00000000005CF907 Unknown Unknown Unknown xspecfem3D 00000000004F0E18 Unknown Unknown Unknown xspecfem3D 00000000004EF900 Unknown Unknown Unknown xspecfem3D 0000000000507C23 Unknown Unknown Unknown xspecfem3D 00000000005CA25D Unknown Unknown Unknown xspecfem3D 00000000004044DE Unknown Unknown Unknown libc-2.17.so 00002AAAAC6F9C05 __libc_start_main Unknown Unknown xspecfem3D 00000000004043E9 Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source xspecfem3D 00000000006376E4 Unknown Unknown Unknown libpthread-2.17.s 00002AAAAC1C95E0 Unknown Unknown Unknown xspecfem3D 00000000005CF907 Unknown Unknown Unknown xspecfem3D 00000000004F0E18 Unknown Unknown Unknown xspecfem3D 00000000004EF900 Unknown Unknown Unknown xspecfem3D 0000000000507C23 Unknown Unknown Unknown xspecfem3D 00000000005CA25D Unknown Unknown Unknown xspecfem3D 00000000004044DE Unknown Unknown Unknown libc-2.17.so 00002AAAAC6F9C05 __libc_start_main Unknown Unknown xspecfem3D 00000000004043E9 Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source xspecfem3D 00000000006376E4 Unknown Unknown Unknown libpthread-2.17.s 00002AAAAC1C95E0 Unknown Unknown Unknown xspecfem3D 00000000005CF907 Unknown Unknown Unknown xspecfem3D 00000000004F0E18 Unknown Unknown Unknown xspecfem3D 00000000004EF900 Unknown Unknown Unknown xspecfem3D 0000000000507C23 Unknown Unknown Unknown xspecfem3D 00000000005CA25D Unknown Unknown Unknown xspecfem3D 00000000004044DE Unknown Unknown Unknown libc-2.17.so 00002AAAAC6F9C05 __libc_start_main Unknown Unknown xspecfem3D 00000000004043E9 Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source xspecfem3D 00000000006376E4 Unknown Unknown Unknown libpthread-2.17.s 00002AAAAC1C95E0 Unknown Unknown Unknown xspecfem3D 00000000005CF907 Unknown Unknown Unknown xspecfem3D 00000000004F0E18 Unknown Unknown Unknown xspecfem3D 00000000004EF900 Unknown Unknown Unknown xspecfem3D 0000000000507C23 Unknown Unknown Unknown xspecfem3D 00000000005CA25D Unknown Unknown Unknown xspecfem3D 00000000004044DE Unknown Unknown Unknown libc-2.17.so 00002AAAAC6F9C05 __libc_start_main Unknown Unknown xspecfem3D 00000000004043E9 Unknown Unknown Unknown …………. I compile using: ./configure FC=mpiifort MPIFC=mpiifort -mcmodel=medium-shared-intel And my modules are: intel/compiler/64/2017/17.0.5 intel/mpi/64/2017/5.239 I found this issue raised earlier (https://github.com/geodynamics/specfem3d/issues/512), but with running of the model by itself and not for movie… Could you provide a direction where to find a reason for that? Thank you Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From komatitsch at lma.cnrs-mrs.fr Wed Mar 28 14:39:37 2018 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Wed, 28 Mar 2018 23:39:37 +0200 Subject: [CIG-SEISMO] Specfem3d_Globe Movie problem In-Reply-To: <582758FB-944A-430B-8DFC-1BB2314D5AB8@my.erau.edu> References: <582758FB-944A-430B-8DFC-1BB2314D5AB8@my.erau.edu> Message-ID: <5d5097c4-a49f-1661-8041-688d1b784d9d@lma.cnrs-mrs.fr> Hi, Thanks. If your model is big it is maybe a movie array for which your system runs out of memory and for which we do not test the exit value of the allocate() statement. Could you configure with --enable-debug and let us know if the run then detects anything useful? Thank you, Best regards, Dimitri. On 03/28/2018 04:58 PM, Inchin, Pavel wrote: > Good day, > > I have a problem with running of SPECFEM3D Globe on a cluster. > > When I run it with > MOVIE_SURFACE = .false. and MOVIE_VOLUME=.false., the simulation runs > without problems. > > But if I want to output movie, xspecfem3D gives error: > > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image              PC                Routine            Line        Source > xspecfem3D         00000000006376E4  Unknown               Unknown  Unknown > libpthread-2.17.s  00002AAAAC1C95E0  Unknown               Unknown  Unknown > xspecfem3D         00000000005CF907  Unknown               Unknown  Unknown > xspecfem3D         00000000004F0E18  Unknown               Unknown  Unknown > xspecfem3D         00000000004EF900  Unknown               Unknown  Unknown > xspecfem3D         0000000000507C23  Unknown               Unknown  Unknown > xspecfem3D         00000000005CA25D  Unknown               Unknown  Unknown > xspecfem3D         00000000004044DE  Unknown               Unknown  Unknown > libc-2.17.so  00002AAAAC6F9C05  __libc_start_main     Unknown  Unknown > xspecfem3D         00000000004043E9  Unknown               Unknown  Unknown > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image              PC                Routine            Line        Source > xspecfem3D         00000000006376E4  Unknown               Unknown  Unknown > libpthread-2.17.s  00002AAAAC1C95E0  Unknown               Unknown  Unknown > xspecfem3D         00000000005CF907  Unknown               Unknown  Unknown > xspecfem3D         00000000004F0E18  Unknown               Unknown  Unknown > xspecfem3D         00000000004EF900  Unknown               Unknown  Unknown > xspecfem3D         0000000000507C23  Unknown               Unknown  Unknown > xspecfem3D         00000000005CA25D  Unknown               Unknown  Unknown > xspecfem3D         00000000004044DE  Unknown               Unknown  Unknown > libc-2.17.so  00002AAAAC6F9C05  __libc_start_main     Unknown  Unknown > xspecfem3D         00000000004043E9  Unknown               Unknown  Unknown > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image              PC                Routine            Line        Source > xspecfem3D         00000000006376E4  Unknown               Unknown  Unknown > libpthread-2.17.s  00002AAAAC1C95E0  Unknown               Unknown  Unknown > xspecfem3D         00000000005CF907  Unknown               Unknown  Unknown > xspecfem3D         00000000004F0E18  Unknown               Unknown  Unknown > xspecfem3D         00000000004EF900  Unknown               Unknown  Unknown > xspecfem3D         0000000000507C23  Unknown               Unknown  Unknown > xspecfem3D         00000000005CA25D  Unknown               Unknown  Unknown > xspecfem3D         00000000004044DE  Unknown               Unknown  Unknown > libc-2.17.so  00002AAAAC6F9C05  __libc_start_main     Unknown  Unknown > xspecfem3D         00000000004043E9  Unknown               Unknown  Unknown > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image              PC                Routine            Line        Source > xspecfem3D         00000000006376E4  Unknown               Unknown  Unknown > libpthread-2.17.s  00002AAAAC1C95E0  Unknown               Unknown  Unknown > xspecfem3D         00000000005CF907  Unknown               Unknown  Unknown > xspecfem3D         00000000004F0E18  Unknown               Unknown  Unknown > xspecfem3D         00000000004EF900  Unknown               Unknown  Unknown > xspecfem3D         0000000000507C23  Unknown               Unknown  Unknown > xspecfem3D         00000000005CA25D  Unknown               Unknown  Unknown > xspecfem3D         00000000004044DE  Unknown               Unknown  Unknown > libc-2.17.so  00002AAAAC6F9C05  __libc_start_main     Unknown  Unknown > xspecfem3D         00000000004043E9  Unknown               Unknown  Unknown > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image              PC                Routine            Line        Source > xspecfem3D         00000000006376E4  Unknown               Unknown  Unknown > libpthread-2.17.s  00002AAAAC1C95E0  Unknown               Unknown  Unknown > xspecfem3D         00000000005CF907  Unknown               Unknown  Unknown > xspecfem3D         00000000004F0E18  Unknown               Unknown  Unknown > xspecfem3D         00000000004EF900  Unknown               Unknown  Unknown > xspecfem3D         0000000000507C23  Unknown               Unknown  Unknown > xspecfem3D         00000000005CA25D  Unknown               Unknown  Unknown > xspecfem3D         00000000004044DE  Unknown               Unknown  Unknown > libc-2.17.so  00002AAAAC6F9C05  __libc_start_main     Unknown  Unknown > xspecfem3D         00000000004043E9  Unknown               Unknown  Unknown > …………. > > I compile using: ./configure FC=mpiifort MPIFC=mpiifort > -mcmodel=medium-shared-intel > > And my modules are: > intel/compiler/64/2017/17.0.5 > intel/mpi/64/2017/5.239 > > > I found this issue raised earlier > (https://github.com/geodynamics/specfem3d/issues/512), but with running > of the model by itself and not for movie… > > Could you provide a direction where to find a reason for that? > > Thank you > Paul > > > > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr From komatitsch at lma.cnrs-mrs.fr Wed Mar 28 15:18:56 2018 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Thu, 29 Mar 2018 00:18:56 +0200 Subject: [CIG-SEISMO] Specfem3d_Globe Movie problem In-Reply-To: <8F9BD3F6-76FD-4A33-BF32-CD4BCDC9ECCD@my.erau.edu> References: <582758FB-944A-430B-8DFC-1BB2314D5AB8@my.erau.edu> <5d5097c4-a49f-1661-8041-688d1b784d9d@lma.cnrs-mrs.fr> <8F9BD3F6-76FD-4A33-BF32-CD4BCDC9ECCD@my.erau.edu> Message-ID: Thanks. It is when you run the code that you may then get a useful bug report (unallocated array, array going out of bounds or something like that), since you will be running in debug mode. Please let us know. Thanks, Dimitri. On 03/29/2018 12:07 AM, Inchin, Pavel wrote: > Thank you for response, > > Here is a configuration log (not sure what might be useful). Thank you! > > > running example: Wed Mar 28 18:03:10 EDT 2018 > directory: /scratch/inchinp/specfem3d_globe/EXAMPLES/NEPAL > (will take about 7 minutes) > > >    setting up example... > > ## ---------------------------- ## > ## setting up compilation flags ## > ## ---------------------------- ## > checking build system type... x86_64-unknown-linux-gnu > checking host system type... x86_64-unknown-linux-gnu > checking whether the Fortran compiler works... yes > checking for Fortran compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU Fortran compiler... no > checking whether mpiifort accepts -g... yes > configure: running /bin/sh ./flags.guess > checking how to get verbose linking output from mpiifort... -v > checking for Fortran libraries of mpiifort... > -L/cm/shared/apps/intel/compilers_and_libraries/2017.5.239/mpi/intel64/lib/debug_mt > -L/cm/shared/apps/intel/compilers_and_libraries/2017.5.239/mpi/intel64/lib > -L/cm/shared/apps/intel/compilers_and_libraries/2017.5.239/compiler/lib/intel64 > -L/cm/shared/apps/intel/2017.5.061/compilers_and_libraries_2017.5.239/linux/compiler/lib/intel64_lin > -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/ > -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 > -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/ > -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64 > -L/usr/lib/../lib64/ > -L/cm/shared/apps/intel/compilers_and_libraries/2017.5.239/compiler/lib/intel64/ > -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../ -L/lib64 -L/lib/ > -L/usr/lib64 -L/usr/lib -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread > -lifport -lifcoremt -limf -lsvml -lm -lipgo -lirc -lirc_s > checking for gcc... icc > checking whether we are using the GNU C compiler... yes > checking whether icc accepts -g... yes > checking for icc option to accept ISO C89... none needed > checking for dummy main to link with Fortran libraries... none > checking for Fortran name-mangling scheme... lower case, underscore, no > extra underscore > checking for Fortran flag to compile .f90 files... none > checking for Fortran flag needed to accept free-form source... none > checking for Fortran flag to compile preprocessed .F files... none > checking how to define symbols for preprocessed Fortran... -D > checking for Fortran flag to compile preprocessed .F90 files... none > checking for gcc... (cached) icc > checking whether we are using the GNU C compiler... (cached) yes > checking whether icc accepts -g... (cached) yes > checking for icc option to accept ISO C89... (cached) none needed > ## ----------------- ## > ## module extensions ## > ## ----------------- ## > checking Fortran 90 module extension... mod > checking Fortran 90 module inclusion flag... -I > checking Fortran 90 module output flag... -mod > checking how to run the C preprocessor... icc -E > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/bin/grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking emmintrin.h usability... yes > checking emmintrin.h presence... yes > checking for emmintrin.h... yes > checking xmmintrin.h usability... yes > checking xmmintrin.h presence... yes > checking for xmmintrin.h... yes > checking whether we are using the GNU C++ compiler... yes > checking whether icpc accepts -g... yes > checking how to run the C++ preprocessor... icpc -E > ## ----------------------------------- ## > ## setting up default simulation setup ## > ## ----------------------------------- ## > configure: building from git repository > configure: creating ./config.status > config.status: creating Makefile > config.status: creating setup/constants.h > config.status: creating setup/constants_tomography.h > config.status: creating setup/precision.h > config.status: creating setup/config.fh > config.status: creating DATA/Par_file > config.status: creating DATA/CMTSOLUTION > config.status: creating DATA/STATIONS > config.status: creating setup/config.h > config.status: setup/config.h is unchanged > config.status: executing bin commands > config.status: executing obj commands > config.status: executing OUTPUT_FILES commands > > ## --------------------- ## > ## Specfem3D_Globe 7.0.1 ## > ## --------------------- ## > > ./configure has completed and set up a default configuration to build. > > You may wish to modify the following files before building: >   DATA/Par_file           Set parameters affecting the build and simulation >                           before running make and compiling. >   DATA/CMTSOLUTION        Set the source parameters before running the > solver. >   DATA/STATIONS           Set the receiver stations before running the > solver. > > cleaning all > rm -f  ./obj/shared_par.shared_module.o > ./obj/adios_manager.shared_adios_module.o ./obj/auto_ner.shared.o > ./obj/binary_c_io.cc.o ./obj/broadcast_computed_parameters.shared.o > ./obj/calendar.shared.o ./obj/count_elements.shared.o > ./obj/count_number_of_sources.shared.o ./obj/count_points.shared.o > ./obj/create_name_database.shared.o > ./obj/create_serial_name_database.shared.o > ./obj/define_all_layers.shared.o ./obj/euler_angles.shared.o > ./obj/exit_mpi.shared.o ./obj/flush_system.shared.o > ./obj/get_all_eight_slices.shared.o ./obj/get_global.shared.o > ./obj/get_model_parameters.shared.o > ./obj/get_timestep_and_layers.shared.o ./obj/gll_library.shared.o > ./obj/heap_sort.shared.o ./obj/hex_nodes.shared.o > ./obj/init_openmp.shared.o ./obj/interpolate.shared.o > ./obj/intgrl.shared.o ./obj/lagrange_poly.shared.o > ./obj/make_ellipticity.shared.o ./obj/memory_eval.shared.o > ./obj/model_prem.shared.o ./obj/model_topo_bathy.shared.o > ./obj/parallel.sharedmpi.o ./obj/param_reader.cc.o > ./obj/read_compute_parameters.shared.o > ./obj/read_parameter_file.shared.o ./obj/read_value_parameters.shared.o > ./obj/recompute_jacobian.shared.o ./obj/reduce.shared.o > ./obj/rthetaphi_xyz.shared.o ./obj/save_header_file.shared.o > ./obj/search_kdtree.shared.o ./obj/smooth_weights_vec.shared.o > ./obj/sort_array_coordinates.shared.o ./obj/spline_routines.shared.o > ./obj/write_VTK_file.shared.o  ./obj/adios_method_stubs.cc.o > ./obj/asdf_method_stubs.cc.o  ./obj/constants.mod > ./obj/manager_adios.mod ./obj/manager_adios_par.mod ./obj/my_mpi.mod > ./obj/shared_input_parameters.mod ./obj/shared_compute_parameters.mod > ./obj/shared_parameters.mod ./obj/kdtree_search.mod > ./obj/shared_par.shared_module.o > ./obj/adios_manager.shared_adios_module.o ./obj/auto_ner.shared.o > ./obj/binary_c_io.cc.o ./obj/broadcast_computed_parameters.shared.o > ./obj/calendar.shared.o ./obj/count_elements.shared.o > ./obj/count_number_of_sources.shared.o ./obj/count_points.shared.o > ./obj/create_name_database.shared.o > ./obj/create_serial_name_database.shared.o > ./obj/define_all_layers.shared.o ./obj/euler_angles.shared.o > ./obj/exit_mpi.shared.o ./obj/flush_system.shared.o > ./obj/get_all_eight_slices.shared.o ./obj/get_global.shared.o > ./obj/get_model_parameters.shared.o > ./obj/get_timestep_and_layers.shared.o ./obj/gll_library.shared.o > ./obj/heap_sort.shared.o ./obj/hex_nodes.shared.o > ./obj/init_openmp.shared.o ./obj/interpolate.shared.o > ./obj/intgrl.shared.o ./obj/lagrange_poly.shared.o > ./obj/make_ellipticity.shared.o ./obj/memory_eval.shared.o > ./obj/model_prem.shared.o ./obj/model_topo_bathy.shared.o > ./obj/parallel.sharedmpi.o ./obj/param_reader.cc.o > ./obj/read_compute_parameters.shared.o > ./obj/read_parameter_file.shared.o ./obj/read_value_parameters.shared.o > ./obj/recompute_jacobian.shared.o ./obj/reduce.shared.o > ./obj/rthetaphi_xyz.shared.o ./obj/save_header_file.shared.o > ./obj/search_kdtree.shared.o ./obj/smooth_weights_vec.shared.o > ./obj/sort_array_coordinates.shared.o ./obj/spline_routines.shared.o > ./obj/write_VTK_file.shared.o  ./obj/adios_method_stubs.cc.o > ./obj/asdf_method_stubs.cc.o    ./obj/create_header_file.header.o > ./bin/xcreate_header_file ./OUTPUT_FILES/values_from_mesher.h > ./obj/meshfem3D_par.check_module.o ./obj/meshfem3D.check.o > ./obj/meshfem3D_models.check.o ./obj/add_missing_nodes.check.o > ./obj/add_topography.check.o ./obj/add_topography_410_650.check.o > ./obj/add_topography_cmb.check.o ./obj/add_topography_icb.check.o > ./obj/assemble_MPI_central_cube_mesh.check.o > ./obj/assemble_MPI_scalar_mesh.check.o > ./obj/assemble_MPI_vector_mesh.check.o ./obj/calc_jacobian.check.o > ./obj/check_mesh_resolution.check.o > ./obj/compute_coordinates_grid.check.o > ./obj/compute_element_properties.check.o > ./obj/compute_volumes_and_areas.check.o ./obj/create_addressing.check.o > ./obj/create_central_cube.check.o > ./obj/create_central_cube_buffers.check.o > ./obj/create_chunk_buffers.check.o > ./obj/create_doubling_elements.check.o > ./obj/create_mass_matrices.check.o ./obj/create_meshes.check.o > ./obj/create_MPI_interfaces.check.o ./obj/create_regions_mesh.check.o > ./obj/create_regions_elements.check.o > ./obj/create_regular_elements.check.o ./obj/define_superbrick.check.o > ./obj/finalize_mesher.check.o ./obj/fix_non_blocking_flags.check.o > ./obj/get_absorb.check.o ./obj/get_ellipticity.check.o > ./obj/get_jacobian_boundaries.check.o > ./obj/get_jacobian_discontinuities.check.o ./obj/get_model.check.o > ./obj/get_MPI_1D_buffers.check.o ./obj/get_MPI_cutplanes_eta.check.o > ./obj/get_MPI_cutplanes_xi.check.o ./obj/get_MPI_interfaces.check.o > ./obj/get_perm_color.check.o ./obj/get_shape2D.check.o > ./obj/get_shape3D.check.o ./obj/gravity_integrals.check.o > ./obj/initialize_layers.check.o ./obj/initialize_mesher.check.o > ./obj/lgndr.check.o ./obj/model_1dref.check.o ./obj/model_1066a.check.o > ./obj/model_ak135.check.o ./obj/model_sea1d.check.o > ./obj/model_aniso_inner_core.check.o ./obj/model_aniso_mantle.check.o > ./obj/model_atten3D_QRFSI12.check.o ./obj/model_attenuation.check.o > ./obj/model_crust_1_0.check.o ./obj/model_crust_2_0.check.o > ./obj/model_crustmaps.check.o ./obj/model_eucrust.check.o > ./obj/model_epcrust.check.o ./obj/model_full_sh.check.o > ./obj/model_gapp2.check.o ./obj/model_gll.check.o > ./obj/model_heterogen_mantle.check.o ./obj/model_iasp91.check.o > ./obj/model_jp1d.check.o ./obj/model_jp3d.check.o > ./obj/model_ppm.check.o ./obj/model_s20rts.check.o > ./obj/model_s40rts.check.o ./obj/model_s362ani.check.o > ./obj/model_sea99_s.check.o ./obj/moho_stretching.check.o > ./obj/save_arrays_solver.check.o ./obj/setup_color_perm.check.o > ./obj/setup_counters.check.o ./obj/setup_inner_outer.check.o > ./obj/setup_model.check.o ./obj/setup_MPI_interfaces.check.o > ./obj/stretching_function.check.o ./obj/test_MPI_interfaces.check.o > ./obj/write_AVS_DX_global_chunks_data.check.o > ./obj/write_AVS_DX_global_data.check.o > ./obj/write_AVS_DX_global_faces_data.check.o > ./obj/write_AVS_DX_output.check.o > ./obj/write_AVS_DX_surface_data.check.o > ./obj/create_regions_mesh_par.mod ./obj/create_regions_mesh_par2.mod > ./obj/create_mpi_interfaces_par.mod > ./obj/gapp2_mantle_model_constants.mod ./obj/manager_adios_par.mod > ./obj/meshfem3d_models_par.mod ./obj/meshfem3d_par.mod > ./obj/mpi_crust_mantle_par.mod ./obj/mpi_inner_core_par.mod > ./obj/mpi_outer_core_par.mod ./obj/model_1066a_par.mod > ./obj/model_1dref_par.mod ./obj/model_ak135_par.mod > ./obj/model_aniso_mantle_par.mod ./obj/model_atten3d_qrfsi12_par.mod > ./obj/model_crust_1_0_par.mod ./obj/model_crust_2_0_par.mod > ./obj/model_crustmaps_par.mod ./obj/model_epcrust_par.mod > ./obj/model_eucrust_par.mod ./obj/model_full_sh_crust_par.mod > ./obj/model_full_sh_mantle_par.mod ./obj/model_heterogen_mantle_par.mod > ./obj/model_jp3d_par.mod ./obj/model_ppm_par.mod > ./obj/model_s20rts_par.mod ./obj/model_s362ani_par.mod > ./obj/model_s40rts_par.mod ./obj/model_sea1d_par.mod > ./obj/model_sea99_s_par.mod ./obj/avs_dx_global_chunks_mod.mod > ./obj/avs_dx_global_mod.mod ./obj/avs_dx_global_faces_mod.mod > ./obj/avs_dx_surface_mod.mod ./bin/xmeshfem3D > ./obj/assemble_MPI_scalar.solver.o ./obj/assemble_MPI_vector.solver.o > ./obj/comp_source_spectrum.solver.o > ./obj/compute_adj_source_frechet.solver.o ./obj/convert_time.solver.o > ./obj/define_derivation_matrices.solver.o ./obj/file_io_threads.cc.o > ./obj/force_ftz.cc.o ./obj/get_backazimuth.solver.o > ./obj/get_cmt.solver.o ./obj/get_force.solver.o > ./obj/get_event_info.solver.o ./obj/make_gravity.solver.o > ./obj/netlib_specfun_erf.solver.o  ./obj/asdf_data.solverstatic_module.o > ./obj/comp_source_time_function.solverstatic.o > ./obj/specfem3D_par.solverstatic_module.o > ./obj/write_seismograms.solverstatic.o > ./obj/check_stability.solverstatic.o > ./obj/compute_add_sources.solverstatic.o > ./obj/compute_arrays_source.solverstatic.o > ./obj/compute_boundary_kernel.solverstatic.o > ./obj/compute_coupling.solverstatic.o > ./obj/compute_element.solverstatic.o > ./obj/compute_element_att_memory.solverstatic.o > ./obj/compute_element_strain.solverstatic.o > ./obj/compute_forces_acoustic_calling_routine.solverstatic.o > ./obj/compute_forces_viscoelastic_calling_routine.solverstatic.o > ./obj/compute_forces_crust_mantle_noDev.solverstatic.o > ./obj/compute_forces_crust_mantle_Dev.solverstatic.o > ./obj/compute_forces_inner_core_noDev.solverstatic.o > ./obj/compute_forces_inner_core_Dev.solverstatic.o > ./obj/compute_forces_outer_core_noDev.solverstatic.o > ./obj/compute_forces_outer_core_Dev.solverstatic.o > ./obj/compute_kernels.solverstatic.o > ./obj/compute_seismograms.solverstatic.o > ./obj/compute_stacey_crust_mantle.solverstatic.o > ./obj/compute_stacey_outer_core.solverstatic.o > ./obj/finalize_simulation.solverstatic.o > ./obj/get_attenuation.solverstatic.o > ./obj/initialize_simulation.solverstatic.o > ./obj/iterate_time.solverstatic.o > ./obj/iterate_time_undoatt.solverstatic.o > ./obj/locate_receivers.solverstatic.o > ./obj/locate_regular_points.solverstatic.o > ./obj/locate_sources.solverstatic.o > ./obj/multiply_arrays_source.solverstatic.o > ./obj/noise_tomography.solverstatic.o > ./obj/prepare_attenuation.solverstatic.o > ./obj/prepare_elastic_elements.solverstatic.o > ./obj/prepare_gpu.solverstatic.o ./obj/prepare_gravity.solverstatic.o > ./obj/prepare_movie.solverstatic.o ./obj/prepare_noise.solverstatic.o > ./obj/prepare_oceans.solverstatic.o > ./obj/prepare_optimized_arrays.solverstatic.o > ./obj/prepare_stacey.solverstatic.o ./obj/prepare_timerun.solverstatic.o > ./obj/prepare_vtk_window.solverstatic.o > ./obj/prepare_wavefields.solverstatic.o > ./obj/read_adjoint_sources.solverstatic.o > ./obj/read_arrays_solver.solverstatic.o > ./obj/read_forward_arrays.solverstatic.o > ./obj/read_mesh_databases.solverstatic.o > ./obj/read_topography_bathymetry.solverstatic.o > ./obj/save_forward_arrays.solverstatic.o > ./obj/save_kernels.solverstatic.o > ./obj/save_regular_kernels.solverstatic.o > ./obj/setup_GLL_points.solverstatic.o > ./obj/setup_sources_receivers.solverstatic.o > ./obj/specfem3D.solverstatic.o > ./obj/update_displacement_LDDRK.solverstatic.o > ./obj/update_displacement_Newmark.solverstatic.o > ./obj/write_movie_output.solverstatic.o > ./obj/write_movie_volume.solverstatic.o > ./obj/write_movie_surface.solverstatic.o > ./obj/write_output_ASCII.solverstatic.o > ./obj/write_output_SAC.solverstatic.o > ./obj/specfem3D_gpu_method_stubs.cc.o > ./obj/visual_vtk_stubs.visualc.o  ./obj/asdf_data.mod > ./obj/constants_solver.mod ./obj/manager_adios_par.mod > ./obj/specfem_par.mod ./obj/specfem_par_crustmantle.mod > ./obj/specfem_par_innercore.mod ./obj/specfem_par_outercore.mod > ./obj/specfem_par_noise.mod ./obj/specfem_par_movie.mod > ./bin/xspecfem3D   ./obj/convolve_source_timefunction.aux.o > ./obj/detect_duplicates_stations_file.aux.o  ./obj/combine_AVS_DX.aux.o > ./obj/get_cmt.solver.o ./obj/combine_paraview_strain_data.auxsolver.o > ./obj/combine_surf_data.auxsolver.o  ./obj/combine_vol_data.auxsolver.o > ./obj/combine_vol_data.auxadios.o > ./obj/combine_vol_data_adios_impl.auxmpi.o > ./obj/combine_vol_data.auxsolver_vtk.o > ./obj/combine_vol_data.auxadios_vtk.o > ./obj/combine_vol_data_adios_impl.auxmpi.o > ./obj/create_movie_AVS_DX.aux.o  ./obj/create_movie_GMT_global.aux.o > ./obj/extract_database.aux.o    ./bin/xconvolve_source_timefunction > ./bin/xdetect_duplicates_stations_file ./bin/xcombine_AVS_DX > ./bin/xcombine_paraview_strain_data ./bin/xcombine_vol_data > ./bin/xcombine_vol_data_vtk ./bin/xcombine_surf_data > ./bin/xcreate_movie_AVS_DX ./bin/xcreate_movie_GMT_global > ./bin/xextract_database   ./obj/postprocess_par.postprocess_module.o > ./obj/addition_sem.postprocess.o > ./obj/postprocess_par.postprocess_module.o > ./obj/parse_kernel_names.postprocess.o ./obj/clip_sem.postprocess.o > ./obj/postprocess_par.postprocess_module.o > ./obj/parse_kernel_names.postprocess.o ./obj/combine_sem.postprocess.o > ./obj/postprocess_par.postprocess_module.o > ./obj/difference_sem.postprocess.o > ./obj/postprocess_par.postprocess_module.o > ./obj/interpolate_model.postprocess.o > ./obj/postprocess_par.postprocess_module.o > ./obj/create_cross_section.postprocess.o > ./obj/parse_kernel_names.postprocess.o > ./obj/postprocess_par.postprocess_module.o > ./obj/parse_kernel_names.postprocess.o ./obj/smooth_sem.postprocess.o > ./obj/convert_model_file_adios.postprocess_adios.o > ./obj/postprocess_par.mod  ./bin/xaddition_sem ./bin/xclip_sem > ./bin/xcombine_sem ./bin/xdifference_sem ./bin/xinterpolate_model > ./bin/xcreate_cross_section ./bin/xsmooth_sem > ./obj/add_model_iso.tomo.o ./obj/tomography_par.tomo_module.o > ./obj/compute_kernel_integral.tomo.o ./obj/get_cg_direction.tomo.o > ./obj/get_sd_direction.tomo.o ./obj/read_kernels.tomo.o > ./obj/read_kernels_cg.tomo.o ./obj/read_model.tomo.o > ./obj/read_parameters_tomo.tomo.o ./obj/write_gradient.tomo.o > ./obj/write_new_model.tomo.o ./obj/write_new_model_perturbations.tomo.o >   ./obj/add_model_tiso.tomo.o ./obj/tomography_par.tomo_module.o > ./obj/compute_kernel_integral.tomo.o ./obj/get_cg_direction.tomo.o > ./obj/get_sd_direction.tomo.o ./obj/read_kernels.tomo.o > ./obj/read_kernels_cg.tomo.o ./obj/read_model.tomo.o > ./obj/read_parameters_tomo.tomo.o ./obj/write_gradient.tomo.o > ./obj/write_new_model.tomo.o ./obj/write_new_model_perturbations.tomo.o >   ./obj/add_model_tiso_cg.tomo.o ./obj/tomography_par.tomo_module.o > ./obj/compute_kernel_integral.tomo.o ./obj/get_cg_direction.tomo.o > ./obj/get_sd_direction.tomo.o ./obj/read_kernels.tomo.o > ./obj/read_kernels_cg.tomo.o ./obj/read_model.tomo.o > ./obj/read_parameters_tomo.tomo.o ./obj/write_gradient.tomo.o > ./obj/write_new_model.tomo.o ./obj/write_new_model_perturbations.tomo.o >   ./obj/add_model_tiso_iso.tomo.o ./obj/tomography_par.tomo_module.o > ./obj/compute_kernel_integral.tomo.o ./obj/get_cg_direction.tomo.o > ./obj/get_sd_direction.tomo.o ./obj/read_kernels.tomo.o > ./obj/read_kernels_cg.tomo.o ./obj/read_model.tomo.o > ./obj/read_parameters_tomo.tomo.o ./obj/write_gradient.tomo.o > ./obj/write_new_model.tomo.o ./obj/write_new_model_perturbations.tomo.o >   ./obj/tomography_par.tomo_module.o ./obj/sum_kernels.tomo.o > ./obj/tomography_par.tomo_module.o > ./obj/sum_preconditioned_kernels.tomo.o   ./obj/tomography_par.mod > ./obj/tomography_kernels_iso.mod ./obj/tomography_kernels_tiso.mod > ./obj/tomography_kernels_tiso_cg.mod ./obj/tomography_model_tiso.mod > ./obj/tomography_model_iso.mod  ./bin/xadd_model_iso > ./bin/xadd_model_tiso ./bin/xadd_model_tiso_cg ./bin/xadd_model_tiso_iso > ./bin/xsum_kernels ./bin/xsum_preconditioned_kernels > rm -f ./bin/*__genmod.* > rm -f ./obj/*__genmod.* > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/shared_par.shared_module.o src/shared/shared_par.f90 > icc -c -I./setup    -g -O2 -o obj/param_reader.cc.o > src/shared/param_reader.c > icc -c -I./setup    -g -O2 -o obj/binary_c_io.cc.o src/shared/binary_c_io.c > icc -c -I./setup    -g -O2 -o obj/adios_method_stubs.cc.o > src/shared/adios_method_stubs.c > icc -c -I./setup    -g -O2 -o obj/file_io_threads.cc.o > src/specfem3D/file_io_threads.c > icc -c -I./setup    -g -O2 -o obj/force_ftz.cc.o src/specfem3D/force_ftz.c > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_backazimuth.solver.o src/specfem3D/get_backazimuth.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_cmt.solver.o src/specfem3D/get_cmt.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_force.solver.o src/specfem3D/get_force.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_event_info.solver.o src/specfem3D/get_event_info.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/make_gravity.solver.o src/specfem3D/make_gravity.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/netlib_specfun_erf.solver.o src/specfem3D/netlib_specfun_erf.f90 > icc -c -I./setup    -g -O2 -o obj/specfem3D_gpu_method_stubs.cc.o > src/specfem3D/specfem3D_gpu_method_stubs.c > icc -c -I./setup     -o obj/visual_vtk_stubs.visualc.o > src/specfem3D/visual_vtk_stubs.c > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/calendar.shared.o src/shared/calendar.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/recompute_jacobian.shared.o src/shared/recompute_jacobian.f90 > icc -c -I./setup    -g -O2 -o obj/asdf_method_stubs.cc.o > src/shared/asdf_method_stubs.c > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_serial_name_database.shared.o > src/shared/create_serial_name_database.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/search_kdtree.shared.o src/shared/search_kdtree.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/interpolate.shared.o src/shared/interpolate.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/auto_ner.shared.o src/shared/auto_ner.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/count_elements.shared.o src/shared/count_elements.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/count_number_of_sources.shared.o src/shared/count_number_of_sources.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/count_points.shared.o src/shared/count_points.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/define_all_layers.shared.o src/shared/define_all_layers.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/euler_angles.shared.o src/shared/euler_angles.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_model_parameters.shared.o src/shared/get_model_parameters.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_timestep_and_layers.shared.o src/shared/get_timestep_and_layers.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/memory_eval.shared.o src/shared/memory_eval.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/read_compute_parameters.shared.o src/shared/read_compute_parameters.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/read_parameter_file.shared.o src/shared/read_parameter_file.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/read_value_parameters.shared.o src/shared/read_value_parameters.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/reduce.shared.o src/shared/reduce.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/rthetaphi_xyz.shared.o src/shared/rthetaphi_xyz.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/save_header_file.shared.o src/shared/save_header_file.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_header_file.header.o > src/create_header_file/create_header_file.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/adios_manager.shared_adios_module.o src/shared/adios_manager.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/broadcast_computed_parameters.shared.o > src/shared/broadcast_computed_parameters.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_name_database.shared.o src/shared/create_name_database.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/exit_mpi.shared.o src/shared/exit_mpi.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/flush_system.shared.o src/shared/flush_system.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_all_eight_slices.shared.o src/shared/get_all_eight_slices.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_global.shared.o src/shared/get_global.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/gll_library.shared.o src/shared/gll_library.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/heap_sort.shared.o src/shared/heap_sort.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/hex_nodes.shared.o src/shared/hex_nodes.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/init_openmp.shared.o src/shared/init_openmp.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/intgrl.shared.o src/shared/intgrl.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/lagrange_poly.shared.o src/shared/lagrange_poly.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/make_ellipticity.shared.o src/shared/make_ellipticity.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_prem.shared.o src/shared/model_prem.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_topo_bathy.shared.o src/shared/model_topo_bathy.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/parallel.sharedmpi.o src/shared/parallel.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/smooth_weights_vec.shared.o src/shared/smooth_weights_vec.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/sort_array_coordinates.shared.o src/shared/sort_array_coordinates.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/spline_routines.shared.o src/shared/spline_routines.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_VTK_file.shared.o src/shared/write_VTK_file.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/meshfem3D_par.check_module.o src/meshfem3D/meshfem3D_par.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/assemble_MPI_scalar.solver.o src/specfem3D/assemble_MPI_scalar.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/assemble_MPI_vector.solver.o src/specfem3D/assemble_MPI_vector.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/comp_source_spectrum.solver.o src/specfem3D/comp_source_spectrum.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_adj_source_frechet.solver.o > src/specfem3D/compute_adj_source_frechet.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/convert_time.solver.o src/specfem3D/convert_time.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/define_derivation_matrices.solver.o > src/specfem3D/define_derivation_matrices.f90 > mpiifort -g      -o bin/xcreate_header_file > obj/shared_par.shared_module.o obj/auto_ner.shared.o > obj/count_elements.shared.o obj/count_number_of_sources.shared.o > obj/count_points.shared.o obj/define_all_layers.shared.o > obj/euler_angles.shared.o obj/get_model_parameters.shared.o > obj/get_timestep_and_layers.shared.o obj/memory_eval.shared.o > obj/param_reader.cc.o obj/read_compute_parameters.shared.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > obj/reduce.shared.o obj/rthetaphi_xyz.shared.o > obj/save_header_file.shared.o obj/create_header_file.header.o > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/meshfem3D.check.o src/meshfem3D/meshfem3D.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/meshfem3D_models.check.o src/meshfem3D/meshfem3D_models.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/add_missing_nodes.check.o src/meshfem3D/add_missing_nodes.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/add_topography.check.o src/meshfem3D/add_topography.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/add_topography_410_650.check.o src/meshfem3D/add_topography_410_650.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/add_topography_cmb.check.o src/meshfem3D/add_topography_cmb.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/add_topography_icb.check.o src/meshfem3D/add_topography_icb.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/assemble_MPI_central_cube_mesh.check.o > src/meshfem3D/assemble_MPI_central_cube_mesh.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/assemble_MPI_scalar_mesh.check.o > src/meshfem3D/assemble_MPI_scalar_mesh.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/assemble_MPI_vector_mesh.check.o > src/meshfem3D/assemble_MPI_vector_mesh.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/calc_jacobian.check.o src/meshfem3D/calc_jacobian.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/check_mesh_resolution.check.o src/meshfem3D/check_mesh_resolution.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_coordinates_grid.check.o > src/meshfem3D/compute_coordinates_grid.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_element_properties.check.o > src/meshfem3D/compute_element_properties.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_volumes_and_areas.check.o > src/meshfem3D/compute_volumes_and_areas.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_addressing.check.o src/meshfem3D/create_addressing.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_central_cube.check.o src/meshfem3D/create_central_cube.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_central_cube_buffers.check.o > src/meshfem3D/create_central_cube_buffers.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_chunk_buffers.check.o src/meshfem3D/create_chunk_buffers.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_doubling_elements.check.o > src/meshfem3D/create_doubling_elements.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_mass_matrices.check.o src/meshfem3D/create_mass_matrices.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_meshes.check.o src/meshfem3D/create_meshes.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_MPI_interfaces.check.o src/meshfem3D/create_MPI_interfaces.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_regions_mesh.check.o src/meshfem3D/create_regions_mesh.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_regions_elements.check.o > src/meshfem3D/create_regions_elements.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_regular_elements.check.o > src/meshfem3D/create_regular_elements.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/define_superbrick.check.o src/meshfem3D/define_superbrick.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/finalize_mesher.check.o src/meshfem3D/finalize_mesher.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/fix_non_blocking_flags.check.o src/meshfem3D/fix_non_blocking_flags.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_absorb.check.o src/meshfem3D/get_absorb.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_ellipticity.check.o src/meshfem3D/get_ellipticity.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_jacobian_boundaries.check.o > src/meshfem3D/get_jacobian_boundaries.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_jacobian_discontinuities.check.o > src/meshfem3D/get_jacobian_discontinuities.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_model.check.o src/meshfem3D/get_model.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_MPI_1D_buffers.check.o src/meshfem3D/get_MPI_1D_buffers.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_MPI_cutplanes_eta.check.o src/meshfem3D/get_MPI_cutplanes_eta.