From rene.gassmoeller at mailbox.org Sat Mar 3 17:07:40 2018 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Sat, 3 Mar 2018 18:07:40 -0700 Subject: [CIG-MC] Segmentation fault - docker image - Mac In-Reply-To: References: Message-ID: <20e921eb-15bd-cb6b-50f6-a2faf9c8b70a@mailbox.org> Hi Diego, sorry for the late reply. I created the docker image, but I did not test it on Mac recently (though I think I tested it when I created it, not sure though). To make sure it is not your model setup or the read only folder that you mount, could you try running one of the cookbooks that are included in the container (e.g. cookbooks/convection-box.prm) and see if that works? If it does not work we need to look for reasons why a docker image would run on linux, but not on Mac. Best, Rene On 02/22/2018 02:00 PM, Diego Fernando Usma Aristizabal wrote: > Hi, > > I'm having a problem with the aspect docker image, after i try to run > a model  i get a segmentation fault error. I’m running in a mac laptop > with the next specifications: > > -os x high sierra > -8 gb ram > -1,8 GHz Intel Core i5 > -1600 MHz DDR3 > > I hope anybody can help me. > > Thanks for your atention, > > Diego Usma, > > Work flow and error: > > MacBook-Air-de-Diego:~ diegousma$ cd dealii/ > MacBook-Air-de-Diego:dealii diegousma$ cd aspect/ > MacBook-Air-de-Diego:aspect diegousma$ cd model_input/ > MacBook-Air-de-Diego:model_input diegousma$ docker run -it -v > "$(pwd):/$HOME/dealii/aspect/model_input:ro" \ > > gassmoeller/aspect:latest bash > dealii at 1db9d807a3cc:~/aspect$ ./aspect model_input/convection-box.prm > Segmentation fault > dealii at 1db9d807a3cc:~/aspect$  > > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc -- Rene Gassmoeller http://www.math.colostate.edu/~gassmoel/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdk at vt.edu Tue Mar 6 05:17:56 2018 From: sdk at vt.edu (Scott King) Date: Tue, 6 Mar 2018 08:17:56 -0500 Subject: [CIG-MC] AGU's new data policy Message-ID: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> AGU journals have a new data policy requiring that all the data from the work must be in a publicly accessible repository. In general I think this is a good thing. They provide several possible solutions. From the editor letter… "AGU requires that data needed to understand and build upon the published research be available in public repositories following best practices . This includes an explicit statement in the Acknowledgments section on where users can access or find the data for this paper. Citations to archived data should be included in your reference list and all references, including those cited in the supplement, should be included in the main reference list. All listed references must be available to the general reader by the time of acceptance.” They list several possible repositories, none of which seem appropriate for 2.9 TB of CicomS results. Set aside the philosophical issue that model results are not “data” (they don’t accept that). I have the output used in the published figures down to a reasonable size but. I’m curious what others are doing. Has anyone else run into this yet? (If not you will.) I’m curious if there is a community consensus regarding a repository where all geodynamics results would/could end up, as opposed to ending up with them scattered across 3-4 (or more) potential repositories. Maybe that’s not something to worry about, but since this is new and to me at least I’ve had no time to think it through, I’m curious what others are doing. Thoughts? Cheers, Scott -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.bower at csh.unibe.ch Tue Mar 6 05:59:45 2018 From: daniel.bower at csh.unibe.ch (Dan Bower) Date: Tue, 6 Mar 2018 14:59:45 +0100 Subject: [CIG-MC] AGU's new data policy In-Reply-To: <1e51989f8e0a4eb3989f6c95a726406b@aai-mail-02.campus.unibe.ch> References: <1e51989f8e0a4eb3989f6c95a726406b@aai-mail-02.campus.unibe.ch> Message-ID: Hi Scott, The SNSF (Switzerland) is also working on this: http://www.snf.ch/en/theSNSF/research-policies/open_research_data/Pages/data-management-plan-dmp-guidelines-for-researchers.aspx At the moment they only provide loose guidelines and try to let the researchers themselves decide on the best course of action. In fact, the SNSF don't even state what "data" actually is (since it varies between fields and disciplines, and particularly between the humanities and sciences). Anyway, hope the link above is of some use to you (and others), perhaps to compare with what AGU (and other science organisations) are doing. Cheers, Dan On 6 March 2018 at 14:17, wrote: > > AGU journals have a new data policy requiring that all the data from the > work must be in a publicly accessible repository. In general I think this > is a good thing. They provide several possible solutions. From the > editor letter… > > "*AGU requires that data needed to understand and build upon the > published research be available in public repositories following **best > practices > . > This includes an explicit statement in the Acknowledgments section on where > users can access or find the data for this paper. Citations to archived > data should be included in your reference list and all references, > including those cited in the supplement, should be included in the main > reference list. All listed references must be available to the general > reader by the time of acceptance.*” > > They list several possible repositories, none of which seem appropriate > for 2.9 TB of CicomS results. Set aside the philosophical issue that model > results are not “data” (they don’t accept that). I have the output used > in the published figures down to a reasonable size but. I’m curious what > others are doing. Has anyone else run into this yet? (If not you will.) > I’m curious if there is a community consensus regarding a repository where > all geodynamics results would/could end up, as opposed to ending up with > them scattered across 3-4 (or more) potential repositories. Maybe that’s > not something to worry about, but since this is new and to me at least I’ve > had no time to think it through, I’m curious what others are doing. > > Thoughts? > > Cheers, > > Scott > > > > -- Dan J. Bower, PhD Oberassistent SNSF Ambizione Fellow and CSH Fellow Center for Space and Habitability (CSH) University of Bern Gesellschaftsstrasse 6 3012 Bern, Switzerland +41 31 631 3703 daniel.bower at csh.unibe.ch https://danjbower.wordpress.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljhwang at ucdavis.edu Tue Mar 6 07:28:48 2018 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Tue, 6 Mar 2018 07:28:48 -0800 Subject: [CIG-MC] AGU's new data policy In-Reply-To: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> Message-ID: Currently CIG maintains a zenodo community: https://zenodo.org/communities/geodynamics/?page=1&size=20 The current description indicates that: This community is intended for use for codes in the CIG repository and their associated research products as it was initiated to grab DOIs for code. Should the scope be broaden? What are the pro’s and cons’s? This is an issue across our communities. AGU guidance is currently what is considered Best Practices though I agree that spreading it across repo’s does not encourage discovery by other means than direct DOI link. Best, -Lorraine ***************************** Lorraine Hwang, Ph.D. Associate Director, CIG 530.752.3656 > On Mar 6, 2018, at 5:17 AM, Scott King wrote: > > > AGU journals have a new data policy requiring that all the data from the work must be in a publicly accessible repository. In general I think this is a good thing. They provide several possible solutions. From the editor letter… > > "AGU requires that data needed to understand and build upon the published research be available in public repositories following best practices . This includes an explicit statement in the Acknowledgments section on where users can access or find the data for this paper. Citations to archived data should be included in your reference list and all references, including those cited in the supplement, should be included in the main reference list. All listed references must be available to the general reader by the time of acceptance.” > > They list several possible repositories, none of which seem appropriate for 2.9 TB of CicomS results. Set aside the philosophical issue that model results are not “data” (they don’t accept that). I have the output used in the published figures down to a reasonable size but. I’m curious what others are doing. Has anyone else run into this yet? (If not you will.) I’m curious if there is a community consensus regarding a repository where all geodynamics results would/could end up, as opposed to ending up with them scattered across 3-4 (or more) potential repositories. Maybe that’s not something to worry about, but since this is new and to me at least I’ve had no time to think it through, I’m curious what others are doing. > > Thoughts? > > Cheers, > > Scott > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From twb at ig.utexas.edu Tue Mar 6 08:39:01 2018 From: twb at ig.utexas.edu (Thorsten Becker) Date: Tue, 6 Mar 2018 10:39:01 -0600 Subject: [CIG-MC] AGU's new data policy In-Reply-To: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> Message-ID: The way I have interpreted AGU's guidelines for geodynamic studies as AGU editor is to not ask for archiving of model output, but to ask for general access to all material that would be needed to recreate that output, or some simpler version of it that is proof of concept. I.e. input data, input files, and a DOI to version of code, for example, if a community code is used. The general idea is, of course, to make things reproducible, and AGU and Wiley are among those who realize that this can cause problems, and are working on solutions with the community. One particular issue is that I have not asked for verification that results are actually reproducible, and taken authors assurances that codes will be shared at face value (besides when the publications were of technical nature, and we ask reviewers to actually try to download and run the software, for example (which usually never works)). I think that part might change, in that publishers may ask for a code access link and somehow archive this. I can also see some solutions akin to asking for a Docker set up, archived somewhere, that will allow anyone to rerun the models. There are interesting challenges involved, but in the end, I think moving to more openness and reproducibility is a good thing, and the success of CIG shows how some issues that were raised before we moved into this model resolved themselves. Things are perfect, but we're making progress. My personal experience with publishing numerical stuff in highly visible journals is that, within a week, there are people actually asking to get all the code and all the input files to rerun our models, and we've always shared all of our stuff, of course. I realize that this is a significant workload (particularly for my grad students who actually put this stuff together...) and somehow AGU and publishers need to do more to support people with large data volumes, seismological inversions being another example. Thorsten Becker - UTIG & DGS, JSG, UT Austin On Tue, Mar 6, 2018 at 7:17 AM, Scott King wrote: > > AGU journals have a new data policy requiring that all the data from the > work must be in a publicly accessible repository. In general I think this > is a good thing. They provide several possible solutions. From the > editor letter… > > "*AGU requires that data needed to understand and build upon the > published research be available in public repositories following **best > practices > . > This includes an explicit statement in the Acknowledgments section on where > users can access or find the data for this paper. Citations to archived > data should be included in your reference list and all references, > including those cited in the supplement, should be included in the main > reference list. All listed references must be available to the general > reader by the time of acceptance.