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_MPI_cutplanes_xi.check.o src/meshfem3D/get_MPI_cutplanes_xi.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_MPI_interfaces.check.o src/meshfem3D/get_MPI_interfaces.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_perm_color.check.o src/meshfem3D/get_perm_color.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_shape2D.check.o src/meshfem3D/get_shape2D.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_shape3D.check.o src/meshfem3D/get_shape3D.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/gravity_integrals.check.o src/meshfem3D/gravity_integrals.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/initialize_layers.check.o src/meshfem3D/initialize_layers.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/initialize_mesher.check.o src/meshfem3D/initialize_mesher.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/lgndr.check.o src/meshfem3D/lgndr.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_1dref.check.o src/meshfem3D/model_1dref.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_1066a.check.o src/meshfem3D/model_1066a.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_ak135.check.o src/meshfem3D/model_ak135.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_sea1d.check.o src/meshfem3D/model_sea1d.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_aniso_inner_core.check.o src/meshfem3D/model_aniso_inner_core.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_aniso_mantle.check.o src/meshfem3D/model_aniso_mantle.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_atten3D_QRFSI12.check.o src/meshfem3D/model_atten3D_QRFSI12.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_crust_1_0.check.o src/meshfem3D/model_crust_1_0.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_crust_2_0.check.o src/meshfem3D/model_crust_2_0.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_crustmaps.check.o src/meshfem3D/model_crustmaps.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_eucrust.check.o src/meshfem3D/model_eucrust.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_epcrust.check.o src/meshfem3D/model_epcrust.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_full_sh.check.o src/meshfem3D/model_full_sh.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_gapp2.check.o src/meshfem3D/model_gapp2.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_gll.check.o src/meshfem3D/model_gll.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_heterogen_mantle.check.o src/meshfem3D/model_heterogen_mantle.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_iasp91.check.o src/meshfem3D/model_iasp91.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_jp1d.check.o src/meshfem3D/model_jp1d.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_jp3d.check.o src/meshfem3D/model_jp3d.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_ppm.check.o src/meshfem3D/model_ppm.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_s20rts.check.o src/meshfem3D/model_s20rts.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_s40rts.check.o src/meshfem3D/model_s40rts.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_s362ani.check.o src/meshfem3D/model_s362ani.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_sea99_s.check.o src/meshfem3D/model_sea99_s.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/moho_stretching.check.o src/meshfem3D/moho_stretching.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/save_arrays_solver.check.o src/meshfem3D/save_arrays_solver.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/setup_color_perm.check.o src/meshfem3D/setup_color_perm.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/setup_counters.check.o src/meshfem3D/setup_counters.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/setup_inner_outer.check.o src/meshfem3D/setup_inner_outer.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/setup_model.check.o src/meshfem3D/setup_model.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/setup_MPI_interfaces.check.o src/meshfem3D/setup_MPI_interfaces.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/stretching_function.check.o src/meshfem3D/stretching_function.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/test_MPI_interfaces.check.o src/meshfem3D/test_MPI_interfaces.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_AVS_DX_global_chunks_data.check.o > src/meshfem3D/write_AVS_DX_global_chunks_data.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_AVS_DX_global_data.check.o > src/meshfem3D/write_AVS_DX_global_data.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_AVS_DX_global_faces_data.check.o > src/meshfem3D/write_AVS_DX_global_faces_data.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_AVS_DX_output.check.o src/meshfem3D/write_AVS_DX_output.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_AVS_DX_surface_data.check.o > src/meshfem3D/write_AVS_DX_surface_data.f90 > > running xcreate_header_file... > > ./bin/xcreate_header_file > > >  creating file OUTPUT_FILES/values_from_mesher.h to compile solver with > correct >  values > > >  edit file OUTPUT_FILES/values_from_mesher.h to see >  some statistics about the mesh > > >  number of processors =          216 > > >  maximum number of points per region =      1060349 > > >  total elements per slice =        18325 >  total points per slice =      1222043 > > >  the time step of the solver will be DT =   0.1900000      (s) >  the (approximate) minimum period resolved will be =    18.13333      (s) > > >  current record length is =    60.00000     min >  current minimum number of time steps will be =        19000 > > >  MOVIE_VOLUME : T >  MOVIE_SURFACE: F >  Saving movie frames every         100 > > >  on NEC SX, make sure "loopcnt=" parameter >  in Makefile is greater than max vector length =      3181047 > > >  approximate static memory needed by the solver: >  ---------------------------------------------- > > >  (lower bound, usually the real amount used is 5% to 10% higher) > > >  (you can get a more precise estimate of the size used per MPI process >   by typing "size -d bin/xspecfem3D" >   after compiling the code with the DATA/Par_file you plan to use) > > >  size of static arrays per slice =    751.438408000000       MB >                                  =    716.627510070801       MiB >                                  =   0.751438408000000       GB >                                  =   0.699831552803516       GiB > > >     (should be below 80% or 90% of the memory installed per core) >     (if significantly more, the job will not run by lack of memory) >     (note that if significantly less, you waste a significant amount >      of memory per processor core) >     (but that can be perfectly acceptable if you can afford it and >      want faster results by using more cores) > > >  size of static arrays for all slices =    162.310696128000       GB >                                       =    151.163615405560       GiB >                                       =   0.162310696128000       TB >                                       =   0.147620718169492       TiB > > >  ******************************************************************************* >  Estimating optimal disk dumping interval for UNDO_ATTENUATION: >  ******************************************************************************* > > >  without undoing of attenuation you are using    1.17753139200000 >   GB per core >    i.e.    29.43828     % of the installed memory > > >  each time step to store in memory to undo attenuation will require > storing >   1.425235200000000E-002  GB per core > > >  ******************************************************************************* >  the optimal value is thus NT_DUMP_ATTENUATION =          155 >  ******************************************************************************* > > >  we will need to save a total of          123  dumpings (restart files) > to disk > > >  each dumping on the disk to undo attenuation will require storing >   0.169208064000000       GB per core > > >  each dumping on the disk will require storing    36.5489418240000 >   GB for all cores > > >  ALL dumpings on the disk will require storing    20.8125918720000 >   GB per core > > >  ******************************************************************************* >  ALL dumpings on the disk will require storing    4495.51984435200 >   GB for all cores >    i.e.    4.49551984435200       TB >  ******************************************************************************* > > > > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/model_attenuation.check.o src/meshfem3D/model_attenuation.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/asdf_data.solverstatic_module.o src/specfem3D/asdf_data.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/specfem3D_par.solverstatic_module.o src/specfem3D/specfem3D_par.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/combine_AVS_DX.aux.o src/auxiliaries/combine_AVS_DX.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/combine_surf_data.auxsolver.o src/auxiliaries/combine_surf_data.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/combine_vol_data.auxsolver.o src/auxiliaries/combine_vol_data.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/combine_vol_data.auxsolver_vtk.o > src/auxiliaries/combine_vol_data.F90 -DUSE_VTK_INSTEAD_OF_MESH > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/convolve_source_timefunction.aux.o > src/auxiliaries/convolve_source_timefunction.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_movie_AVS_DX.aux.o src/auxiliaries/create_movie_AVS_DX.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_movie_GMT_global.aux.o > src/auxiliaries/create_movie_GMT_global.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/detect_duplicates_stations_file.aux.o > src/auxiliaries/detect_duplicates_stations_file.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/combine_paraview_strain_data.auxsolver.o > src/auxiliaries/combine_paraview_strain_data.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/extract_database.aux.o src/auxiliaries/extract_database.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/postprocess_par.postprocess_module.o > src/tomography/postprocess_sensitivity_kernels/postprocess_par.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/tomography_par.tomo_module.o src/tomography/tomography_par.f90 > mpiifort -g      -o bin/xcombine_surf_data > obj/combine_surf_data.auxsolver.o obj/shared_par.shared_module.o > obj/binary_c_io.cc.o obj/flush_system.shared.o > mpiifort -g      -o bin/xcombine_vol_data_vtk > obj/combine_vol_data.auxsolver_vtk.o obj/shared_par.shared_module.o > obj/binary_c_io.cc.o obj/exit_mpi.shared.o obj/flush_system.shared.o > obj/intgrl.shared.o obj/make_ellipticity.shared.o > obj/model_prem.shared.o obj/parallel.sharedmpi.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > obj/param_reader.cc.o obj/reduce.shared.o obj/rthetaphi_xyz.shared.o > obj/spline_routines.shared.o > mpiifort -g      -o bin/xconvolve_source_timefunction > obj/convolve_source_timefunction.aux.o obj/shared_par.shared_module.o > mpiifort -g      -o bin/xdetect_duplicates_stations_file > obj/detect_duplicates_stations_file.aux.o obj/shared_par.shared_module.o > mpiifort -g      -o bin/xmeshfem3D obj/shared_par.shared_module.o > obj/adios_manager.shared_adios_module.o obj/auto_ner.shared.o > obj/binary_c_io.cc.o obj/broadcast_computed_parameters.shared.o > obj/count_elements.shared.o obj/count_number_of_sources.shared.o > obj/count_points.shared.o obj/create_name_database.shared.o > obj/define_all_layers.shared.o obj/euler_angles.shared.o > obj/exit_mpi.shared.o obj/flush_system.shared.o > obj/get_all_eight_slices.shared.o obj/get_global.shared.o > obj/get_model_parameters.shared.o obj/get_timestep_and_layers.shared.o > obj/gll_library.shared.o obj/heap_sort.shared.o obj/hex_nodes.shared.o > obj/init_openmp.shared.o obj/intgrl.shared.o obj/lagrange_poly.shared.o > obj/make_ellipticity.shared.o obj/memory_eval.shared.o > obj/model_prem.shared.o obj/model_topo_bathy.shared.o > obj/parallel.sharedmpi.o obj/param_reader.cc.o > obj/read_compute_parameters.shared.o obj/read_parameter_file.shared.o > obj/read_value_parameters.shared.o obj/reduce.shared.o > obj/rthetaphi_xyz.shared.o obj/save_header_file.shared.o > obj/smooth_weights_vec.shared.o obj/sort_array_coordinates.shared.o > obj/spline_routines.shared.o obj/write_VTK_file.shared.o > obj/adios_method_stubs.cc.o obj/meshfem3D_par.check_module.o > obj/meshfem3D.check.o obj/meshfem3D_models.check.o > obj/add_missing_nodes.check.o obj/add_topography.check.o > obj/add_topography_410_650.check.o obj/add_topography_cmb.check.o > obj/add_topography_icb.check.o > obj/assemble_MPI_central_cube_mesh.check.o > obj/assemble_MPI_scalar_mesh.check.o > obj/assemble_MPI_vector_mesh.check.o obj/calc_jacobian.check.o > obj/check_mesh_resolution.check.o obj/compute_coordinates_grid.check.o > obj/compute_element_properties.check.o > obj/compute_volumes_and_areas.check.o obj/create_addressing.check.o > obj/create_central_cube.check.o obj/create_central_cube_buffers.check.o > obj/create_chunk_buffers.check.o obj/create_doubling_elements.check.o > obj/create_mass_matrices.check.o obj/create_meshes.check.o > obj/create_MPI_interfaces.check.o obj/create_regions_mesh.check.o > obj/create_regions_elements.check.o obj/create_regular_elements.check.o > obj/define_superbrick.check.o obj/finalize_mesher.check.o > obj/fix_non_blocking_flags.check.o obj/get_absorb.check.o > obj/get_ellipticity.check.o obj/get_jacobian_boundaries.check.o > obj/get_jacobian_discontinuities.check.o obj/get_model.check.o > obj/get_MPI_1D_buffers.check.o obj/get_MPI_cutplanes_eta.check.o > obj/get_MPI_cutplanes_xi.check.o obj/get_MPI_interfaces.check.o > obj/get_perm_color.check.o obj/get_shape2D.check.o > obj/get_shape3D.check.o obj/gravity_integrals.check.o > obj/initialize_layers.check.o obj/initialize_mesher.check.o > obj/lgndr.check.o obj/model_1dref.check.o obj/model_1066a.check.o > obj/model_ak135.check.o obj/model_sea1d.check.o > obj/model_aniso_inner_core.check.o obj/model_aniso_mantle.check.o > obj/model_atten3D_QRFSI12.check.o obj/model_attenuation.check.o > obj/model_crust_1_0.check.o obj/model_crust_2_0.check.o > obj/model_crustmaps.check.o obj/model_eucrust.check.o > obj/model_epcrust.check.o obj/model_full_sh.check.o > obj/model_gapp2.check.o obj/model_gll.check.o > obj/model_heterogen_mantle.check.o obj/model_iasp91.check.o > obj/model_jp1d.check.o obj/model_jp3d.check.o obj/model_ppm.check.o > obj/model_s20rts.check.o obj/model_s40rts.check.o > obj/model_s362ani.check.o obj/model_sea99_s.check.o > obj/moho_stretching.check.o obj/save_arrays_solver.check.o > obj/setup_color_perm.check.o obj/setup_counters.check.o > obj/setup_inner_outer.check.o obj/setup_model.check.o > obj/setup_MPI_interfaces.check.o obj/stretching_function.check.o > obj/test_MPI_interfaces.check.o > obj/write_AVS_DX_global_chunks_data.check.o > obj/write_AVS_DX_global_data.check.o > obj/write_AVS_DX_global_faces_data.check.o > obj/write_AVS_DX_output.check.o obj/write_AVS_DX_surface_data.check.o > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/comp_source_time_function.solverstatic.o > src/specfem3D/comp_source_time_function.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_seismograms.solverstatic.o src/specfem3D/write_seismograms.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/check_stability.solverstatic.o src/specfem3D/check_stability.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_add_sources.solverstatic.o src/specfem3D/compute_add_sources.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_boundary_kernel.solverstatic.o > src/specfem3D/compute_boundary_kernel.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_coupling.solverstatic.o src/specfem3D/compute_coupling.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_element.solverstatic.o src/specfem3D/compute_element.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_element_att_memory.solverstatic.o > src/specfem3D/compute_element_att_memory.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_element_strain.solverstatic.o > src/specfem3D/compute_element_strain.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_forces_acoustic_calling_routine.solverstatic.o > src/specfem3D/compute_forces_acoustic_calling_routine.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_forces_viscoelastic_calling_routine.solverstatic.o > src/specfem3D/compute_forces_viscoelastic_calling_routine.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_forces_crust_mantle_noDev.solverstatic.o > src/specfem3D/compute_forces_crust_mantle_noDev.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_forces_crust_mantle_Dev.solverstatic.o > src/specfem3D/compute_forces_crust_mantle_Dev.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_forces_inner_core_noDev.solverstatic.o > src/specfem3D/compute_forces_inner_core_noDev.f90 > src/specfem3D/compute_element.F90(1383): remark #5082: Directive ignored > - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: > ; RECURSIVE > !DIR$ INLINEALWAYS compute_element_stress_attenuation_contrib > ------------^ > src/specfem3D/compute_element.F90(1486): remark #5082: Directive ignored > - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: > ; RECURSIVE > !DIR$ INLINEALWAYS compute_element_precompute_factors > ------------^ > src/specfem3D/compute_element.F90(1587): remark #5082: Directive ignored > - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: > ; RECURSIVE > !DIR$ INLINEALWAYS compute_element_deviatoric_strain > ------------^ > src/specfem3D/compute_element.F90(1677): remark #5082: Directive ignored > - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: > ; RECURSIVE > !DIR$ INLINEALWAYS compute_element_dot_product_stress > ------------^ > src/specfem3D/compute_element.F90(1779): remark #5082: Directive ignored > - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: > ; RECURSIVE > !DIR$ INLINEALWAYS compute_element_gravity > ------------^ > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_forces_inner_core_Dev.solverstatic.o > src/specfem3D/compute_forces_inner_core_Dev.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_forces_outer_core_noDev.solverstatic.o > src/specfem3D/compute_forces_outer_core_noDev.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_forces_outer_core_Dev.solverstatic.o > src/specfem3D/compute_forces_outer_core_Dev.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_kernels.solverstatic.o src/specfem3D/compute_kernels.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_seismograms.solverstatic.o src/specfem3D/compute_seismograms.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_stacey_crust_mantle.solverstatic.o > src/specfem3D/compute_stacey_crust_mantle.f90 > src/specfem3D/compute_forces_crust_mantle_Dev.F90(557): remark #5082: > Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when > expecting one of: ; RECURSIVE > !DIR$ INLINEALWAYS mxm5_3comp_singleA > ------------^ > src/specfem3D/compute_forces_crust_mantle_Dev.F90(622): remark #5082: > Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when > expecting one of: ; RECURSIVE > !DIR$ INLINEALWAYS mxm5_3comp_singleB > ------------^ > src/specfem3D/compute_forces_crust_mantle_Dev.F90(687): remark #5082: > Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when > expecting one of: ; RECURSIVE > !DIR$ INLINEALWAYS mxm5_3comp_3dmat_singleB > ------------^ > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_stacey_outer_core.solverstatic.o > src/specfem3D/compute_stacey_outer_core.f90 > src/specfem3D/compute_forces_inner_core_Dev.F90(420): remark #5082: > Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when > expecting one of: ; RECURSIVE > !DIR$ INLINEALWAYS mxm5_3comp_singleA > ------------^ > src/specfem3D/compute_forces_inner_core_Dev.F90(485): remark #5082: > Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when > expecting one of: ; RECURSIVE > !DIR$ INLINEALWAYS mxm5_3comp_singleB > ------------^ > src/specfem3D/compute_forces_inner_core_Dev.F90(550): remark #5082: > Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when > expecting one of: ; RECURSIVE > !DIR$ INLINEALWAYS mxm5_3comp_3dmat_singleB > ------------^ > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/finalize_simulation.solverstatic.o src/specfem3D/finalize_simulation.