*” > > They list several possible repositories, none of which seem appropriate > for 2.9 TB of CicomS results. Set aside the philosophical issue that model > results are not “data” (they don’t accept that). I have the output used > in the published figures down to a reasonable size but. I’m curious what > others are doing. Has anyone else run into this yet? (If not you will.) > I’m curious if there is a community consensus regarding a repository where > all geodynamics results would/could end up, as opposed to ending up with > them scattered across 3-4 (or more) potential repositories. Maybe that’s > not something to worry about, but since this is new and to me at least I’ve > had no time to think it through, I’m curious what others are doing. > > Thoughts? > > Cheers, > > Scott > > > > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shijie.zhong at colorado.edu Tue Mar 6 07:33:53 2018 From: shijie.zhong at colorado.edu (Shijie Zhong) Date: Tue, 6 Mar 2018 15:33:53 +0000 Subject: [CIG-MC] AGU's new data policy In-Reply-To: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> Message-ID: <8925D28E-8061-4A43-B6CA-3FAC84954C3C@colorado.edu> Hi Scott, You raised an excellent question. We published a paper last month in GRL. Although the paper is not about convection modeling with only small amount of data all generated from semi-analytical solutions (of deformation and gravity anomalies for a tidally driven planet), as we worked on the data/code availability statement in the acknowledgement section, we struggled on what to do and also anticipated questions like yours for mantle convection modeling studies. For modeling studies, it seems that modeling codes and input files should be sufficient. One does not need a lot of storage space for these files. I was also curious what public repositories our colleagues have been using. Another question that is probably more relevant to AGU is what type of codes they expect authors to put into the repositories, executables or the source codes? For codes publically available such as CitcomS or ASPECT, this is not an issue, but how about some new codes that authors are not ready to put to public domain? I was curious whether you all have any thoughts to share. All the best, Shijie Shijie Zhong, Professor Department of Physics University of Colorado at Boulder Boulder, CO 80309 http://mathis.colorado.edu/szhong Tel: 303-735-5095; Fax: 303-492-7935 From: CIG-MC on behalf of Scott King Reply-To: "cig-mc at geodynamics.org" Date: Tuesday, March 6, 2018 at 6:17 AM To: "cig-mc at geodynamics.org" Cc: Louise Kellogg Subject: [CIG-MC] AGU's new data policy AGU journals have a new data policy requiring that all the data from the work must be in a publicly accessible repository. In general I think this is a good thing. They provide several possible solutions. From the editor letter… "AGU requires that data needed to understand and build upon the published research be available in public repositories following best practices. This includes an explicit statement in the Acknowledgments section on where users can access or find the data for this paper. Citations to archived data should be included in your reference list and all references, including those cited in the supplement, should be included in the main reference list. All listed references must be available to the general reader by the time of acceptance.” They list several possible repositories, none of which seem appropriate for 2.9 TB of CicomS results. Set aside the philosophical issue that model results are not “data” (they don’t accept that). I have the output used in the published figures down to a reasonable size but. I’m curious what others are doing. Has anyone else run into this yet? (If not you will.) I’m curious if there is a community consensus regarding a repository where all geodynamics results would/could end up, as opposed to ending up with them scattered across 3-4 (or more) potential repositories. Maybe that’s not something to worry about, but since this is new and to me at least I’ve had no time to think it through, I’m curious what others are doing. Thoughts? Cheers, Scott -------------- next part -------------- An HTML attachment was scrubbed... URL: From judannberg at gmail.com Tue Mar 6 09:01:33 2018 From: judannberg at gmail.com (Juliane Dannberg) Date: Tue, 6 Mar 2018 10:01:33 -0700 Subject: [CIG-MC] AGU's new data policy In-Reply-To: References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> Message-ID: <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> My experience with this is similar to what Thorsten describes. I also regularly have TB-sized model output, and usually include the doi of the version of the code I used in the paper, upload all input files/scripts etc. I used as supplementary material, and include a sentence that "all input files necessary to reproduce the model results are included in the supplementary material". So far, that seemed to be an acceptable solution, also for AGU journals. But I agree that there doesn't seem to be a good way to archive TB-sized model output over long periods of time... Best, Juliane ---------------------------------------------------------------------- Juliane Dannberg Postdoctoral Fellow, Colorado State University http://www.math.colostate.edu/~dannberg/ Am 3/6/2018 um 9:39 AM schrieb Thorsten Becker: > The way I have interpreted AGU's guidelines for geodynamic studies as > AGU editor is to not ask for archiving of model output, but to ask for > general access to all material that would be needed to recreate that > output, or some simpler version of it that is proof of concept. I.e. > input data, input files, and a DOI to version of code, for example, if > a community code is used. > > The general idea is, of course, to make things reproducible, and AGU > and Wiley are among those who realize that this can cause problems, > and are working on solutions with the community. > > One particular issue is that I have not asked for verification that > results are actually reproducible, and taken authors assurances that > codes will be shared at face value (besides when the publications were > of technical nature, and we ask reviewers to actually try to download > and run the software, for example (which usually never works)). I > think that part might change, in that publishers may ask for a code > access link and somehow archive this. > > I can also see some solutions akin to asking for a Docker set up, > archived somewhere, that will allow anyone to rerun the models. There > are interesting challenges involved, but in the end, I think moving to > more openness and reproducibility is a good thing, and the success of > CIG shows how some issues that were raised before we moved into this > model resolved themselves. Things are perfect, but we're making progress. > > My personal experience with publishing numerical stuff in highly > visible journals is that, within a week, there are people actually > asking to get all the code and all the input files to rerun our > models, and we've always shared all of our stuff, of course. I realize > that this is a significant workload (particularly for my grad students > who actually put this stuff together...) and somehow AGU and > publishers need to do more to support people with large data volumes, > seismological inversions being another example. > > > Thorsten Becker - UTIG & DGS, JSG, UT Austin > > > On Tue, Mar 6, 2018 at 7:17 AM, Scott King > wrote: > > > AGU journals have a new data policy requiring that all the data > from the work must be in a publicly accessible repository.  In > general I think this is a good thing.   They provide several > possible solutions. From the editor letter… > > "/AGU requires that data needed to understand and build upon the > published research be available in public repositories following > //best practices > . > This includes an explicit statement in the Acknowledgments section > on where users can access or find the data for this paper. > Citations to archived data should be included in your reference > list and all references, including those cited in the supplement, > should be included in the main reference list. All listed > references must be available to the general reader by the time of > acceptance./” > > They list several possible repositories, none of which seem > appropriate for 2.9 TB of CicomS results. Set aside the > philosophical issue that model results are not “data” (they don’t > accept that).   I have the output used in the published figures > down to a reasonable size but. I’m curious what others are doing.  > Has anyone else run into this yet?  (If not you will.)  I’m > curious if there is a community consensus regarding a repository > where all geodynamics results would/could end up, as opposed to > ending up with them scattered across 3-4 (or more) potential > repositories.  Maybe that’s not something to worry about, but > since this is new and to me at least I’ve had no time to think it > through, I’m curious what others are doing. > > Thoughts? > > Cheers, > > Scott > > > > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc > > > > > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdk at vt.edu Tue Mar 6 09:31:07 2018 From: sdk at vt.edu (Scott King) Date: Tue, 6 Mar 2018 12:31:07 -0500 Subject: [CIG-MC] AGU's new data policy In-Reply-To: <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> Message-ID: Just to explain/clarify. What you and Thorsten describe is no longer acceptable, at least with JGR Planets, as of January 2018. The editor is insisting on the specific data used to generate the figures (at a minimum) in addition to referencing an open source code and putting the input files in a repository. This might be something that is being enforced/interpreted on an editor by editor basis. It seems (not unlike other instances with AGU) that they have come up with a policy, have lots of instructions with MUST, but don’t really have a clear plan or even understand whether the resources are available to do what one MUST do. Scott > On Mar 6, 2018, at 12:01 PM, Juliane Dannberg wrote: > > My experience with this is similar to what Thorsten describes. I also regularly have TB-sized model output, and usually include the doi of the version of the code I used in the paper, upload all input files/scripts etc. I used as supplementary material, and include a sentence that "all input files necessary to reproduce the model results are included in the supplementary material". So far, that seemed to be an acceptable solution, also for AGU journals. > But I agree that there doesn't seem to be a good way to archive TB-sized model output over long periods of time... > > Best, > Juliane > > > ---------------------------------------------------------------------- > Juliane Dannberg > Postdoctoral Fellow, Colorado State University > http://www.math.colostate.edu/~dannberg/ > > > Am 3/6/2018 um 9:39 AM schrieb Thorsten Becker: >> The way I have interpreted AGU's guidelines for geodynamic studies as AGU editor is to not ask for archiving of model output, but to ask for general access to all material that would be needed to recreate that output, or some simpler version of it that is proof of concept. I.e. input data, input files, and a DOI to version of code, for example, if a community code is used. >> >> The general idea is, of course, to make things reproducible, and AGU and Wiley are among those who realize that this can cause problems, and are working on solutions with the community. >> >> One particular issue is that I have not asked for verification that results are actually reproducible, and taken authors assurances that codes will be shared at face value (besides when the publications were of technical nature, and we ask reviewers to actually try to download and run the software, for example (which usually never works)). I think that part might change, in that publishers may ask for a code access link and somehow archive this. >> >> I can also see some solutions akin to asking for a Docker set up, archived somewhere, that will allow anyone to rerun the models. There are interesting challenges involved, but in the end, I think moving to more openness and reproducibility is a good thing, and the success of CIG shows how some issues that were raised before we moved into this model resolved themselves. Things are perfect, but we're making progress. >> >> My personal experience with publishing numerical stuff in highly visible journals is that, within a week, there are people actually asking to get all the code and all the input files to rerun our models, and we've always shared all of our stuff, of course. I realize that this is a significant workload (particularly for my grad students who actually put this stuff together...) and somehow AGU and publishers need to do more to support people with large data volumes, seismological inversions being another example. >> >> >> Thorsten Becker - UTIG & DGS, JSG, UT Austin >> On Tue, Mar 6, 2018 at 7:17 AM, Scott King > wrote: >> >> AGU journals have a new data policy requiring that all the data from the work must be in a publicly accessible repository. In general I think this is a good thing. They provide several possible solutions. From the editor letter… >> >> "AGU requires that data needed to understand and build upon the published research be available in public repositories following best practices . This includes an explicit statement in the Acknowledgments section on where users can access or find the data for this paper. Citations to archived data should be included in your reference list and all references, including those cited in the supplement, should be included