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_attenuation.solverstatic.o src/specfem3D/get_attenuation.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/initialize_simulation.solverstatic.o > src/specfem3D/initialize_simulation.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/iterate_time.solverstatic.o src/specfem3D/iterate_time.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/iterate_time_undoatt.solverstatic.o > src/specfem3D/iterate_time_undoatt.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/locate_receivers.solverstatic.o src/specfem3D/locate_receivers.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/locate_regular_points.solverstatic.o > src/specfem3D/locate_regular_points.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/locate_sources.solverstatic.o src/specfem3D/locate_sources.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/multiply_arrays_source.solverstatic.o > src/specfem3D/multiply_arrays_source.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/noise_tomography.solverstatic.o src/specfem3D/noise_tomography.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/prepare_attenuation.solverstatic.o src/specfem3D/prepare_attenuation.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/prepare_elastic_elements.solverstatic.o > src/specfem3D/prepare_elastic_elements.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/prepare_gpu.solverstatic.o src/specfem3D/prepare_gpu.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/prepare_gravity.solverstatic.o src/specfem3D/prepare_gravity.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/prepare_movie.solverstatic.o src/specfem3D/prepare_movie.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/prepare_noise.solverstatic.o src/specfem3D/prepare_noise.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/prepare_oceans.solverstatic.o src/specfem3D/prepare_oceans.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/prepare_optimized_arrays.solverstatic.o > src/specfem3D/prepare_optimized_arrays.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/prepare_stacey.solverstatic.o src/specfem3D/prepare_stacey.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/prepare_timerun.solverstatic.o src/specfem3D/prepare_timerun.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/prepare_vtk_window.solverstatic.o src/specfem3D/prepare_vtk_window.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/prepare_wavefields.solverstatic.o src/specfem3D/prepare_wavefields.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/read_adjoint_sources.solverstatic.o > src/specfem3D/read_adjoint_sources.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/read_arrays_solver.solverstatic.o src/specfem3D/read_arrays_solver.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/read_forward_arrays.solverstatic.o src/specfem3D/read_forward_arrays.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/read_mesh_databases.solverstatic.o src/specfem3D/read_mesh_databases.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/read_topography_bathymetry.solverstatic.o > src/specfem3D/read_topography_bathymetry.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/save_forward_arrays.solverstatic.o src/specfem3D/save_forward_arrays.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/save_kernels.solverstatic.o src/specfem3D/save_kernels.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/save_regular_kernels.solverstatic.o > src/specfem3D/save_regular_kernels.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/setup_GLL_points.solverstatic.o src/specfem3D/setup_GLL_points.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/setup_sources_receivers.solverstatic.o > src/specfem3D/setup_sources_receivers.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/specfem3D.solverstatic.o src/specfem3D/specfem3D.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/update_displacement_LDDRK.solverstatic.o > src/specfem3D/update_displacement_LDDRK.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/update_displacement_Newmark.solverstatic.o > src/specfem3D/update_displacement_Newmark.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_movie_output.solverstatic.o src/specfem3D/write_movie_output.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_movie_volume.solverstatic.o src/specfem3D/write_movie_volume.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_movie_surface.solverstatic.o src/specfem3D/write_movie_surface.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_output_ASCII.solverstatic.o src/specfem3D/write_output_ASCII.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_output_SAC.solverstatic.o src/specfem3D/write_output_SAC.f90 > mpiifort -g      -o bin/xcombine_AVS_DX obj/combine_AVS_DX.aux.o > obj/get_cmt.solver.o obj/shared_par.shared_module.o > obj/auto_ner.shared.o obj/calendar.shared.o obj/count_elements.shared.o > obj/count_number_of_sources.shared.o obj/count_points.shared.o > obj/create_serial_name_database.shared.o obj/define_all_layers.shared.o > obj/get_model_parameters.shared.o obj/get_timestep_and_layers.shared.o > obj/param_reader.cc.o obj/read_compute_parameters.shared.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > obj/reduce.shared.o obj/rthetaphi_xyz.shared.o > mpiifort -g      -o bin/xcombine_vol_data > obj/combine_vol_data.auxsolver.o obj/shared_par.shared_module.o > obj/binary_c_io.cc.o obj/exit_mpi.shared.o obj/flush_system.shared.o > obj/intgrl.shared.o obj/make_ellipticity.shared.o > obj/model_prem.shared.o obj/parallel.sharedmpi.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > obj/param_reader.cc.o obj/reduce.shared.o obj/rthetaphi_xyz.shared.o > obj/spline_routines.shared.o > mpiifort -g      -o bin/xcreate_movie_AVS_DX > obj/create_movie_AVS_DX.aux.o obj/shared_par.shared_module.o > obj/auto_ner.shared.o obj/count_elements.shared.o > obj/count_number_of_sources.shared.o obj/count_points.shared.o > obj/define_all_layers.shared.o obj/get_global.shared.o > obj/get_model_parameters.shared.o obj/get_timestep_and_layers.shared.o > obj/param_reader.cc.o obj/read_compute_parameters.shared.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > obj/reduce.shared.o obj/rthetaphi_xyz.shared.o > obj/sort_array_coordinates.shared.o > mpiifort -g      -o bin/xcreate_movie_GMT_global > obj/create_movie_GMT_global.aux.o obj/shared_par.shared_module.o > obj/auto_ner.shared.o obj/count_elements.shared.o > obj/count_number_of_sources.shared.o obj/count_points.shared.o > obj/define_all_layers.shared.o obj/get_model_parameters.shared.o > obj/get_timestep_and_layers.shared.o obj/param_reader.cc.o > obj/read_compute_parameters.shared.o obj/read_parameter_file.shared.o > obj/read_value_parameters.shared.o obj/reduce.shared.o > obj/rthetaphi_xyz.shared.o > mpiifort -g      -o bin/xcombine_paraview_strain_data > obj/combine_paraview_strain_data.auxsolver.o > obj/shared_par.shared_module.o obj/binary_c_io.cc.o > mpiifort -g      -o bin/xextract_database obj/extract_database.aux.o > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/addition_sem.postprocess.o > src/tomography/postprocess_sensitivity_kernels/addition_sem.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/parse_kernel_names.postprocess.o > src/tomography/postprocess_sensitivity_kernels/parse_kernel_names.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/clip_sem.postprocess.o > src/tomography/postprocess_sensitivity_kernels/clip_sem.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/combine_sem.postprocess.o > src/tomography/postprocess_sensitivity_kernels/combine_sem.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/difference_sem.postprocess.o > src/tomography/postprocess_sensitivity_kernels/difference_sem.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/interpolate_model.postprocess.o > src/tomography/postprocess_sensitivity_kernels/interpolate_model.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/create_cross_section.postprocess.o > src/tomography/postprocess_sensitivity_kernels/create_cross_section.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/smooth_sem.postprocess.o > src/tomography/postprocess_sensitivity_kernels/smooth_sem.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/add_model_iso.tomo.o src/tomography/add_model_iso.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_kernel_integral.tomo.o > src/tomography/compute_kernel_integral.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_cg_direction.tomo.o src/tomography/get_cg_direction.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/get_sd_direction.tomo.o src/tomography/get_sd_direction.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/read_kernels.tomo.o src/tomography/read_kernels.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/read_kernels_cg.tomo.o src/tomography/read_kernels_cg.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/read_model.tomo.o src/tomography/read_model.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/read_parameters_tomo.tomo.o src/tomography/read_parameters_tomo.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_gradient.tomo.o src/tomography/write_gradient.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_new_model.tomo.o src/tomography/write_new_model.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/write_new_model_perturbations.tomo.o > src/tomography/write_new_model_perturbations.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/add_model_tiso.tomo.o src/tomography/add_model_tiso.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/add_model_tiso_cg.tomo.o src/tomography/add_model_tiso_cg.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/add_model_tiso_iso.tomo.o src/tomography/add_model_tiso_iso.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/sum_kernels.tomo.o src/tomography/sum_kernels.F90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/sum_preconditioned_kernels.tomo.o > src/tomography/sum_preconditioned_kernels.f90 > mpiifort -g      -mod ./obj -I./obj -I.  -I. -I./setup -c -o > obj/compute_arrays_source.solverstatic.o > src/specfem3D/compute_arrays_source.f90 > mpiifort -g      -o bin/xaddition_sem > obj/postprocess_par.postprocess_module.o obj/addition_sem.postprocess.o > obj/shared_par.shared_module.o obj/parallel.sharedmpi.o > obj/exit_mpi.shared.o obj/param_reader.cc.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > mpiifort -g      -o bin/xclip_sem > obj/postprocess_par.postprocess_module.o > obj/parse_kernel_names.postprocess.o obj/clip_sem.postprocess.o > obj/shared_par.shared_module.o obj/parallel.sharedmpi.o > obj/param_reader.cc.o obj/read_parameter_file.shared.o > obj/read_value_parameters.shared.o > mpiifort -g      -o bin/xcombine_sem > obj/postprocess_par.postprocess_module.o > obj/parse_kernel_names.postprocess.o obj/combine_sem.postprocess.o > obj/shared_par.shared_module.o obj/parallel.sharedmpi.o > obj/param_reader.cc.o obj/read_parameter_file.shared.o > obj/read_value_parameters.shared.o > mpiifort -g      -o bin/xdifference_sem > obj/postprocess_par.postprocess_module.o > obj/difference_sem.postprocess.o obj/shared_par.shared_module.o > obj/parallel.sharedmpi.o obj/exit_mpi.shared.o obj/param_reader.cc.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > mpiifort -g      -o bin/xinterpolate_model > obj/postprocess_par.postprocess_module.o > obj/interpolate_model.postprocess.o obj/shared_par.shared_module.o > obj/parallel.sharedmpi.o obj/gll_library.shared.o obj/heap_sort.shared.o > obj/hex_nodes.shared.o obj/interpolate.shared.o > obj/lagrange_poly.shared.o obj/recompute_jacobian.shared.o > obj/search_kdtree.shared.o obj/param_reader.cc.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > mpiifort -g      -o bin/xcreate_cross_section > obj/postprocess_par.postprocess_module.o > obj/create_cross_section.postprocess.o > obj/parse_kernel_names.postprocess.o obj/shared_par.shared_module.o > obj/parallel.sharedmpi.o obj/binary_c_io.cc.o > obj/create_name_database.shared.o obj/exit_mpi.shared.o > obj/flush_system.shared.o obj/gll_library.shared.o > obj/heap_sort.shared.o obj/hex_nodes.shared.o obj/interpolate.shared.o > obj/intgrl.shared.o obj/lagrange_poly.shared.o > obj/make_ellipticity.shared.o obj/model_prem.shared.o > obj/model_topo_bathy.shared.o obj/recompute_jacobian.shared.o > obj/reduce.shared.o obj/rthetaphi_xyz.shared.o > obj/search_kdtree.shared.o obj/spline_routines.shared.o > obj/param_reader.cc.o obj/read_parameter_file.shared.o > obj/read_value_parameters.shared.o > mpiifort -g      -o bin/xsmooth_sem > obj/postprocess_par.postprocess_module.o > obj/parse_kernel_names.postprocess.o obj/smooth_sem.postprocess.o > obj/shared_par.shared_module.o obj/parallel.sharedmpi.o > obj/exit_mpi.shared.o obj/get_all_eight_slices.shared.o > obj/gll_library.shared.o obj/heap_sort.shared.o obj/reduce.shared.o > obj/rthetaphi_xyz.shared.o obj/search_kdtree.shared.o > obj/smooth_weights_vec.shared.o obj/write_VTK_file.shared.o > obj/param_reader.cc.o obj/read_parameter_file.shared.o > obj/read_value_parameters.shared.o > mpiifort -g      -o bin/xadd_model_iso obj/add_model_iso.tomo.o > obj/tomography_par.tomo_module.o obj/compute_kernel_integral.tomo.o > obj/get_cg_direction.tomo.o obj/get_sd_direction.tomo.o > obj/read_kernels.tomo.o obj/read_kernels_cg.tomo.o obj/read_model.tomo.o > obj/read_parameters_tomo.tomo.o obj/write_gradient.tomo.o > obj/write_new_model.tomo.o obj/write_new_model_perturbations.tomo.o > obj/shared_par.shared_module.o obj/parallel.sharedmpi.o > obj/exit_mpi.shared.o obj/gll_library.shared.o obj/param_reader.cc.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > mpiifort -g      -o bin/xadd_model_tiso obj/add_model_tiso.tomo.o > obj/tomography_par.tomo_module.o obj/compute_kernel_integral.tomo.o > obj/get_cg_direction.tomo.o obj/get_sd_direction.tomo.o > obj/read_kernels.tomo.o obj/read_kernels_cg.tomo.o obj/read_model.tomo.o > obj/read_parameters_tomo.tomo.o obj/write_gradient.tomo.o > obj/write_new_model.tomo.o obj/write_new_model_perturbations.tomo.o > obj/shared_par.shared_module.o obj/parallel.sharedmpi.o > obj/exit_mpi.shared.o obj/gll_library.shared.o obj/param_reader.cc.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > mpiifort -g      -o bin/xadd_model_tiso_cg obj/add_model_tiso_cg.tomo.o > obj/tomography_par.tomo_module.o obj/compute_kernel_integral.tomo.o > obj/get_cg_direction.tomo.o obj/get_sd_direction.tomo.o > obj/read_kernels.tomo.o obj/read_kernels_cg.tomo.o obj/read_model.tomo.o > obj/read_parameters_tomo.tomo.o obj/write_gradient.tomo.o > obj/write_new_model.tomo.o obj/write_new_model_perturbations.tomo.o > obj/shared_par.shared_module.o obj/parallel.sharedmpi.o > obj/exit_mpi.shared.o obj/gll_library.shared.o obj/param_reader.cc.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > mpiifort -g      -o bin/xadd_model_tiso_iso > obj/add_model_tiso_iso.tomo.o obj/tomography_par.tomo_module.o > obj/compute_kernel_integral.tomo.o obj/get_cg_direction.tomo.o > obj/get_sd_direction.tomo.o obj/read_kernels.tomo.o > obj/read_kernels_cg.tomo.o obj/read_model.tomo.o > obj/read_parameters_tomo.tomo.o obj/write_gradient.tomo.o > obj/write_new_model.tomo.o obj/write_new_model_perturbations.tomo.o > obj/shared_par.shared_module.o obj/parallel.sharedmpi.o > obj/exit_mpi.shared.o obj/gll_library.shared.o obj/param_reader.cc.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > mpiifort -g      -o bin/xsum_kernels obj/tomography_par.tomo_module.o > obj/sum_kernels.tomo.o obj/shared_par.shared_module.o > obj/parallel.sharedmpi.o obj/param_reader.cc.o > obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o > mpiifort -g      -o bin/xsum_preconditioned_kernels > obj/tomography_par.tomo_module.o obj/sum_preconditioned_kernels.tomo.o > obj/shared_par.shared_module.o obj/parallel.sharedmpi.o > obj/param_reader.cc.o obj/read_parameter_file.shared.o > obj/read_value_parameters.shared.o > > building xspecfem3D > > mpiifort -g      -o ./bin/xspecfem3D ./obj/assemble_MPI_scalar.solver.o > ./obj/assemble_MPI_vector.solver.o ./obj/comp_source_spectrum.solver.o > ./obj/compute_adj_source_frechet.solver.o ./obj/convert_time.solver.o > ./obj/define_derivation_matrices.solver.o ./obj/file_io_threads.cc.o > ./obj/force_ftz.cc.o ./obj/get_backazimuth.solver.o > ./obj/get_cmt.solver.o ./obj/get_force.solver.o > ./obj/get_event_info.solver.o ./obj/make_gravity.solver.o > ./obj/netlib_specfun_erf.solver.o ./obj/asdf_data.solverstatic_module.o > ./obj/comp_source_time_function.solverstatic.o > ./obj/specfem3D_par.solverstatic_module.o > ./obj/write_seismograms.solverstatic.o > ./obj/check_stability.solverstatic.o > ./obj/compute_add_sources.solverstatic.o > ./obj/compute_arrays_source.solverstatic.o > ./obj/compute_boundary_kernel.solverstatic.o > ./obj/compute_coupling.solverstatic.o > ./obj/compute_element.solverstatic.o > ./obj/compute_element_att_memory.solverstatic.o > ./obj/compute_element_strain.solverstatic.o > ./obj/compute_forces_acoustic_calling_routine.solverstatic.o > ./obj/compute_forces_viscoelastic_calling_routine.solverstatic.o > ./obj/compute_forces_crust_mantle_noDev.solverstatic.o > ./obj/compute_forces_crust_mantle_Dev.solverstatic.o > ./obj/compute_forces_inner_core_noDev.solverstatic.o > ./obj/compute_forces_inner_core_Dev.solverstatic.o > ./obj/compute_forces_outer_core_noDev.solverstatic.o > ./obj/compute_forces_outer_core_Dev.solverstatic.o > ./obj/compute_kernels.solverstatic.o > ./obj/compute_seismograms.solverstatic.o > ./obj/compute_stacey_crust_mantle.solverstatic.o > ./obj/compute_stacey_outer_core.solverstatic.o > ./obj/finalize_simulation.solverstatic.o > ./obj/get_attenuation.solverstatic.o > ./obj/initialize_simulation.solverstatic.o > ./obj/iterate_time.solverstatic.o > ./obj/iterate_time_undoatt.solverstatic.o > ./obj/locate_receivers.solverstatic.o > ./obj/locate_regular_points.solverstatic.o > ./obj/locate_sources.solverstatic.o > ./obj/multiply_arrays_source.solverstatic.o > ./obj/noise_tomography.solverstatic.o > ./obj/prepare_attenuation.solverstatic.o > ./obj/prepare_elastic_elements.solverstatic.o > ./obj/prepare_gpu.solverstatic.o ./obj/prepare_gravity.solverstatic.o > ./obj/prepare_movie.solverstatic.o ./obj/prepare_noise.solverstatic.o > ./obj/prepare_oceans.solverstatic.o > ./obj/prepare_optimized_arrays.solverstatic.o > ./obj/prepare_stacey.solverstatic.o ./obj/prepare_timerun.solverstatic.o > ./obj/prepare_vtk_window.solverstatic.o > ./obj/prepare_wavefields.solverstatic.o > ./obj/read_adjoint_sources.solverstatic.o > ./obj/read_arrays_solver.solverstatic.o > ./obj/read_forward_arrays.solverstatic.o > ./obj/read_mesh_databases.solverstatic.o > ./obj/read_topography_bathymetry.solverstatic.o > ./obj/save_forward_arrays.solverstatic.o > ./obj/save_kernels.solverstatic.o > ./obj/save_regular_kernels.solverstatic.o > ./obj/setup_GLL_points.solverstatic.o > ./obj/setup_sources_receivers.solverstatic.o > ./obj/specfem3D.solverstatic.o > ./obj/update_displacement_LDDRK.solverstatic.o > ./obj/update_displacement_Newmark.solverstatic.o > ./obj/write_movie_output.solverstatic.o > ./obj/write_movie_volume.solverstatic.o > ./obj/write_movie_surface.solverstatic.o > ./obj/write_output_ASCII.solverstatic.o > ./obj/write_output_SAC.solverstatic.o > ./obj/specfem3D_gpu_method_stubs.cc.o   ./obj/visual_vtk_stubs.visualc.o > ./obj/shared_par.shared_module.o > ./obj/adios_manager.shared_adios_module.o ./obj/auto_ner.shared.o > ./obj/binary_c_io.cc.o ./obj/broadcast_computed_parameters.shared.o > ./obj/calendar.shared.o ./obj/count_elements.shared.o > ./obj/count_number_of_sources.shared.o ./obj/count_points.shared.o > ./obj/create_name_database.shared.o ./obj/define_all_layers.shared.o > ./obj/exit_mpi.shared.o ./obj/flush_system.shared.o > ./obj/get_model_parameters.shared.o > ./obj/get_timestep_and_layers.shared.o ./obj/gll_library.shared.o > ./obj/hex_nodes.shared.o ./obj/init_openmp.shared.o > ./obj/intgrl.shared.o ./obj/lagrange_poly.shared.o > ./obj/make_ellipticity.shared.o ./obj/model_prem.shared.o > ./obj/model_topo_bathy.shared.o ./obj/parallel.sharedmpi.o > ./obj/param_reader.cc.o ./obj/read_compute_parameters.shared.o > ./obj/read_parameter_file.shared.o ./obj/read_value_parameters.shared.o > ./obj/recompute_jacobian.shared.o ./obj/reduce.shared.o > ./obj/rthetaphi_xyz.shared.o ./obj/spline_routines.shared.o > ./obj/write_VTK_file.shared.o  ./obj/adios_method_stubs.cc.o > ./obj/asdf_method_stubs.cc.o > > cp: omitting directory ‘setup/adios_xml_files’ > ln: failed to create symbolic link ‘./crust2.0’: File exists > ln: failed to create symbolic link ‘./s362ani’: File exists > ln: failed to create symbolic link ‘./QRFSI12’: File exists > ln: failed to create symbolic link ‘./topo_bathy’: File exists > >   running script... > > Wed Mar 28 18:03:52 EDT 2018 > > > >> On Mar 28, 2018, at 5:39 PM, Dimitri Komatitsch >> > wrote: >> >> >> Hi, >> >> Thanks. If your model is big it is maybe a movie array for which your >> system runs out of memory and for which we do not test the exit value >> of the allocate() statement. >> >> Could you configure with --enable-debug and let us know if the run >> then detects anything useful? >> >> Thank you, >> Best regards, >> Dimitri. >> >> On 03/28/2018 04:58 PM, Inchin, Pavel wrote: >>> Good day, >>> I have a problem with running of SPECFEM3D Globe on a cluster. >>> When I run it with >>> MOVIE_SURFACE = .false. and MOVIE_VOLUME=.false., the simulation runs >>> without problems. >>> But if I want to output movie, xspecfem3D gives error: >>> forrtl: severe (174): SIGSEGV, segmentation fault occurred >>> Image              PC                Routine            Line >>> Source >>> xspecfem3D         00000000006376E4  Unknown               Unknown >>> Unknown >>> libpthread-2.17.s  00002AAAAC1C95E0  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000005CF907  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004F0E18  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004EF900  Unknown               Unknown >>> Unknown >>> xspecfem3D         0000000000507C23  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000005CA25D  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004044DE  Unknown               Unknown >>> Unknown >>> libc-2.17.so  00002AAAAC6F9C05  __libc_start_main     Unknown  Unknown >>> xspecfem3D         00000000004043E9  Unknown               Unknown >>> Unknown >>> forrtl: severe (174): SIGSEGV, segmentation fault occurred >>> Image              PC                Routine            Line >>> Source >>> xspecfem3D         00000000006376E4  Unknown               Unknown >>> Unknown >>> libpthread-2.17.s  00002AAAAC1C95E0  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000005CF907  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004F0E18  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004EF900  Unknown               Unknown >>> Unknown >>> xspecfem3D         0000000000507C23  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000005CA25D  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004044DE  Unknown               Unknown >>> Unknown >>> libc-2.17.so  00002AAAAC6F9C05  __libc_start_main     Unknown  Unknown >>> xspecfem3D         00000000004043E9  Unknown               Unknown >>> Unknown >>> forrtl: severe (174): SIGSEGV, segmentation fault occurred >>> Image              PC                Routine            Line >>> Source >>> xspecfem3D         00000000006376E4  Unknown               Unknown >>> Unknown >>> libpthread-2.17.s  00002AAAAC1C95E0  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000005CF907  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004F0E18  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004EF900  Unknown               Unknown >>> Unknown >>> xspecfem3D         0000000000507C23  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000005CA25D  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004044DE  Unknown               Unknown >>> Unknown >>> libc-2.17.so  00002AAAAC6F9C05  __libc_start_main     Unknown  Unknown >>> xspecfem3D         00000000004043E9  Unknown               Unknown >>> Unknown >>> forrtl: severe (174): SIGSEGV, segmentation fault occurred >>> Image              PC                Routine            Line >>> Source >>> xspecfem3D         00000000006376E4  Unknown               Unknown >>> Unknown >>> libpthread-2.17.s  00002AAAAC1C95E0  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000005CF907  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004F0E18  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004EF900  Unknown               Unknown >>> Unknown >>> xspecfem3D         0000000000507C23  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000005CA25D  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004044DE  Unknown               Unknown >>> Unknown >>> libc-2.17.so  00002AAAAC6F9C05  __libc_start_main     Unknown  Unknown >>> xspecfem3D         00000000004043E9  Unknown               Unknown >>> Unknown >>> forrtl: severe (174): SIGSEGV, segmentation fault occurred >>> Image              PC                Routine            Line >>> Source >>> xspecfem3D         00000000006376E4  Unknown               Unknown >>> Unknown >>> libpthread-2.17.s  00002AAAAC1C95E0  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000005CF907  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004F0E18  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004EF900  Unknown               Unknown >>> Unknown >>> xspecfem3D         0000000000507C23  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000005CA25D  Unknown               Unknown >>> Unknown >>> xspecfem3D         00000000004044DE  Unknown               Unknown >>> Unknown >>> libc-2.17.so  00002AAAAC6F9C05  __libc_start_main     Unknown  Unknown >>> xspecfem3D         00000000004043E9  Unknown               Unknown >>> Unknown >>> …………. >>> I compile using: ./configure FC=mpiifort MPIFC=mpiifort >>> -mcmodel=medium-shared-intel >>> And my modules are: >>> intel/compiler/64/2017/17.0.5 >>> intel/mpi/64/2017/5.239 >>> I found this issue raised earlier >>> (https://github.com/geodynamics/specfem3d/issues/512), but with >>> running of the model by itself and not for movie… >>> Could you provide a direction where to find a reason for that? >>> Thank you >>> Paul >>> _______________________________________________ >>> CIG-SEISMO mailing list >>> CIG-SEISMO at geodynamics.org >>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >> >> -- >> Dimitri Komatitsch, CNRS Research Director (DR CNRS) >> Laboratory of Mechanics and Acoustics, Marseille, France >> http://komatitsch.free.fr > -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr From INCHINP at my.erau.edu Wed Mar 28 15:07:15 2018 From: INCHINP at my.erau.edu (Inchin, Pavel) Date: Wed, 28 Mar 2018 22:07:15 +0000 Subject: [CIG-SEISMO] Specfem3d_Globe Movie problem In-Reply-To: <5d5097c4-a49f-1661-8041-688d1b784d9d@lma.cnrs-mrs.fr> References: <582758FB-944A-430B-8DFC-1BB2314D5AB8@my.erau.edu> <5d5097c4-a49f-1661-8041-688d1b784d9d@lma.cnrs-mrs.fr> Message-ID: <8F9BD3F6-76FD-4A33-BF32-CD4BCDC9ECCD@my.erau.edu> Thank you for response, Here is a configuration log (not sure what might be useful). Thank you! running example: Wed Mar 28 18:03:10 EDT 2018 directory: /scratch/inchinp/specfem3d_globe/EXAMPLES/NEPAL (will take about 7 minutes) setting up example... ## ---------------------------- ## ## setting up compilation flags ## ## ---------------------------- ## checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking whether the Fortran compiler works... yes checking for Fortran compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU Fortran compiler... no checking whether mpiifort accepts -g... yes configure: running /bin/sh ./flags.guess checking how to get verbose linking output from mpiifort... -v checking for Fortran libraries of mpiifort... -L/cm/shared/apps/intel/compilers_and_libraries/2017.5.239/mpi/intel64/lib/debug_mt -L/cm/shared/apps/intel/compilers_and_libraries/2017.5.239/mpi/intel64/lib -L/cm/shared/apps/intel/compilers_and_libraries/2017.5.239/compiler/lib/intel64 -L/cm/shared/apps/intel/2017.5.061/compilers_and_libraries_2017.5.239/linux/compiler/lib/intel64_lin -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/ -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/ -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64 -L/usr/lib/../lib64/ -L/cm/shared/apps/intel/compilers_and_libraries/2017.5.239/compiler/lib/intel64/ -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../ -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread -lifport -lifcoremt -limf -lsvml -lm -lipgo -lirc -lirc_s checking for gcc... icc checking whether we are using the GNU C compiler... yes checking whether icc accepts -g... yes checking for icc option to accept ISO C89... none needed checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking for Fortran flag to compile .f90 files... none checking for Fortran flag needed to accept free-form source... none checking for Fortran flag to compile preprocessed .F files... none checking how to define symbols for preprocessed Fortran... -D checking for Fortran flag to compile preprocessed .F90 files... none checking for gcc... (cached) icc checking whether we are using the GNU C compiler... (cached) yes checking whether icc accepts -g... (cached) yes checking for icc option to accept ISO C89... (cached) none needed ## ----------------- ## ## module extensions ## ## ----------------- ## checking Fortran 90 module extension... mod checking Fortran 90 module inclusion flag... -I checking Fortran 90 module output flag... -mod checking how to run the C preprocessor... icc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking emmintrin.h usability... yes checking emmintrin.h presence... yes checking for emmintrin.h... yes checking xmmintrin.h usability... yes checking xmmintrin.h presence... yes checking for xmmintrin.h... yes checking whether we are using the GNU C++ compiler... yes checking whether icpc accepts -g... yes checking how to run the C++ preprocessor... icpc -E ## ----------------------------------- ## ## setting up default simulation setup ## ## ----------------------------------- ## configure: building from git repository configure: creating ./config.status config.status: creating Makefile config.status: creating setup/constants.h config.status: creating setup/constants_tomography.h config.status: creating setup/precision.h config.status: creating setup/config.fh config.status: creating DATA/Par_file config.status: creating DATA/CMTSOLUTION config.status: creating DATA/STATIONS config.status: creating setup/config.h config.status: setup/config.h is unchanged config.status: executing bin commands config.status: executing obj commands config.status: executing OUTPUT_FILES commands ## --------------------- ## ## Specfem3D_Globe 7.0.1 ## ## --------------------- ## ./configure has completed and set up a default configuration to build. You may wish to modify the following files before building: DATA/Par_file Set parameters affecting the build and simulation before running make and compiling. DATA/CMTSOLUTION Set the source parameters before running the solver. DATA/STATIONS Set the receiver stations before running the solver. cleaning all rm -f ./obj/shared_par.shared_module.o ./obj/adios_manager.shared_adios_module.o ./obj/auto_ner.shared.o ./obj/binary_c_io.cc.o ./obj/broadcast_computed_parameters.shared.o ./obj/calendar.shared.o ./obj/count_elements.shared.o ./obj/count_number_of_sources.shared.o ./obj/count_points.shared.o ./obj/create_name_database.shared.o ./obj/create_serial_name_database.shared.o ./obj/define_all_layers.shared.o ./obj/euler_angles.shared.o ./obj/exit_mpi.shared.o ./obj/flush_system.shared.o ./obj/get_all_eight_slices.shared.o ./obj/get_global.shared.o ./obj/get_model_parameters.shared.o ./obj/get_timestep_and_layers.shared.o ./obj/gll_library.shared.o ./obj/heap_sort.shared.o ./obj/hex_nodes.shared.o ./obj/init_openmp.shared.o ./obj/interpolate.shared.o ./obj/intgrl.shared.o ./obj/lagrange_poly.shared.o ./obj/make_ellipticity.shared.o ./obj/memory_eval.shared.o ./obj/model_prem.shared.o ./obj/model_topo_bathy.shared.o ./obj/parallel.sharedmpi.o ./obj/param_reader.cc.o ./obj/read_compute_parameters.shared.o ./obj/read_parameter_file.shared.o ./obj/read_value_parameters.shared.o ./obj/recompute_jacobian.shared.o ./obj/reduce.shared.o ./obj/rthetaphi_xyz.shared.o ./obj/save_header_file.shared.o ./obj/search_kdtree.shared.o ./obj/smooth_weights_vec.shared.o ./obj/sort_array_coordinates.shared.o ./obj/spline_routines.shared.o ./obj/write_VTK_file.shared.o ./obj/adios_method_stubs.cc.o ./obj/asdf_method_stubs.cc.o ./obj/constants.mod ./obj/manager_adios.mod ./obj/manager_adios_par.mod ./obj/my_mpi.mod ./obj/shared_input_parameters.mod ./obj/shared_compute_parameters.mod ./obj/shared_parameters.mod ./obj/kdtree_search.mod ./obj/shared_par.shared_module.o ./obj/adios_manager.shared_adios_module.o ./obj/auto_ner.shared.o ./obj/binary_c_io.cc.o ./obj/broadcast_computed_parameters.shared.o ./obj/calendar.shared.o ./obj/count_elements.shared.o ./obj/count_number_of_sources.shared.o ./obj/count_points.shared.o ./obj/create_name_database.shared.o ./obj/create_serial_name_database.shared.o ./obj/define_all_layers.shared.o ./obj/euler_angles.shared.o ./obj/exit_mpi.shared.o ./obj/flush_system.shared.o ./obj/get_all_eight_slices.shared.o ./obj/get_global.shared.o ./obj/get_model_parameters.shared.o ./obj/get_timestep_and_layers.shared.o ./obj/gll_library.shared.o ./obj/heap_sort.shared.o ./obj/hex_nodes.shared.o ./obj/init_openmp.shared.o ./obj/interpolate.shared.o ./obj/intgrl.shared.o ./obj/lagrange_poly.shared.o ./obj/make_ellipticity.shared.o ./obj/memory_eval.shared.o ./obj/model_prem.shared.o ./obj/model_topo_bathy.shared.o ./obj/parallel.sharedmpi.o ./obj/param_reader.cc.o ./obj/read_compute_parameters.shared.o ./obj/read_parameter_file.shared.o ./obj/read_value_parameters.shared.o ./obj/recompute_jacobian.shared.o ./obj/reduce.shared.o ./obj/rthetaphi_xyz.shared.o ./obj/save_header_file.shared.o ./obj/search_kdtree.shared.o ./obj/smooth_weights_vec.shared.o ./obj/sort_array_coordinates.shared.o ./obj/spline_routines.shared.o ./obj/write_VTK_file.shared.o ./obj/adios_method_stubs.cc.o ./obj/asdf_method_stubs.cc.o ./obj/create_header_file.header.o ./bin/xcreate_header_file ./OUTPUT_FILES/values_from_mesher.h ./obj/meshfem3D_par.check_module.o ./obj/meshfem3D.check.o ./obj/meshfem3D_models.check.o ./obj/add_missing_nodes.check.o ./obj/add_topography.check.o ./obj/add_topography_410_650.check.o ./obj/add_topography_cmb.check.o ./obj/add_topography_icb.check.o ./obj/assemble_MPI_central_cube_mesh.check.o ./obj/assemble_MPI_scalar_mesh.check.o ./obj/assemble_MPI_vector_mesh.check.o ./obj/calc_jacobian.check.o ./obj/check_mesh_resolution.check.o ./obj/compute_coordinates_grid.check.o ./obj/compute_element_properties.check.o ./obj/compute_volumes_and_areas.check.o ./obj/create_addressing.check.o ./obj/create_central_cube.check.o ./obj/create_central_cube_buffers.check.o ./obj/create_chunk_buffers.check.o ./obj/create_doubling_elements.check.o ./obj/create_mass_matrices.check.o ./obj/create_meshes.check.o ./obj/create_MPI_interfaces.check.o ./obj/create_regions_mesh.check.o ./obj/create_regions_elements.check.o ./obj/create_regular_elements.check.o ./obj/define_superbrick.check.o ./obj/finalize_mesher.check.o ./obj/fix_non_blocking_flags.check.o ./obj/get_absorb.check.o ./obj/get_ellipticity.check.o ./obj/get_jacobian_boundaries.check.o ./obj/get_jacobian_discontinuities.check.o ./obj/get_model.check.o ./obj/get_MPI_1D_buffers.check.o ./obj/get_MPI_cutplanes_eta.check.o ./obj/get_MPI_cutplanes_xi.check.o ./obj/get_MPI_interfaces.check.o ./obj/get_perm_color.check.o ./obj/get_shape2D.check.o ./obj/get_shape3D.check.o ./obj/gravity_integrals.check.o ./obj/initialize_layers.check.o ./obj/initialize_mesher.check.o ./obj/lgndr.check.o ./obj/model_1dref.check.o ./obj/model_1066a.check.o ./obj/model_ak135.check.o ./obj/model_sea1d.check.o ./obj/model_aniso_inner_core.check.o ./obj/model_aniso_mantle.check.o ./obj/model_atten3D_QRFSI12.check.o ./obj/model_attenuation.check.o ./obj/model_crust_1_0.check.o ./obj/model_crust_2_0.check.o ./obj/model_crustmaps.check.o ./obj/model_eucrust.check.o ./obj/model_epcrust.check.o ./obj/model_full_sh.check.o ./obj/model_gapp2.check.o ./obj/model_gll.check.o ./obj/model_heterogen_mantle.check.o ./obj/model_iasp91.check.o ./obj/model_jp1d.check.o ./obj/model_jp3d.check.o ./obj/model_ppm.check.o ./obj/model_s20rts.check.o ./obj/model_s40rts.check.o ./obj/model_s362ani.check.o ./obj/model_sea99_s.check.o ./obj/moho_stretching.check.o ./obj/save_arrays_solver.check.o ./obj/setup_color_perm.check.o ./obj/setup_counters.check.o ./obj/setup_inner_outer.check.o ./obj/setup_model.check.o ./obj/setup_MPI_interfaces.check.o ./obj/stretching_function.check.o ./obj/test_MPI_interfaces.check.o ./obj/write_AVS_DX_global_chunks_data.check.o ./obj/write_AVS_DX_global_data.check.o ./obj/write_AVS_DX_global_faces_data.check.o ./obj/write_AVS_DX_output.check.o ./obj/write_AVS_DX_surface_data.check.o ./obj/create_regions_mesh_par.mod ./obj/create_regions_mesh_par2.mod ./obj/create_mpi_interfaces_par.mod ./obj/gapp2_mantle_model_constants.mod ./obj/manager_adios_par.mod ./obj/meshfem3d_models_par.mod ./obj/meshfem3d_par.mod ./obj/mpi_crust_mantle_par.mod ./obj/mpi_inner_core_par.mod ./obj/mpi_outer_core_par.mod ./obj/model_1066a_par.mod ./obj/model_1dref_par.mod ./obj/model_ak135_par.mod ./obj/model_aniso_mantle_par.mod ./obj/model_atten3d_qrfsi12_par.mod ./obj/model_crust_1_0_par.mod ./obj/model_crust_2_0_par.mod ./obj/model_crustmaps_par.mod ./obj/model_epcrust_par.mod ./obj/model_eucrust_par.mod ./obj/model_full_sh_crust_par.mod ./obj/model_full_sh_mantle_par.mod ./obj/model_heterogen_mantle_par.mod ./obj/model_jp3d_par.mod ./obj/model_ppm_par.mod ./obj/model_s20rts_par.mod ./obj/model_s362ani_par.mod ./obj/model_s40rts_par.mod ./obj/model_sea1d_par.mod ./obj/model_sea99_s_par.mod ./obj/avs_dx_global_chunks_mod.mod ./obj/avs_dx_global_mod.mod ./obj/avs_dx_global_faces_mod.mod ./obj/avs_dx_surface_mod.mod ./bin/xmeshfem3D ./obj/assemble_MPI_scalar.solver.o ./obj/assemble_MPI_vector.solver.o ./obj/comp_source_spectrum.solver.o ./obj/compute_adj_source_frechet.solver.o ./obj/convert_time.solver.o ./obj/define_derivation_matrices.solver.o ./obj/file_io_threads.cc.o ./obj/force_ftz.cc.o ./obj/get_backazimuth.solver.o ./obj/get_cmt.solver.o ./obj/get_force.solver.o ./obj/get_event_info.solver.o ./obj/make_gravity.solver.o ./obj/netlib_specfun_erf.solver.o ./obj/asdf_data.solverstatic_module.o ./obj/comp_source_time_function.solverstatic.o ./obj/specfem3D_par.solverstatic_module.o ./obj/write_seismograms.solverstatic.o ./obj/check_stability.solverstatic.o ./obj/compute_add_sources.solverstatic.o ./obj/compute_arrays_source.solverstatic.o ./obj/compute_boundary_kernel.solverstatic.o ./obj/compute_coupling.solverstatic.o ./obj/compute_element.solverstatic.o ./obj/compute_element_att_memory.solverstatic.o ./obj/compute_element_strain.solverstatic.o ./obj/compute_forces_acoustic_calling_routine.solverstatic.o ./obj/compute_forces_viscoelastic_calling_routine.solverstatic.o ./obj/compute_forces_crust_mantle_noDev.solverstatic.o ./obj/compute_forces_crust_mantle_Dev.solverstatic.o ./obj/compute_forces_inner_core_noDev.solverstatic.o ./obj/compute_forces_inner_core_Dev.solverstatic.o ./obj/compute_forces_outer_core_noDev.solverstatic.o ./obj/compute_forces_outer_core_Dev.solverstatic.o ./obj/compute_kernels.solverstatic.o ./obj/compute_seismograms.solverstatic.o ./obj/compute_stacey_crust_mantle.solverstatic.o ./obj/compute_stacey_outer_core.solverstatic.o ./obj/finalize_simulation.solverstatic.o ./obj/get_attenuation.solverstatic.o ./obj/initialize_simulation.solverstatic.o ./obj/iterate_time.solverstatic.o ./obj/iterate_time_undoatt.solverstatic.o ./obj/locate_receivers.solverstatic.o ./obj/locate_regular_points.solverstatic.o ./obj/locate_sources.solverstatic.o ./obj/multiply_arrays_source.solverstatic.o ./obj/noise_tomography.solverstatic.o ./obj/prepare_attenuation.solverstatic.o ./obj/prepare_elastic_elements.solverstatic.o ./obj/prepare_gpu.solverstatic.o ./obj/prepare_gravity.solverstatic.o ./obj/prepare_movie.solverstatic.o ./obj/prepare_noise.solverstatic.o ./obj/prepare_oceans.solverstatic.o ./obj/prepare_optimized_arrays.solverstatic.o ./obj/prepare_stacey.solverstatic.o ./obj/prepare_timerun.solverstatic.o ./obj/prepare_vtk_window.solverstatic.o ./obj/prepare_wavefields.solverstatic.o ./obj/read_adjoint_sources.solverstatic.o ./obj/read_arrays_solver.solverstatic.o ./obj/read_forward_arrays.solverstatic.o ./obj/read_mesh_databases.solverstatic.o ./obj/read_topography_bathymetry.solverstatic.o ./obj/save_forward_arrays.solverstatic.o ./obj/save_kernels.solverstatic.o ./obj/save_regular_kernels.solverstatic.o ./obj/setup_GLL_points.solverstatic.o ./obj/setup_sources_receivers.solverstatic.o ./obj/specfem3D.solverstatic.o ./obj/update_displacement_LDDRK.solverstatic.o ./obj/update_displacement_Newmark.solverstatic.o ./obj/write_movie_output.solverstatic.o ./obj/write_movie_volume.solverstatic.o ./obj/write_movie_surface.solverstatic.o ./obj/write_output_ASCII.solverstatic.o ./obj/write_output_SAC.solverstatic.o ./obj/specfem3D_gpu_method_stubs.cc.o ./obj/visual_vtk_stubs.visualc.o ./obj/asdf_data.mod ./obj/constants_solver.mod ./obj/manager_adios_par.mod ./obj/specfem_par.mod ./obj/specfem_par_crustmantle.mod ./obj/specfem_par_innercore.mod ./obj/specfem_par_outercore.mod ./obj/specfem_par_noise.mod ./obj/specfem_par_movie.mod ./bin/xspecfem3D ./obj/convolve_source_timefunction.aux.o ./obj/detect_duplicates_stations_file.aux.o ./obj/combine_AVS_DX.aux.o ./obj/get_cmt.solver.o ./obj/combine_paraview_strain_data.auxsolver.o ./obj/combine_surf_data.auxsolver.o ./obj/combine_vol_data.auxsolver.o ./obj/combine_vol_data.auxadios.o ./obj/combine_vol_data_adios_impl.auxmpi.o ./obj/combine_vol_data.auxsolver_vtk.o ./obj/combine_vol_data.auxadios_vtk.o ./obj/combine_vol_data_adios_impl.auxmpi.o ./obj/create_movie_AVS_DX.aux.o ./obj/create_movie_GMT_global.aux.o ./obj/extract_database.aux.o ./bin/xconvolve_source_timefunction ./bin/xdetect_duplicates_stations_file ./bin/xcombine_AVS_DX ./bin/xcombine_paraview_strain_data ./bin/xcombine_vol_data ./bin/xcombine_vol_data_vtk ./bin/xcombine_surf_data ./bin/xcreate_movie_AVS_DX ./bin/xcreate_movie_GMT_global ./bin/xextract_database ./obj/postprocess_par.postprocess_module.o ./obj/addition_sem.postprocess.o ./obj/postprocess_par.postprocess_module.o ./obj/parse_kernel_names.postprocess.o ./obj/clip_sem.postprocess.o ./obj/postprocess_par.postprocess_module.o ./obj/parse_kernel_names.postprocess.o ./obj/combine_sem.postprocess.o ./obj/postprocess_par.postprocess_module.o ./obj/difference_sem.postprocess.o ./obj/postprocess_par.postprocess_module.o ./obj/interpolate_model.postprocess.o ./obj/postprocess_par.postprocess_module.o ./obj/create_cross_section.postprocess.o ./obj/parse_kernel_names.postprocess.o ./obj/postprocess_par.postprocess_module.o ./obj/parse_kernel_names.postprocess.o ./obj/smooth_sem.postprocess.o ./obj/convert_model_file_adios.postprocess_adios.o ./obj/postprocess_par.mod ./bin/xaddition_sem ./bin/xclip_sem ./bin/xcombine_sem ./bin/xdifference_sem ./bin/xinterpolate_model ./bin/xcreate_cross_section ./bin/xsmooth_sem ./obj/add_model_iso.tomo.o ./obj/tomography_par.tomo_module.o ./obj/compute_kernel_integral.tomo.o ./obj/get_cg_direction.tomo.o ./obj/get_sd_direction.tomo.o ./obj/read_kernels.tomo.o ./obj/read_kernels_cg.tomo.o ./obj/read_model.tomo.o ./obj/read_parameters_tomo.tomo.o ./obj/write_gradient.tomo.o ./obj/write_new_model.tomo.o ./obj/write_new_model_perturbations.tomo.o ./obj/add_model_tiso.tomo.o ./obj/tomography_par.tomo_module.o ./obj/compute_kernel_integral.tomo.o ./obj/get_cg_direction.tomo.o ./obj/get_sd_direction.tomo.o ./obj/read_kernels.tomo.o ./obj/read_kernels_cg.tomo.o ./obj/read_model.tomo.o ./obj/read_parameters_tomo.tomo.o ./obj/write_gradient.tomo.o ./obj/write_new_model.tomo.o ./obj/write_new_model_perturbations.tomo.o ./obj/add_model_tiso_cg.tomo.o ./obj/tomography_par.tomo_module.o ./obj/compute_kernel_integral.tomo.o ./obj/get_cg_direction.tomo.o ./obj/get_sd_direction.tomo.o ./obj/read_kernels.tomo.o ./obj/read_kernels_cg.tomo.o ./obj/read_model.tomo.o ./obj/read_parameters_tomo.tomo.o ./obj/write_gradient.tomo.o ./obj/write_new_model.tomo.o ./obj/write_new_model_perturbations.tomo.o ./obj/add_model_tiso_iso.tomo.o ./obj/tomography_par.tomo_module.o ./obj/compute_kernel_integral.tomo.o ./obj/get_cg_direction.tomo.o ./obj/get_sd_direction.tomo.o ./obj/read_kernels.tomo.o ./obj/read_kernels_cg.tomo.o ./obj/read_model.tomo.o ./obj/read_parameters_tomo.tomo.o ./obj/write_gradient.tomo.o ./obj/write_new_model.tomo.o ./obj/write_new_model_perturbations.tomo.o ./obj/tomography_par.tomo_module.o ./obj/sum_kernels.tomo.o ./obj/tomography_par.tomo_module.o ./obj/sum_preconditioned_kernels.tomo.o ./obj/tomography_par.mod ./obj/tomography_kernels_iso.mod ./obj/tomography_kernels_tiso.mod ./obj/tomography_kernels_tiso_cg.mod ./obj/tomography_model_tiso.mod ./obj/tomography_model_iso.mod ./bin/xadd_model_iso ./bin/xadd_model_tiso ./bin/xadd_model_tiso_cg ./bin/xadd_model_tiso_iso ./bin/xsum_kernels ./bin/xsum_preconditioned_kernels rm -f ./bin/*__genmod.* rm -f ./obj/*__genmod.* mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/shared_par.shared_module.o src/shared/shared_par.f90 icc -c -I./setup -g -O2 -o obj/param_reader.cc.o src/shared/param_reader.c icc -c -I./setup -g -O2 -o obj/binary_c_io.cc.o src/shared/binary_c_io.c icc -c -I./setup -g -O2 -o obj/adios_method_stubs.cc.o src/shared/adios_method_stubs.c icc -c -I./setup -g -O2 -o obj/file_io_threads.cc.o src/specfem3D/file_io_threads.c icc -c -I./setup -g -O2 -o obj/force_ftz.cc.o src/specfem3D/force_ftz.c mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_backazimuth.solver.o src/specfem3D/get_backazimuth.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_cmt.solver.o src/specfem3D/get_cmt.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_force.solver.o src/specfem3D/get_force.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_event_info.solver.o src/specfem3D/get_event_info.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/make_gravity.solver.o src/specfem3D/make_gravity.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/netlib_specfun_erf.solver.o src/specfem3D/netlib_specfun_erf.f90 icc -c -I./setup -g -O2 -o obj/specfem3D_gpu_method_stubs.cc.o src/specfem3D/specfem3D_gpu_method_stubs.c icc -c -I./setup -o obj/visual_vtk_stubs.visualc.o src/specfem3D/visual_vtk_stubs.c mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/calendar.shared.o src/shared/calendar.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/recompute_jacobian.shared.o src/shared/recompute_jacobian.f90 icc -c -I./setup -g -O2 -o obj/asdf_method_stubs.cc.o src/shared/asdf_method_stubs.c mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_serial_name_database.shared.o src/shared/create_serial_name_database.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/search_kdtree.shared.o src/shared/search_kdtree.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/interpolate.shared.o src/shared/interpolate.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/auto_ner.shared.o src/shared/auto_ner.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/count_elements.shared.o src/shared/count_elements.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/count_number_of_sources.shared.o src/shared/count_number_of_sources.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/count_points.shared.o src/shared/count_points.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/define_all_layers.shared.o src/shared/define_all_layers.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/euler_angles.shared.o src/shared/euler_angles.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_model_parameters.shared.o src/shared/get_model_parameters.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_timestep_and_layers.shared.o src/shared/get_timestep_and_layers.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/memory_eval.shared.o src/shared/memory_eval.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/read_compute_parameters.shared.o src/shared/read_compute_parameters.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/read_parameter_file.shared.o src/shared/read_parameter_file.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/read_value_parameters.shared.o src/shared/read_value_parameters.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/reduce.shared.o src/shared/reduce.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/rthetaphi_xyz.shared.o src/shared/rthetaphi_xyz.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/save_header_file.shared.o src/shared/save_header_file.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_header_file.header.o src/create_header_file/create_header_file.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/adios_manager.shared_adios_module.o src/shared/adios_manager.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/broadcast_computed_parameters.shared.o src/shared/broadcast_computed_parameters.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_name_database.shared.o src/shared/create_name_database.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/exit_mpi.shared.o src/shared/exit_mpi.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/flush_system.shared.o src/shared/flush_system.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_all_eight_slices.shared.o src/shared/get_all_eight_slices.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_global.shared.o src/shared/get_global.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/gll_library.shared.o src/shared/gll_library.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/heap_sort.shared.o src/shared/heap_sort.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/hex_nodes.shared.o src/shared/hex_nodes.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/init_openmp.shared.o src/shared/init_openmp.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/intgrl.shared.o src/shared/intgrl.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/lagrange_poly.shared.o src/shared/lagrange_poly.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/make_ellipticity.shared.o src/shared/make_ellipticity.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_prem.shared.o src/shared/model_prem.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_topo_bathy.shared.o src/shared/model_topo_bathy.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/parallel.sharedmpi.o src/shared/parallel.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/smooth_weights_vec.shared.o src/shared/smooth_weights_vec.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/sort_array_coordinates.shared.o src/shared/sort_array_coordinates.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/spline_routines.shared.o src/shared/spline_routines.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_VTK_file.shared.o src/shared/write_VTK_file.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/meshfem3D_par.check_module.o src/meshfem3D/meshfem3D_par.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/assemble_MPI_scalar.solver.o src/specfem3D/assemble_MPI_scalar.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/assemble_MPI_vector.solver.o src/specfem3D/assemble_MPI_vector.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/comp_source_spectrum.solver.o src/specfem3D/comp_source_spectrum.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_adj_source_frechet.solver.o src/specfem3D/compute_adj_source_frechet.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/convert_time.solver.o src/specfem3D/convert_time.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/define_derivation_matrices.solver.o src/specfem3D/define_derivation_matrices.f90 mpiifort -g -o bin/xcreate_header_file obj/shared_par.shared_module.o obj/auto_ner.shared.o obj/count_elements.shared.o obj/count_number_of_sources.shared.o obj/count_points.shared.o obj/define_all_layers.shared.o obj/euler_angles.shared.o obj/get_model_parameters.shared.o obj/get_timestep_and_layers.shared.o obj/memory_eval.shared.o obj/param_reader.cc.o obj/read_compute_parameters.shared.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o obj/reduce.shared.o obj/rthetaphi_xyz.shared.o obj/save_header_file.shared.o obj/create_header_file.header.o mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/meshfem3D.check.o src/meshfem3D/meshfem3D.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/meshfem3D_models.check.o src/meshfem3D/meshfem3D_models.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/add_missing_nodes.check.o src/meshfem3D/add_missing_nodes.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/add_topography.check.o src/meshfem3D/add_topography.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/add_topography_410_650.check.o src/meshfem3D/add_topography_410_650.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/add_topography_cmb.check.o src/meshfem3D/add_topography_cmb.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/add_topography_icb.check.o src/meshfem3D/add_topography_icb.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/assemble_MPI_central_cube_mesh.check.o src/meshfem3D/assemble_MPI_central_cube_mesh.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/assemble_MPI_scalar_mesh.check.o src/meshfem3D/assemble_MPI_scalar_mesh.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/assemble_MPI_vector_mesh.check.o src/meshfem3D/assemble_MPI_vector_mesh.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/calc_jacobian.check.o src/meshfem3D/calc_jacobian.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/check_mesh_resolution.check.o src/meshfem3D/check_mesh_resolution.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_coordinates_grid.check.o src/meshfem3D/compute_coordinates_grid.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_element_properties.check.o src/meshfem3D/compute_element_properties.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_volumes_and_areas.check.o src/meshfem3D/compute_volumes_and_areas.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_addressing.check.o src/meshfem3D/create_addressing.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_central_cube.check.o src/meshfem3D/create_central_cube.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_central_cube_buffers.check.o src/meshfem3D/create_central_cube_buffers.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_chunk_buffers.check.o src/meshfem3D/create_chunk_buffers.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_doubling_elements.check.o src/meshfem3D/create_doubling_elements.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_mass_matrices.check.o src/meshfem3D/create_mass_matrices.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_meshes.check.o src/meshfem3D/create_meshes.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_MPI_interfaces.check.o src/meshfem3D/create_MPI_interfaces.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_regions_mesh.check.o src/meshfem3D/create_regions_mesh.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_regions_elements.check.o src/meshfem3D/create_regions_elements.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_regular_elements.check.o src/meshfem3D/create_regular_elements.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/define_superbrick.check.o src/meshfem3D/define_superbrick.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/finalize_mesher.check.o src/meshfem3D/finalize_mesher.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/fix_non_blocking_flags.check.o src/meshfem3D/fix_non_blocking_flags.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_absorb.check.o src/meshfem3D/get_absorb.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_ellipticity.check.o src/meshfem3D/get_ellipticity.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_jacobian_boundaries.check.o src/meshfem3D/get_jacobian_boundaries.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_jacobian_discontinuities.check.o src/meshfem3D/get_jacobian_discontinuities.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_model.check.o src/meshfem3D/get_model.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_MPI_1D_buffers.check.o src/meshfem3D/get_MPI_1D_buffers.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_MPI_cutplanes_eta.check.o src/meshfem3D/get_MPI_cutplanes_eta.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_MPI_cutplanes_xi.check.o src/meshfem3D/get_MPI_cutplanes_xi.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_MPI_interfaces.check.o src/meshfem3D/get_MPI_interfaces.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_perm_color.check.o src/meshfem3D/get_perm_color.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_shape2D.check.o src/meshfem3D/get_shape2D.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_shape3D.check.o src/meshfem3D/get_shape3D.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/gravity_integrals.check.o src/meshfem3D/gravity_integrals.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/initialize_layers.check.o src/meshfem3D/initialize_layers.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/initialize_mesher.check.o src/meshfem3D/initialize_mesher.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/lgndr.check.o src/meshfem3D/lgndr.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_1dref.check.o src/meshfem3D/model_1dref.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_1066a.check.o src/meshfem3D/model_1066a.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_ak135.check.o src/meshfem3D/model_ak135.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_sea1d.check.o src/meshfem3D/model_sea1d.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_aniso_inner_core.check.o src/meshfem3D/model_aniso_inner_core.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_aniso_mantle.check.o src/meshfem3D/model_aniso_mantle.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_atten3D_QRFSI12.check.o src/meshfem3D/model_atten3D_QRFSI12.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_crust_1_0.check.o src/meshfem3D/model_crust_1_0.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_crust_2_0.check.o src/meshfem3D/model_crust_2_0.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_crustmaps.check.o src/meshfem3D/model_crustmaps.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_eucrust.check.o src/meshfem3D/model_eucrust.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_epcrust.check.o src/meshfem3D/model_epcrust.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_full_sh.check.o src/meshfem3D/model_full_sh.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_gapp2.check.o src/meshfem3D/model_gapp2.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_gll.check.o src/meshfem3D/model_gll.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_heterogen_mantle.check.o src/meshfem3D/model_heterogen_mantle.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_iasp91.check.o src/meshfem3D/model_iasp91.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_jp1d.check.o src/meshfem3D/model_jp1d.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_jp3d.check.o src/meshfem3D/model_jp3d.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_ppm.check.o src/meshfem3D/model_ppm.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_s20rts.check.o src/meshfem3D/model_s20rts.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_s40rts.check.o src/meshfem3D/model_s40rts.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_s362ani.check.o src/meshfem3D/model_s362ani.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_sea99_s.check.o src/meshfem3D/model_sea99_s.