in the main reference list. All listed references must be available to the general reader by the time of acceptance.” >> >> They list several possible repositories, none of which seem appropriate for 2.9 TB of CicomS results. Set aside the philosophical issue that model results are not “data” (they don’t accept that). I have the output used in the published figures down to a reasonable size but. I’m curious what others are doing. Has anyone else run into this yet? (If not you will.) I’m curious if there is a community consensus regarding a repository where all geodynamics results would/could end up, as opposed to ending up with them scattered across 3-4 (or more) potential repositories. Maybe that’s not something to worry about, but since this is new and to me at least I’ve had no time to think it through, I’m curious what others are doing. >> >> Thoughts? >> >> Cheers, >> >> Scott >> >> >> >> >> _______________________________________________ >> CIG-MC mailing list >> CIG-MC at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc >> >> >> >> _______________________________________________ >> CIG-MC mailing list >> CIG-MC at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc -------------- next part -------------- An HTML attachment was scrubbed... URL: From legendcit at gmail.com Tue Mar 6 08:12:08 2018 From: legendcit at gmail.com (Lijun Liu) Date: Tue, 6 Mar 2018 10:12:08 -0600 Subject: [CIG-MC] CIG-MC Digest, Vol 122, Issue 3 In-Reply-To: References: Message-ID: My 2 cents: I also find this issue a bit confusing and troublesome. Not only AGU journals, others like Nature Geoscience also started to have a similar requirement call ‘Data availability’. As Scott said, there is no clear way we can really upload these model outputs, but it seems these journals are not clear on what they need either. We do try to cite every relevant publication so that readers can track down the work, but that’s probably no different from what’s discussed here. Either way, readers still don’t get the access to the raw model outputs. Maybe the most practical way is still what the tomographers are doing, as is to provide the outputs on their own server. This seems something hard to avoid for a while. Cheers, Lijun --------------------------------------------------- Lijun Liu Associate Professor Lincoln Excellence Scholar & Geo Thrust Professorial Scholar University of Illinois at Urbana-Champaign Email: ljliu at illinois.edu Web: https://www.geology.illinois.edu/cms/One.aspx?portalId=127672&pageId=230146 > On Mar 6, 2018, at 9:43 AM, cig-mc-request at geodynamics.org wrote: > > Send CIG-MC mailing list submissions to > cig-mc at geodynamics.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc > or, via email, send a message with subject or body 'help' to > cig-mc-request at geodynamics.org > > You can reach the person managing the list at > cig-mc-owner at geodynamics.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of CIG-MC digest..." > > > Today's Topics: > > 1. AGU's new data policy (Scott King) > 2. Re: AGU's new data policy (Dan Bower) > 3. Re: AGU's new data policy (Lorraine Hwang) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 6 Mar 2018 08:17:56 -0500 > From: Scott King > To: cig-mc at geodynamics.org > Cc: Louise Kellogg > Subject: [CIG-MC] AGU's new data policy > Message-ID: <975B089E-2E3A-439E-BA70-B5182109D221 at vt.edu> > Content-Type: text/plain; charset="utf-8" > > > AGU journals have a new data policy requiring that all the data from the work must be in a publicly accessible repository. In general I think this is a good thing. They provide several possible solutions. From the editor letter… > > "AGU requires that data needed to understand and build upon the published research be available in public repositories following best practices . This includes an explicit statement in the Acknowledgments section on where users can access or find the data for this paper. Citations to archived data should be included in your reference list and all references, including those cited in the supplement, should be included in the main reference list. All listed references must be available to the general reader by the time of acceptance.” > > They list several possible repositories, none of which seem appropriate for 2.9 TB of CicomS results. Set aside the philosophical issue that model results are not “data” (they don’t accept that). I have the output used in the published figures down to a reasonable size but. I’m curious what others are doing. Has anyone else run into this yet? (If not you will.) I’m curious if there is a community consensus regarding a repository where all geodynamics results would/could end up, as opposed to ending up with them scattered across 3-4 (or more) potential repositories. Maybe that’s not something to worry about, but since this is new and to me at least I’ve had no time to think it through, I’m curious what others are doing. > > Thoughts? > > Cheers, > > Scott > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Tue, 6 Mar 2018 14:59:45 +0100 > From: Dan Bower > To: > Cc: lhkellogg at ucdavis.edu > Subject: Re: [CIG-MC] AGU's new data policy > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Scott, > > The SNSF (Switzerland) is also working on this: > > http://www.snf.ch/en/theSNSF/research-policies/open_research_data/Pages/data-management-plan-dmp-guidelines-for-researchers.aspx > > At the moment they only provide loose guidelines and try to let the > researchers themselves decide on the best course of action. In fact, the > SNSF don't even state what "data" actually is (since it varies between > fields and disciplines, and particularly between the humanities and > sciences). Anyway, hope the link above is of some use to you (and others), > perhaps to compare with what AGU (and other science organisations) are > doing. > > Cheers, > > Dan > > > On 6 March 2018 at 14:17, wrote: > >> >> AGU journals have a new data policy requiring that all the data from the >> work must be in a publicly accessible repository. In general I think this >> is a good thing. They provide several possible solutions. From the >> editor letter… >> >> "*AGU requires that data needed to understand and build upon the >> published research be available in public repositories following **best >> practices >> . >> This includes an explicit statement in the Acknowledgments section on where >> users can access or find the data for this paper. Citations to archived >> data should be included in your reference list and all references, >> including those cited in the supplement, should be included in the main >> reference list. All listed references must be available to the general >> reader by the time of acceptance.*” >> >> They list several possible repositories, none of which seem appropriate >> for 2.9 TB of CicomS results. Set aside the philosophical issue that model >> results are not “data” (they don’t accept that). I have the output used >> in the published figures down to a reasonable size but. I’m curious what >> others are doing. Has anyone else run into this yet? (If not you will.) >> I’m curious if there is a community consensus regarding a repository where >> all geodynamics results would/could end up, as opposed to ending up with >> them scattered across 3-4 (or more) potential repositories. Maybe that’s >> not something to worry about, but since this is new and to me at least I’ve >> had no time to think it through, I’m curious what others are doing. >> >> Thoughts? >> >> Cheers, >> >> Scott >> >> >> >> > > > -- > Dan J. Bower, PhD > Oberassistent > SNSF Ambizione Fellow and CSH Fellow > Center for Space and Habitability (CSH) > University of Bern > Gesellschaftsstrasse 6 > 3012 Bern, Switzerland > +41 31 631 3703 > daniel.bower at csh.unibe.ch > https://danjbower.wordpress.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 3 > Date: Tue, 6 Mar 2018 07:28:48 -0800 > From: Lorraine Hwang > To: Scott King > Cc: Louise Kellogg , cig-mc at geodynamics.org > Subject: Re: [CIG-MC] AGU's new data policy > Message-ID: > Content-Type: text/plain; charset="utf-8" > > Currently CIG maintains a zenodo community: > https://zenodo.org/communities/geodynamics/?page=1&size=20 > > The current description indicates that: > > This community is intended for use for codes in the CIG repository and their associated research products > > as it was initiated to grab DOIs for code. Should the scope be broaden? What are the pro’s and cons’s? This is an issue across our communities. > > AGU guidance is currently what is considered Best Practices though I agree that spreading it across repo’s does not encourage discovery by other means than direct DOI link. > > Best, > -Lorraine > > ***************************** > Lorraine Hwang, Ph.D. > Associate Director, CIG > 530.752.3656 > > > >> On Mar 6, 2018, at 5:17 AM, Scott King wrote: >> >> >> AGU journals have a new data policy requiring that all the data from the work must be in a publicly accessible repository. In general I think this is a good thing. They provide several possible solutions. From the editor letter… >> >> "AGU requires that data needed to understand and build upon the published research be available in public repositories following best practices . This includes an explicit statement in the Acknowledgments section on where users can access or find the data for this paper. Citations to archived data should be included in your reference list and all references, including those cited in the supplement, should be included in the main reference list. All listed references must be available to the general reader by the time of acceptance.” >> >> They list several possible repositories, none of which seem appropriate for 2.9 TB of CicomS results. Set aside the philosophical issue that model results are not “data” (they don’t accept that). I have the output used in the published figures down to a reasonable size but. I’m curious what others are doing. Has anyone else run into this yet? (If not you will.) I’m curious if there is a community consensus regarding a repository where all geodynamics results would/could end up, as opposed to ending up with them scattered across 3-4 (or more) potential repositories. Maybe that’s not something to worry about, but since this is new and to me at least I’ve had no time to think it through, I’m curious what others are doing. >> >> Thoughts? >> >> Cheers, >> >> Scott >> >> >> > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc > > ------------------------------ > > End of CIG-MC Digest, Vol 122, Issue 3 > ************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From cmcooper at wsu.edu Tue Mar 6 09:28:04 2018 From: cmcooper at wsu.edu (Cooper, Catherine M) Date: Tue, 6 Mar 2018 17:28:04 +0000 Subject: [CIG-MC] AGU's new data policy In-Reply-To: <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> Message-ID: <277B34AD-D981-4A95-B8D6-586EF8DB3706@wsu.edu> I wonder if it wouldn’t be helpful to have a community statement as to what we consider “data” and what we agree needs to be shared for reproducibility (which we all agree is important)? But it seems like we might need to do some outreach on this if there is some misunderstanding about model output as data amongst AGU and NASA (this has come up in proposal reviews). On Mar 6, 2018, at 9:01 AM, Juliane Dannberg > wrote: My experience with this is similar to what Thorsten describes. I also regularly have TB-sized model output, and usually include the doi of the version of the code I used in the paper, upload all input files/scripts etc. I used as supplementary material, and include a sentence that "all input files necessary to reproduce the model results are included in the supplementary material". So far, that seemed to be an acceptable solution, also for AGU journals. But I agree that there doesn't seem to be a good way to archive TB-sized model output over long periods of time... Best, Juliane ---------------------------------------------------------------------- Juliane Dannberg Postdoctoral Fellow, Colorado State University http://www.math.colostate.edu/~dannberg/ Am 3/6/2018 um 9:39 AM schrieb Thorsten Becker: The way I have interpreted AGU's guidelines for geodynamic studies as AGU editor is to not ask for archiving of model output, but to ask for general access to all material that would be needed to recreate that output, or some simpler version of it that is proof of concept. I.e. input data, input files, and a DOI to version of code, for example, if a community code is used. The general idea is, of course, to make things reproducible, and AGU and Wiley are among those who realize that this can cause problems, and are working on solutions with the community. One particular issue is that I have not asked for verification that results are actually reproducible, and taken authors assurances that codes will be shared at face value (besides when the publications were