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/moho_stretching.check.o src/meshfem3D/moho_stretching.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/save_arrays_solver.check.o src/meshfem3D/save_arrays_solver.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/setup_color_perm.check.o src/meshfem3D/setup_color_perm.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/setup_counters.check.o src/meshfem3D/setup_counters.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/setup_inner_outer.check.o src/meshfem3D/setup_inner_outer.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/setup_model.check.o src/meshfem3D/setup_model.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/setup_MPI_interfaces.check.o src/meshfem3D/setup_MPI_interfaces.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/stretching_function.check.o src/meshfem3D/stretching_function.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/test_MPI_interfaces.check.o src/meshfem3D/test_MPI_interfaces.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_AVS_DX_global_chunks_data.check.o src/meshfem3D/write_AVS_DX_global_chunks_data.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_AVS_DX_global_data.check.o src/meshfem3D/write_AVS_DX_global_data.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_AVS_DX_global_faces_data.check.o src/meshfem3D/write_AVS_DX_global_faces_data.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_AVS_DX_output.check.o src/meshfem3D/write_AVS_DX_output.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_AVS_DX_surface_data.check.o src/meshfem3D/write_AVS_DX_surface_data.f90 running xcreate_header_file... ./bin/xcreate_header_file creating file OUTPUT_FILES/values_from_mesher.h to compile solver with correct values edit file OUTPUT_FILES/values_from_mesher.h to see some statistics about the mesh number of processors = 216 maximum number of points per region = 1060349 total elements per slice = 18325 total points per slice = 1222043 the time step of the solver will be DT = 0.1900000 (s) the (approximate) minimum period resolved will be = 18.13333 (s) current record length is = 60.00000 min current minimum number of time steps will be = 19000 MOVIE_VOLUME : T MOVIE_SURFACE: F Saving movie frames every 100 on NEC SX, make sure "loopcnt=" parameter in Makefile is greater than max vector length = 3181047 approximate static memory needed by the solver: ---------------------------------------------- (lower bound, usually the real amount used is 5% to 10% higher) (you can get a more precise estimate of the size used per MPI process by typing "size -d bin/xspecfem3D" after compiling the code with the DATA/Par_file you plan to use) size of static arrays per slice = 751.438408000000 MB = 716.627510070801 MiB = 0.751438408000000 GB = 0.699831552803516 GiB (should be below 80% or 90% of the memory installed per core) (if significantly more, the job will not run by lack of memory) (note that if significantly less, you waste a significant amount of memory per processor core) (but that can be perfectly acceptable if you can afford it and want faster results by using more cores) size of static arrays for all slices = 162.310696128000 GB = 151.163615405560 GiB = 0.162310696128000 TB = 0.147620718169492 TiB ******************************************************************************* Estimating optimal disk dumping interval for UNDO_ATTENUATION: ******************************************************************************* without undoing of attenuation you are using 1.17753139200000 GB per core i.e. 29.43828 % of the installed memory each time step to store in memory to undo attenuation will require storing 1.425235200000000E-002 GB per core ******************************************************************************* the optimal value is thus NT_DUMP_ATTENUATION = 155 ******************************************************************************* we will need to save a total of 123 dumpings (restart files) to disk each dumping on the disk to undo attenuation will require storing 0.169208064000000 GB per core each dumping on the disk will require storing 36.5489418240000 GB for all cores ALL dumpings on the disk will require storing 20.8125918720000 GB per core ******************************************************************************* ALL dumpings on the disk will require storing 4495.51984435200 GB for all cores i.e. 4.49551984435200 TB ******************************************************************************* mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/model_attenuation.check.o src/meshfem3D/model_attenuation.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/asdf_data.solverstatic_module.o src/specfem3D/asdf_data.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/specfem3D_par.solverstatic_module.o src/specfem3D/specfem3D_par.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/combine_AVS_DX.aux.o src/auxiliaries/combine_AVS_DX.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/combine_surf_data.auxsolver.o src/auxiliaries/combine_surf_data.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/combine_vol_data.auxsolver.o src/auxiliaries/combine_vol_data.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/combine_vol_data.auxsolver_vtk.o src/auxiliaries/combine_vol_data.F90 -DUSE_VTK_INSTEAD_OF_MESH mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/convolve_source_timefunction.aux.o src/auxiliaries/convolve_source_timefunction.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_movie_AVS_DX.aux.o src/auxiliaries/create_movie_AVS_DX.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_movie_GMT_global.aux.o src/auxiliaries/create_movie_GMT_global.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/detect_duplicates_stations_file.aux.o src/auxiliaries/detect_duplicates_stations_file.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/combine_paraview_strain_data.auxsolver.o src/auxiliaries/combine_paraview_strain_data.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/extract_database.aux.o src/auxiliaries/extract_database.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/postprocess_par.postprocess_module.o src/tomography/postprocess_sensitivity_kernels/postprocess_par.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/tomography_par.tomo_module.o src/tomography/tomography_par.f90 mpiifort -g -o bin/xcombine_surf_data obj/combine_surf_data.auxsolver.o obj/shared_par.shared_module.o obj/binary_c_io.cc.o obj/flush_system.shared.o mpiifort -g -o bin/xcombine_vol_data_vtk obj/combine_vol_data.auxsolver_vtk.o obj/shared_par.shared_module.o obj/binary_c_io.cc.o obj/exit_mpi.shared.o obj/flush_system.shared.o obj/intgrl.shared.o obj/make_ellipticity.shared.o obj/model_prem.shared.o obj/parallel.sharedmpi.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o obj/param_reader.cc.o obj/reduce.shared.o obj/rthetaphi_xyz.shared.o obj/spline_routines.shared.o mpiifort -g -o bin/xconvolve_source_timefunction obj/convolve_source_timefunction.aux.o obj/shared_par.shared_module.o mpiifort -g -o bin/xdetect_duplicates_stations_file obj/detect_duplicates_stations_file.aux.o obj/shared_par.shared_module.o mpiifort -g -o bin/xmeshfem3D obj/shared_par.shared_module.o obj/adios_manager.shared_adios_module.o obj/auto_ner.shared.o obj/binary_c_io.cc.o obj/broadcast_computed_parameters.shared.o obj/count_elements.shared.o obj/count_number_of_sources.shared.o obj/count_points.shared.o obj/create_name_database.shared.o obj/define_all_layers.shared.o obj/euler_angles.shared.o obj/exit_mpi.shared.o obj/flush_system.shared.o obj/get_all_eight_slices.shared.o obj/get_global.shared.o obj/get_model_parameters.shared.o obj/get_timestep_and_layers.shared.o obj/gll_library.shared.o obj/heap_sort.shared.o obj/hex_nodes.shared.o obj/init_openmp.shared.o obj/intgrl.shared.o obj/lagrange_poly.shared.o obj/make_ellipticity.shared.o obj/memory_eval.shared.o obj/model_prem.shared.o obj/model_topo_bathy.shared.o obj/parallel.sharedmpi.o obj/param_reader.cc.o obj/read_compute_parameters.shared.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o obj/reduce.shared.o obj/rthetaphi_xyz.shared.o obj/save_header_file.shared.o obj/smooth_weights_vec.shared.o obj/sort_array_coordinates.shared.o obj/spline_routines.shared.o obj/write_VTK_file.shared.o obj/adios_method_stubs.cc.o obj/meshfem3D_par.check_module.o obj/meshfem3D.check.o obj/meshfem3D_models.check.o obj/add_missing_nodes.check.o obj/add_topography.check.o obj/add_topography_410_650.check.o obj/add_topography_cmb.check.o obj/add_topography_icb.check.o obj/assemble_MPI_central_cube_mesh.check.o obj/assemble_MPI_scalar_mesh.check.o obj/assemble_MPI_vector_mesh.check.o obj/calc_jacobian.check.o obj/check_mesh_resolution.check.o obj/compute_coordinates_grid.check.o obj/compute_element_properties.check.o obj/compute_volumes_and_areas.check.o obj/create_addressing.check.o obj/create_central_cube.check.o obj/create_central_cube_buffers.check.o obj/create_chunk_buffers.check.o obj/create_doubling_elements.check.o obj/create_mass_matrices.check.o obj/create_meshes.check.o obj/create_MPI_interfaces.check.o obj/create_regions_mesh.check.o obj/create_regions_elements.check.o obj/create_regular_elements.check.o obj/define_superbrick.check.o obj/finalize_mesher.check.o obj/fix_non_blocking_flags.check.o obj/get_absorb.check.o obj/get_ellipticity.check.o obj/get_jacobian_boundaries.check.o obj/get_jacobian_discontinuities.check.o obj/get_model.check.o obj/get_MPI_1D_buffers.check.o obj/get_MPI_cutplanes_eta.check.o obj/get_MPI_cutplanes_xi.check.o obj/get_MPI_interfaces.check.o obj/get_perm_color.check.o obj/get_shape2D.check.o obj/get_shape3D.check.o obj/gravity_integrals.check.o obj/initialize_layers.check.o obj/initialize_mesher.check.o obj/lgndr.check.o obj/model_1dref.check.o obj/model_1066a.check.o obj/model_ak135.check.o obj/model_sea1d.check.o obj/model_aniso_inner_core.check.o obj/model_aniso_mantle.check.o obj/model_atten3D_QRFSI12.check.o obj/model_attenuation.check.o obj/model_crust_1_0.check.o obj/model_crust_2_0.check.o obj/model_crustmaps.check.o obj/model_eucrust.check.o obj/model_epcrust.check.o obj/model_full_sh.check.o obj/model_gapp2.check.o obj/model_gll.check.o obj/model_heterogen_mantle.check.o obj/model_iasp91.check.o obj/model_jp1d.check.o obj/model_jp3d.check.o obj/model_ppm.check.o obj/model_s20rts.check.o obj/model_s40rts.check.o obj/model_s362ani.check.o obj/model_sea99_s.check.o obj/moho_stretching.check.o obj/save_arrays_solver.check.o obj/setup_color_perm.check.o obj/setup_counters.check.o obj/setup_inner_outer.check.o obj/setup_model.check.o obj/setup_MPI_interfaces.check.o obj/stretching_function.check.o obj/test_MPI_interfaces.check.o obj/write_AVS_DX_global_chunks_data.check.o obj/write_AVS_DX_global_data.check.o obj/write_AVS_DX_global_faces_data.check.o obj/write_AVS_DX_output.check.o obj/write_AVS_DX_surface_data.check.o mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/comp_source_time_function.solverstatic.o src/specfem3D/comp_source_time_function.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_seismograms.solverstatic.o src/specfem3D/write_seismograms.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/check_stability.solverstatic.o src/specfem3D/check_stability.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_add_sources.solverstatic.o src/specfem3D/compute_add_sources.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_boundary_kernel.solverstatic.o src/specfem3D/compute_boundary_kernel.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_coupling.solverstatic.o src/specfem3D/compute_coupling.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_element.solverstatic.o src/specfem3D/compute_element.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_element_att_memory.solverstatic.o src/specfem3D/compute_element_att_memory.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_element_strain.solverstatic.o src/specfem3D/compute_element_strain.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_forces_acoustic_calling_routine.solverstatic.o src/specfem3D/compute_forces_acoustic_calling_routine.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_forces_viscoelastic_calling_routine.solverstatic.o src/specfem3D/compute_forces_viscoelastic_calling_routine.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_forces_crust_mantle_noDev.solverstatic.o src/specfem3D/compute_forces_crust_mantle_noDev.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_forces_crust_mantle_Dev.solverstatic.o src/specfem3D/compute_forces_crust_mantle_Dev.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_forces_inner_core_noDev.solverstatic.o src/specfem3D/compute_forces_inner_core_noDev.f90 src/specfem3D/compute_element.F90(1383): remark #5082: Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: ; RECURSIVE !DIR$ INLINEALWAYS compute_element_stress_attenuation_contrib ------------^ src/specfem3D/compute_element.F90(1486): remark #5082: Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: ; RECURSIVE !DIR$ INLINEALWAYS compute_element_precompute_factors ------------^ src/specfem3D/compute_element.F90(1587): remark #5082: Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: ; RECURSIVE !DIR$ INLINEALWAYS compute_element_deviatoric_strain ------------^ src/specfem3D/compute_element.F90(1677): remark #5082: Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: ; RECURSIVE !DIR$ INLINEALWAYS compute_element_dot_product_stress ------------^ src/specfem3D/compute_element.F90(1779): remark #5082: Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: ; RECURSIVE !DIR$ INLINEALWAYS compute_element_gravity ------------^ mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_forces_inner_core_Dev.solverstatic.o src/specfem3D/compute_forces_inner_core_Dev.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_forces_outer_core_noDev.solverstatic.o src/specfem3D/compute_forces_outer_core_noDev.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_forces_outer_core_Dev.solverstatic.o src/specfem3D/compute_forces_outer_core_Dev.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_kernels.solverstatic.o src/specfem3D/compute_kernels.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_seismograms.solverstatic.o src/specfem3D/compute_seismograms.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_stacey_crust_mantle.solverstatic.o src/specfem3D/compute_stacey_crust_mantle.f90 src/specfem3D/compute_forces_crust_mantle_Dev.F90(557): remark #5082: Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: ; RECURSIVE !DIR$ INLINEALWAYS mxm5_3comp_singleA ------------^ src/specfem3D/compute_forces_crust_mantle_Dev.F90(622): remark #5082: Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: ; RECURSIVE !DIR$ INLINEALWAYS mxm5_3comp_singleB ------------^ src/specfem3D/compute_forces_crust_mantle_Dev.F90(687): remark #5082: Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: ; RECURSIVE !DIR$ INLINEALWAYS mxm5_3comp_3dmat_singleB ------------^ mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_stacey_outer_core.solverstatic.o src/specfem3D/compute_stacey_outer_core.f90 src/specfem3D/compute_forces_inner_core_Dev.F90(420): remark #5082: Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: ; RECURSIVE !DIR$ INLINEALWAYS mxm5_3comp_singleA ------------^ src/specfem3D/compute_forces_inner_core_Dev.F90(485): remark #5082: Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: ; RECURSIVE !DIR$ INLINEALWAYS mxm5_3comp_singleB ------------^ src/specfem3D/compute_forces_inner_core_Dev.F90(550): remark #5082: Directive ignored - Syntax error, found IDENTIFIER 'ALWAYS' when expecting one of: ; RECURSIVE !DIR$ INLINEALWAYS mxm5_3comp_3dmat_singleB ------------^ mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/finalize_simulation.solverstatic.o src/specfem3D/finalize_simulation.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_attenuation.solverstatic.o src/specfem3D/get_attenuation.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/initialize_simulation.solverstatic.o src/specfem3D/initialize_simulation.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/iterate_time.solverstatic.o src/specfem3D/iterate_time.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/iterate_time_undoatt.solverstatic.o src/specfem3D/iterate_time_undoatt.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/locate_receivers.solverstatic.o src/specfem3D/locate_receivers.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/locate_regular_points.solverstatic.o src/specfem3D/locate_regular_points.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/locate_sources.solverstatic.o src/specfem3D/locate_sources.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/multiply_arrays_source.solverstatic.o src/specfem3D/multiply_arrays_source.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/noise_tomography.solverstatic.o src/specfem3D/noise_tomography.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/prepare_attenuation.solverstatic.o src/specfem3D/prepare_attenuation.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/prepare_elastic_elements.solverstatic.o src/specfem3D/prepare_elastic_elements.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/prepare_gpu.solverstatic.o src/specfem3D/prepare_gpu.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/prepare_gravity.solverstatic.o src/specfem3D/prepare_gravity.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/prepare_movie.solverstatic.o src/specfem3D/prepare_movie.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/prepare_noise.solverstatic.o src/specfem3D/prepare_noise.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/prepare_oceans.solverstatic.o src/specfem3D/prepare_oceans.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/prepare_optimized_arrays.solverstatic.o src/specfem3D/prepare_optimized_arrays.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/prepare_stacey.solverstatic.o src/specfem3D/prepare_stacey.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/prepare_timerun.solverstatic.o src/specfem3D/prepare_timerun.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/prepare_vtk_window.solverstatic.o src/specfem3D/prepare_vtk_window.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/prepare_wavefields.solverstatic.o src/specfem3D/prepare_wavefields.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/read_adjoint_sources.solverstatic.o src/specfem3D/read_adjoint_sources.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/read_arrays_solver.solverstatic.o src/specfem3D/read_arrays_solver.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/read_forward_arrays.solverstatic.o src/specfem3D/read_forward_arrays.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/read_mesh_databases.solverstatic.o src/specfem3D/read_mesh_databases.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/read_topography_bathymetry.solverstatic.o src/specfem3D/read_topography_bathymetry.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/save_forward_arrays.solverstatic.o src/specfem3D/save_forward_arrays.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/save_kernels.solverstatic.o src/specfem3D/save_kernels.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/save_regular_kernels.solverstatic.o src/specfem3D/save_regular_kernels.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/setup_GLL_points.solverstatic.o src/specfem3D/setup_GLL_points.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/setup_sources_receivers.solverstatic.o src/specfem3D/setup_sources_receivers.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/specfem3D.solverstatic.o src/specfem3D/specfem3D.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/update_displacement_LDDRK.solverstatic.o src/specfem3D/update_displacement_LDDRK.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/update_displacement_Newmark.solverstatic.o src/specfem3D/update_displacement_Newmark.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_movie_output.solverstatic.o src/specfem3D/write_movie_output.