of technical nature, and we ask reviewers to actually try to download and run the software, for example (which usually never works)). I think that part might change, in that publishers may ask for a code access link and somehow archive this. I can also see some solutions akin to asking for a Docker set up, archived somewhere, that will allow anyone to rerun the models. There are interesting challenges involved, but in the end, I think moving to more openness and reproducibility is a good thing, and the success of CIG shows how some issues that were raised before we moved into this model resolved themselves. Things are perfect, but we're making progress. My personal experience with publishing numerical stuff in highly visible journals is that, within a week, there are people actually asking to get all the code and all the input files to rerun our models, and we've always shared all of our stuff, of course. I realize that this is a significant workload (particularly for my grad students who actually put this stuff together...) and somehow AGU and publishers need to do more to support people with large data volumes, seismological inversions being another example. Thorsten Becker - UTIG & DGS, JSG, UT Austin On Tue, Mar 6, 2018 at 7:17 AM, Scott King > wrote: AGU journals have a new data policy requiring that all the data from the work must be in a publicly accessible repository. In general I think this is a good thing. They provide several possible solutions. From the editor letter… "AGU requires that data needed to understand and build upon the published research be available in public repositories following best practices. This includes an explicit statement in the Acknowledgments section on where users can access or find the data for this paper. Citations to archived data should be included in your reference list and all references, including those cited in the supplement, should be included in the main reference list. All listed references must be available to the general reader by the time of acceptance.” They list several possible repositories, none of which seem appropriate for 2.9 TB of CicomS results. Set aside the philosophical issue that model results are not “data” (they don’t accept that). I have the output used in the published figures down to a reasonable size but. I’m curious what others are doing. Has anyone else run into this yet? (If not you will.) I’m curious if there is a community consensus regarding a repository where all geodynamics results would/could end up, as opposed to ending up with them scattered across 3-4 (or more) potential repositories. Maybe that’s not something to worry about, but since this is new and to me at least I’ve had no time to think it through, I’m curious what others are doing. Thoughts? Cheers, Scott _______________________________________________ CIG-MC mailing list CIG-MC at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc _______________________________________________ CIG-MC mailing list CIG-MC at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc _______________________________________________ CIG-MC mailing list CIG-MC at geodynamics.org https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_cig-2Dmc&d=DwIGaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=3iAcC0lqlf3gOx4_NidEiA&m=HfT2q7BUNv7lwQ4rNBn6WCxad64-R40vEvd3Ehweq84&s=XOhKoMDTham1Kxbm10gSj_HK0WwQs7oPVG5RjUctuS0&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: From mbweller at ig.utexas.edu Tue Mar 6 13:49:47 2018 From: mbweller at ig.utexas.edu (Matthew Weller) Date: Tue, 6 Mar 2018 15:49:47 -0600 Subject: [CIG-MC] CIG-MC Digest, Vol 122, Issue 7 In-Reply-To: References: Message-ID: I second the idea of a community statement as to what we consider to be data and what we consider the standard of reproducibility to be. This has come up a lot recently, and there has not been a satisfactory response from funding agencies and journals. As stated, if we do indeed need to archive and make available large amounts of data (TB scale) as suggested for JGR Planets, I worry what the implications are for early career researchers? Those who may move institutions frequently, and who may have limited to non-existent funding? The idea of maintaining large amounts of data on personal servers, as done in tomography, is not a very robust option. It creates a potentially significant barrier to publishing, perhaps even barring publication in extreme cases... at least without a clear and well articulated definition of 'data' and a standard of reproducibility within the community and at large. well, that's as far as my 2-cents go. On Tue, Mar 6, 2018 at 3:15 PM, wrote: > Send CIG-MC mailing list submissions to > cig-mc at geodynamics.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc > or, via email, send a message with subject or body 'help' to > cig-mc-request at geodynamics.org > > You can reach the person managing the list at > cig-mc-owner at geodynamics.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of CIG-MC digest..." > > > Today's Topics: > > 1. Re: AGU's new data policy (Cooper, Catherine M) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 6 Mar 2018 17:28:04 +0000 > From: "Cooper, Catherine M" > To: "cig-mc at geodynamics.org" > Subject: Re: [CIG-MC] AGU's new data policy > Message-ID: <277B34AD-D981-4A95-B8D6-586EF8DB3706 at wsu.edu> > Content-Type: text/plain; charset="utf-8" > > > I wonder if it wouldn’t be helpful to have a community statement as to > what we consider “data” and what we agree needs to be shared for > reproducibility (which we all agree is important)? But it seems like we > might need to do some outreach on this if there is some misunderstanding > about model output as data amongst AGU and NASA (this has come up in > proposal reviews). > > > On Mar 6, 2018, at 9:01 AM, Juliane Dannberg judannberg at gmail.com>> wrote: > > My experience with this is similar to what Thorsten describes. I also > regularly have TB-sized model output, and usually include the doi of the > version of the code I used in the paper, upload all input files/scripts > etc. I used as supplementary material, and include a sentence that "all > input files necessary to reproduce the model results are included in the > supplementary material". So far, that seemed to be an acceptable solution, > also for AGU journals. > > But I agree that there doesn't seem to be a good way to archive TB-sized > model output over long periods of