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_movie_volume.solverstatic.o src/specfem3D/write_movie_volume.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_movie_surface.solverstatic.o src/specfem3D/write_movie_surface.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_output_ASCII.solverstatic.o src/specfem3D/write_output_ASCII.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_output_SAC.solverstatic.o src/specfem3D/write_output_SAC.f90 mpiifort -g -o bin/xcombine_AVS_DX obj/combine_AVS_DX.aux.o obj/get_cmt.solver.o obj/shared_par.shared_module.o obj/auto_ner.shared.o obj/calendar.shared.o obj/count_elements.shared.o obj/count_number_of_sources.shared.o obj/count_points.shared.o obj/create_serial_name_database.shared.o obj/define_all_layers.shared.o obj/get_model_parameters.shared.o obj/get_timestep_and_layers.shared.o obj/param_reader.cc.o obj/read_compute_parameters.shared.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o obj/reduce.shared.o obj/rthetaphi_xyz.shared.o mpiifort -g -o bin/xcombine_vol_data obj/combine_vol_data.auxsolver.o obj/shared_par.shared_module.o obj/binary_c_io.cc.o obj/exit_mpi.shared.o obj/flush_system.shared.o obj/intgrl.shared.o obj/make_ellipticity.shared.o obj/model_prem.shared.o obj/parallel.sharedmpi.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o obj/param_reader.cc.o obj/reduce.shared.o obj/rthetaphi_xyz.shared.o obj/spline_routines.shared.o mpiifort -g -o bin/xcreate_movie_AVS_DX obj/create_movie_AVS_DX.aux.o obj/shared_par.shared_module.o obj/auto_ner.shared.o obj/count_elements.shared.o obj/count_number_of_sources.shared.o obj/count_points.shared.o obj/define_all_layers.shared.o obj/get_global.shared.o obj/get_model_parameters.shared.o obj/get_timestep_and_layers.shared.o obj/param_reader.cc.o obj/read_compute_parameters.shared.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o obj/reduce.shared.o obj/rthetaphi_xyz.shared.o obj/sort_array_coordinates.shared.o mpiifort -g -o bin/xcreate_movie_GMT_global obj/create_movie_GMT_global.aux.o obj/shared_par.shared_module.o obj/auto_ner.shared.o obj/count_elements.shared.o obj/count_number_of_sources.shared.o obj/count_points.shared.o obj/define_all_layers.shared.o obj/get_model_parameters.shared.o obj/get_timestep_and_layers.shared.o obj/param_reader.cc.o obj/read_compute_parameters.shared.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o obj/reduce.shared.o obj/rthetaphi_xyz.shared.o mpiifort -g -o bin/xcombine_paraview_strain_data obj/combine_paraview_strain_data.auxsolver.o obj/shared_par.shared_module.o obj/binary_c_io.cc.o mpiifort -g -o bin/xextract_database obj/extract_database.aux.o mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/addition_sem.postprocess.o src/tomography/postprocess_sensitivity_kernels/addition_sem.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/parse_kernel_names.postprocess.o src/tomography/postprocess_sensitivity_kernels/parse_kernel_names.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/clip_sem.postprocess.o src/tomography/postprocess_sensitivity_kernels/clip_sem.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/combine_sem.postprocess.o src/tomography/postprocess_sensitivity_kernels/combine_sem.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/difference_sem.postprocess.o src/tomography/postprocess_sensitivity_kernels/difference_sem.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/interpolate_model.postprocess.o src/tomography/postprocess_sensitivity_kernels/interpolate_model.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/create_cross_section.postprocess.o src/tomography/postprocess_sensitivity_kernels/create_cross_section.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/smooth_sem.postprocess.o src/tomography/postprocess_sensitivity_kernels/smooth_sem.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/add_model_iso.tomo.o src/tomography/add_model_iso.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_kernel_integral.tomo.o src/tomography/compute_kernel_integral.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_cg_direction.tomo.o src/tomography/get_cg_direction.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/get_sd_direction.tomo.o src/tomography/get_sd_direction.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/read_kernels.tomo.o src/tomography/read_kernels.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/read_kernels_cg.tomo.o src/tomography/read_kernels_cg.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/read_model.tomo.o src/tomography/read_model.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/read_parameters_tomo.tomo.o src/tomography/read_parameters_tomo.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_gradient.tomo.o src/tomography/write_gradient.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_new_model.tomo.o src/tomography/write_new_model.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/write_new_model_perturbations.tomo.o src/tomography/write_new_model_perturbations.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/add_model_tiso.tomo.o src/tomography/add_model_tiso.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/add_model_tiso_cg.tomo.o src/tomography/add_model_tiso_cg.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/add_model_tiso_iso.tomo.o src/tomography/add_model_tiso_iso.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/sum_kernels.tomo.o src/tomography/sum_kernels.F90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/sum_preconditioned_kernels.tomo.o src/tomography/sum_preconditioned_kernels.f90 mpiifort -g -mod ./obj -I./obj -I. -I. -I./setup -c -o obj/compute_arrays_source.solverstatic.o src/specfem3D/compute_arrays_source.f90 mpiifort -g -o bin/xaddition_sem obj/postprocess_par.postprocess_module.o obj/addition_sem.postprocess.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/exit_mpi.shared.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o mpiifort -g -o bin/xclip_sem obj/postprocess_par.postprocess_module.o obj/parse_kernel_names.postprocess.o obj/clip_sem.postprocess.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o mpiifort -g -o bin/xcombine_sem obj/postprocess_par.postprocess_module.o obj/parse_kernel_names.postprocess.o obj/combine_sem.postprocess.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o mpiifort -g -o bin/xdifference_sem obj/postprocess_par.postprocess_module.o obj/difference_sem.postprocess.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/exit_mpi.shared.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o mpiifort -g -o bin/xinterpolate_model obj/postprocess_par.postprocess_module.o obj/interpolate_model.postprocess.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/gll_library.shared.o obj/heap_sort.shared.o obj/hex_nodes.shared.o obj/interpolate.shared.o obj/lagrange_poly.shared.o obj/recompute_jacobian.shared.o obj/search_kdtree.shared.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o mpiifort -g -o bin/xcreate_cross_section obj/postprocess_par.postprocess_module.o obj/create_cross_section.postprocess.o obj/parse_kernel_names.postprocess.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/binary_c_io.cc.o obj/create_name_database.shared.o obj/exit_mpi.shared.o obj/flush_system.shared.o obj/gll_library.shared.o obj/heap_sort.shared.o obj/hex_nodes.shared.o obj/interpolate.shared.o obj/intgrl.shared.o obj/lagrange_poly.shared.o obj/make_ellipticity.shared.o obj/model_prem.shared.o obj/model_topo_bathy.shared.o obj/recompute_jacobian.shared.o obj/reduce.shared.o obj/rthetaphi_xyz.shared.o obj/search_kdtree.shared.o obj/spline_routines.shared.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o mpiifort -g -o bin/xsmooth_sem obj/postprocess_par.postprocess_module.o obj/parse_kernel_names.postprocess.o obj/smooth_sem.postprocess.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/exit_mpi.shared.o obj/get_all_eight_slices.shared.o obj/gll_library.shared.o obj/heap_sort.shared.o obj/reduce.shared.o obj/rthetaphi_xyz.shared.o obj/search_kdtree.shared.o obj/smooth_weights_vec.shared.o obj/write_VTK_file.shared.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o mpiifort -g -o bin/xadd_model_iso obj/add_model_iso.tomo.o obj/tomography_par.tomo_module.o obj/compute_kernel_integral.tomo.o obj/get_cg_direction.tomo.o obj/get_sd_direction.tomo.o obj/read_kernels.tomo.o obj/read_kernels_cg.tomo.o obj/read_model.tomo.o obj/read_parameters_tomo.tomo.o obj/write_gradient.tomo.o obj/write_new_model.tomo.o obj/write_new_model_perturbations.tomo.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/exit_mpi.shared.o obj/gll_library.shared.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o mpiifort -g -o bin/xadd_model_tiso obj/add_model_tiso.tomo.o obj/tomography_par.tomo_module.o obj/compute_kernel_integral.tomo.o obj/get_cg_direction.tomo.o obj/get_sd_direction.tomo.o obj/read_kernels.tomo.o obj/read_kernels_cg.tomo.o obj/read_model.tomo.o obj/read_parameters_tomo.tomo.o obj/write_gradient.tomo.o obj/write_new_model.tomo.o obj/write_new_model_perturbations.tomo.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/exit_mpi.shared.o obj/gll_library.shared.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o mpiifort -g -o bin/xadd_model_tiso_cg obj/add_model_tiso_cg.tomo.o obj/tomography_par.tomo_module.o obj/compute_kernel_integral.tomo.o obj/get_cg_direction.tomo.o obj/get_sd_direction.tomo.o obj/read_kernels.tomo.o obj/read_kernels_cg.tomo.o obj/read_model.tomo.o obj/read_parameters_tomo.tomo.o obj/write_gradient.tomo.o obj/write_new_model.tomo.o obj/write_new_model_perturbations.tomo.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/exit_mpi.shared.o obj/gll_library.shared.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o mpiifort -g -o bin/xadd_model_tiso_iso obj/add_model_tiso_iso.tomo.o obj/tomography_par.tomo_module.o obj/compute_kernel_integral.tomo.o obj/get_cg_direction.tomo.o obj/get_sd_direction.tomo.o obj/read_kernels.tomo.o obj/read_kernels_cg.tomo.o obj/read_model.tomo.o obj/read_parameters_tomo.tomo.o obj/write_gradient.tomo.o obj/write_new_model.tomo.o obj/write_new_model_perturbations.tomo.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/exit_mpi.shared.o obj/gll_library.shared.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o mpiifort -g -o bin/xsum_kernels obj/tomography_par.tomo_module.o obj/sum_kernels.tomo.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o mpiifort -g -o bin/xsum_preconditioned_kernels obj/tomography_par.tomo_module.o obj/sum_preconditioned_kernels.tomo.o obj/shared_par.shared_module.o obj/parallel.sharedmpi.o obj/param_reader.cc.o obj/read_parameter_file.shared.o obj/read_value_parameters.shared.o building xspecfem3D mpiifort -g -o ./bin/xspecfem3D ./obj/assemble_MPI_scalar.solver.o ./obj/assemble_MPI_vector.solver.o ./obj/comp_source_spectrum.solver.o ./obj/compute_adj_source_frechet.solver.o ./obj/convert_time.solver.o ./obj/define_derivation_matrices.solver.o ./obj/file_io_threads.cc.o ./obj/force_ftz.cc.o ./obj/get_backazimuth.solver.o ./obj/get_cmt.solver.o ./obj/get_force.solver.o ./obj/get_event_info.solver.o ./obj/make_gravity.solver.o ./obj/netlib_specfun_erf.solver.o ./obj/asdf_data.solverstatic_module.o ./obj/comp_source_time_function.solverstatic.o ./obj/specfem3D_par.solverstatic_module.o ./obj/write_seismograms.solverstatic.o ./obj/check_stability.solverstatic.o ./obj/compute_add_sources.solverstatic.o ./obj/compute_arrays_source.solverstatic.o ./obj/compute_boundary_kernel.solverstatic.o ./obj/compute_coupling.solverstatic.o ./obj/compute_element.solverstatic.o ./obj/compute_element_att_memory.solverstatic.o ./obj/compute_element_strain.solverstatic.o ./obj/compute_forces_acoustic_calling_routine.solverstatic.o ./obj/compute_forces_viscoelastic_calling_routine.solverstatic.o ./obj/compute_forces_crust_mantle_noDev.solverstatic.o ./obj/compute_forces_crust_mantle_Dev.solverstatic.o ./obj/compute_forces_inner_core_noDev.solverstatic.o ./obj/compute_forces_inner_core_Dev.solverstatic.o ./obj/compute_forces_outer_core_noDev.solverstatic.o ./obj/compute_forces_outer_core_Dev.solverstatic.o ./obj/compute_kernels.solverstatic.o ./obj/compute_seismograms.solverstatic.o ./obj/compute_stacey_crust_mantle.solverstatic.o ./obj/compute_stacey_outer_core.solverstatic.o ./obj/finalize_simulation.solverstatic.o ./obj/get_attenuation.solverstatic.o ./obj/initialize_simulation.solverstatic.o ./obj/iterate_time.solverstatic.o ./obj/iterate_time_undoatt.solverstatic.o ./obj/locate_receivers.solverstatic.o ./obj/locate_regular_points.solverstatic.o ./obj/locate_sources.solverstatic.o ./obj/multiply_arrays_source.solverstatic.o ./obj/noise_tomography.solverstatic.o ./obj/prepare_attenuation.solverstatic.o ./obj/prepare_elastic_elements.solverstatic.o ./obj/prepare_gpu.solverstatic.o ./obj/prepare_gravity.solverstatic.o ./obj/prepare_movie.solverstatic.o ./obj/prepare_noise.solverstatic.o ./obj/prepare_oceans.solverstatic.o ./obj/prepare_optimized_arrays.solverstatic.o ./obj/prepare_stacey.solverstatic.o ./obj/prepare_timerun.solverstatic.o ./obj/prepare_vtk_window.solverstatic.o ./obj/prepare_wavefields.solverstatic.o ./obj/read_adjoint_sources.solverstatic.o ./obj/read_arrays_solver.solverstatic.o ./obj/read_forward_arrays.solverstatic.o ./obj/read_mesh_databases.solverstatic.o ./obj/read_topography_bathymetry.solverstatic.o ./obj/save_forward_arrays.solverstatic.o ./obj/save_kernels.solverstatic.o ./obj/save_regular_kernels.solverstatic.o ./obj/setup_GLL_points.solverstatic.o ./obj/setup_sources_receivers.solverstatic.o ./obj/specfem3D.solverstatic.o ./obj/update_displacement_LDDRK.solverstatic.o ./obj/update_displacement_Newmark.solverstatic.o ./obj/write_movie_output.solverstatic.o ./obj/write_movie_volume.solverstatic.o ./obj/write_movie_surface.solverstatic.o ./obj/write_output_ASCII.solverstatic.o ./obj/write_output_SAC.solverstatic.o ./obj/specfem3D_gpu_method_stubs.cc.o ./obj/visual_vtk_stubs.visualc.o ./obj/shared_par.shared_module.o ./obj/adios_manager.shared_adios_module.o ./obj/auto_ner.shared.o ./obj/binary_c_io.cc.o ./obj/broadcast_computed_parameters.shared.o ./obj/calendar.shared.o ./obj/count_elements.shared.o ./obj/count_number_of_sources.shared.o ./obj/count_points.shared.o ./obj/create_name_database.shared.o ./obj/define_all_layers.shared.o ./obj/exit_mpi.shared.o ./obj/flush_system.shared.o ./obj/get_model_parameters.shared.o ./obj/get_timestep_and_layers.shared.o ./obj/gll_library.shared.o ./obj/hex_nodes.shared.o ./obj/init_openmp.shared.o ./obj/intgrl.shared.o ./obj/lagrange_poly.shared.o ./obj/make_ellipticity.shared.o ./obj/model_prem.shared.o ./obj/model_topo_bathy.shared.o ./obj/parallel.sharedmpi.o ./obj/param_reader.cc.o ./obj/read_compute_parameters.shared.o ./obj/read_parameter_file.shared.o ./obj/read_value_parameters.shared.o ./obj/recompute_jacobian.shared.o ./obj/reduce.shared.o ./obj/rthetaphi_xyz.shared.o ./obj/spline_routines.shared.o ./obj/write_VTK_file.shared.o ./obj/adios_method_stubs.cc.o ./obj/asdf_method_stubs.cc.o cp: omitting directory ‘setup/adios_xml_files’ ln: failed to create symbolic link ‘./crust2.0’: File exists ln: failed to create symbolic link ‘./s362ani’: File exists ln: failed to create symbolic link ‘./QRFSI12’: File exists ln: failed to create symbolic link ‘./topo_bathy’: File exists running script... Wed Mar 28 18:03:52 EDT 2018 On Mar 28, 2018, at 5:39 PM, Dimitri Komatitsch > wrote: Hi, Thanks. If your model is big it is maybe a movie array for which your system runs out of memory and for which we do not test the exit value of the allocate() statement. Could you configure with --enable-debug and let us know if the run then detects anything useful? Thank you, Best regards, Dimitri. On 03/28/2018 04:58 PM, Inchin, Pavel wrote: Good day, I have a problem with running of SPECFEM3D Globe on a cluster. When I run it with MOVIE_SURFACE = .false. and MOVIE_VOLUME=.false., the simulation runs without problems. But if I want to output movie, xspecfem3D gives error: forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source xspecfem3D 00000000006376E4 Unknown Unknown Unknown libpthread-2.17.s 00002AAAAC1C95E0 Unknown Unknown Unknown xspecfem3D 00000000005CF907 Unknown Unknown Unknown xspecfem3D 00000000004F0E18 Unknown Unknown Unknown xspecfem3D 00000000004EF900 Unknown Unknown Unknown xspecfem3D 0000000000507C23 Unknown Unknown Unknown xspecfem3D 00000000005CA25D Unknown Unknown Unknown xspecfem3D 00000000004044DE Unknown Unknown Unknown libc-2.17.so 00002AAAAC6F9C05 __libc_start_main Unknown Unknown xspecfem3D 00000000004043E9 Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source xspecfem3D 00000000006376E4 Unknown Unknown Unknown libpthread-2.17.s 00002AAAAC1C95E0 Unknown Unknown Unknown xspecfem3D 00000000005CF907 Unknown Unknown Unknown xspecfem3D 00000000004F0E18 Unknown Unknown Unknown xspecfem3D 00000000004EF900 Unknown Unknown Unknown xspecfem3D 0000000000507C23 Unknown Unknown Unknown xspecfem3D 00000000005CA25D Unknown Unknown Unknown xspecfem3D 00000000004044DE Unknown Unknown Unknown libc-2.17.so 00002AAAAC6F9C05 __libc_start_main Unknown Unknown xspecfem3D 00000000004043E9 Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source xspecfem3D 00000000006376E4 Unknown Unknown Unknown libpthread-2.17.s 00002AAAAC1C95E0 Unknown Unknown Unknown xspecfem3D 00000000005CF907 Unknown Unknown Unknown xspecfem3D 00000000004F0E18 Unknown Unknown Unknown xspecfem3D 00000000004EF900 Unknown Unknown Unknown xspecfem3D 0000000000507C23 Unknown Unknown Unknown xspecfem3D 00000000005CA25D Unknown Unknown Unknown xspecfem3D 00000000004044DE Unknown Unknown Unknown libc-2.17.so 00002AAAAC6F9C05 __libc_start_main Unknown Unknown xspecfem3D 00000000004043E9 Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source xspecfem3D 00000000006376E4 Unknown Unknown Unknown libpthread-2.17.s 00002AAAAC1C95E0 Unknown Unknown Unknown xspecfem3D 00000000005CF907 Unknown Unknown Unknown xspecfem3D 00000000004F0E18 Unknown Unknown Unknown xspecfem3D 00000000004EF900 Unknown Unknown Unknown xspecfem3D 0000000000507C23 Unknown Unknown Unknown xspecfem3D 00000000005CA25D Unknown Unknown Unknown xspecfem3D 00000000004044DE Unknown Unknown Unknown libc-2.17.so 00002AAAAC6F9C05 __libc_start_main Unknown Unknown xspecfem3D 00000000004043E9 Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source xspecfem3D 00000000006376E4 Unknown Unknown Unknown libpthread-2.17.s 00002AAAAC1C95E0 Unknown Unknown Unknown xspecfem3D 00000000005CF907 Unknown Unknown Unknown xspecfem3D 00000000004F0E18 Unknown Unknown Unknown xspecfem3D 00000000004EF900 Unknown Unknown Unknown xspecfem3D 0000000000507C23 Unknown Unknown Unknown xspecfem3D 00000000005CA25D Unknown Unknown Unknown xspecfem3D 00000000004044DE Unknown Unknown Unknown libc-2.17.so 00002AAAAC6F9C05 __libc_start_main Unknown Unknown xspecfem3D 00000000004043E9 Unknown Unknown Unknown …………. I compile using: ./configure FC=mpiifort MPIFC=mpiifort -mcmodel=medium-shared-intel And my modules are: intel/compiler/64/2017/17.0.5 intel/mpi/64/2017/5.239 I found this issue raised earlier (https://github.com/geodynamics/specfem3d/issues/512), but with running of the model by itself and not for movie… Could you provide a direction where to find a reason for that? Thank you Paul _______________________________________________ CIG-SEISMO mailing list CIG-SEISMO at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: From wyc1974 at hotmail.com Wed Mar 28 21:24:30 2018 From: wyc1974 at hotmail.com (weiyu chen) Date: Thu, 29 Mar 2018 04:24:30 +0000 Subject: [CIG-SEISMO] SW4 installation error Message-ID: Hi, I am pretty new to Linux, so was following the SW4 installation step- by-step. I encountered following error messages when "make" xerror.o: In function `xersav_.constprop.2': xerror.f:(.text+0x12c): undefined reference to `_gfortran_st_write' xerror.f:(.text+0x140): undefined reference to `_gfortran_transfer_character_write' xerror.f:(.text+0x14a): undefined reference to `_gfortran_st_write_done' ..... Can you please teach me how to install SW4 properly? Many thanks. weiyu