time... > > Best, > Juliane > > ---------------------------------------------------------------------- > Juliane Dannberg > Postdoctoral Fellow, Colorado State University > http://www.math.colostate.edu/~dannberg/ proofpoint.com/v2/url?u=http-3A__www.math.colostate.edu_- > 257Edannberg_&d=DwMDaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb- > Je7sw&r=3iAcC0lqlf3gOx4_NidEiA&m=HfT2q7BUNv7lwQ4rNBn6WCxad64- > R40vEvd3Ehweq84&s=iVhuH7wc5RA1dEULO5hsENSQBBcmRpe1dBNQMzkZxOU&e=> > > > Am 3/6/2018 um 9:39 AM schrieb Thorsten Becker: > The way I have interpreted AGU's guidelines for geodynamic studies as AGU > editor is to not ask for archiving of model output, but to ask for general > access to all material that would be needed to recreate that output, or > some simpler version of it that is proof of concept. I.e. input data, input > files, and a DOI to version of code, for example, if a community code is > used. > > The general idea is, of course, to make things reproducible, and AGU and > Wiley are among those who realize that this can cause problems, and are > working on solutions with the community. > > One particular issue is that I have not asked for verification that > results are actually reproducible, and taken authors assurances that codes > will be shared at face value (besides when the publications were of > technical nature, and we ask reviewers to actually try to download and run > the software, for example (which usually never works)). I think that part > might change, in that publishers may ask for a code access link and somehow > archive this. > > I can also see some solutions akin to asking for a Docker set up, archived > somewhere, that will allow anyone to rerun the models. There are > interesting challenges involved, but in the end, I think moving to more > openness and reproducibility is a good thing, and the success of CIG shows > how some issues that were raised before we moved into this model resolved > themselves. Things are perfect, but we're making progress. > > My personal experience with publishing numerical stuff in highly visible > journals is that, within a week, there are people actually asking to get > all the code and all the input files to rerun our models, and we've always > shared all of our stuff, of course. I realize that this is a significant > workload (particularly for my grad students who actually put this stuff > together...) and somehow AGU and publishers need to do more to support > people with large data volumes, seismological inversions being another > example. > > > Thorsten Becker - UTIG & DGS, JSG, UT Austin proofpoint.com/v2/url?u=http-3A__www-2Dudc.ig.utexas.edu_ > external_becker_&d=DwMDaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb- > Je7sw&r=3iAcC0lqlf3gOx4_NidEiA&m=HfT2q7BUNv7lwQ4rNBn6WCxad64- > R40vEvd3Ehweq84&s=ht52HpJGdxPfwGDTFHbOvc6DI21TD42eHQ4S-Bm8Iyo&e=> > > On Tue, Mar 6, 2018 at 7:17 AM, Scott King > > wrote: > > AGU journals have a new data policy requiring that all the data from the > work must be in a publicly accessible repository. In general I think this > is a good thing. They provide several possible solutions. From the > editor letter… > > "AGU requires that data needed to understand and build upon the published > research be available in public repositories following best practices< > https://urldefense.proofpoint.com/v2/url?u=http-3A__publications.agu.org_ > author-2Dresource-2Dcenter_publication-2Dpolicies_data- > 2Dpolicy_data-2Dpolicy-2Dfaq_&d=DwMDaQ&c=C3yme8gMkxg_ > ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=3iAcC0lqlf3gOx4_NidEiA&m= > HfT2q7BUNv7lwQ4rNBn6WCxad64-R40vEvd3Ehweq84&s= > ySxEBeS3cBYIOD8hSSkU7WymnOp8M-wucwrFXLBFHss&e=>. This includes an > explicit statement in the Acknowledgments section on where users can access > or find the data for this paper. Citations to archived data should be > included in your reference list and all references, including those cited > in the supplement, should be included in the main reference list. All > listed references must be available to the general reader by the time of > acceptance.” > > They list several possible repositories, none of which seem appropriate > for 2.9 TB of CicomS results. Set aside the philosophical issue that model > results are not “data” (they don’t accept that). I have the output used > in the published figures down to a reasonable size but. I’m curious what > others are doing. Has anyone else run into this yet? (If not you will.) > I’m curious if there is a community consensus regarding a repository where > all geodynamics results would/could end up, as opposed to ending up with > them scattered across 3-4 (or more) potential repositories. Maybe that’s > not something to worry about, but since this is new and to me at least I’ve > had no time to think it through, I’m curious what others are doing. > > Thoughts? > > Cheers, > > Scott > > > > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc< > https://urldefense.proofpoint.com/v2/url?u=http- > 3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_cig- > 2Dmc&d=DwMDaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb- > Je7sw&r=3iAcC0lqlf3gOx4_NidEiA&m=HfT2q7BUNv7lwQ4rNBn6WCxad64- > R40vEvd3Ehweq84&s=XOhKoMDTham1Kxbm10gSj_HK0WwQs7oPVG5RjUctuS0&e=> > > > > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc< > https://urldefense.proofpoint.com/v2/url?u=http- > 3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_cig- > 2Dmc&d=DwMDaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb- > Je7sw&r=3iAcC0lqlf3gOx4_NidEiA&m=HfT2q7BUNv7lwQ4rNBn6WCxad64- > R40vEvd3Ehweq84&s=XOhKoMDTham1Kxbm10gSj_HK0WwQs7oPVG5RjUctuS0&e=> > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists. > geodynamics.org_cgi-2Dbin_mailman_listinfo_cig-2Dmc&d= > DwIGaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=3iAcC0lqlf3gOx4_ > NidEiA&m=HfT2q7BUNv7lwQ4rNBn6WCxad64-R40vEvd3Ehweq84&s= > XOhKoMDTham1Kxbm10gSj_HK0WwQs7oPVG5RjUctuS0&e= > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: 20180306/cc5d87de/attachment.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc > > ------------------------------ > > End of CIG-MC Digest, Vol 122, Issue 7 > ************************************** > -- ________________________________ ________________________________ ________________________________ Matthew B. Weller, Ph.D Institutional Postdoctoral Fellow Institute for Geophysics; Office 2.116A J.J. Pickle Research Campus, Bldg. 196 10100 Burnet Road (R2200) Austin, TX 78758-4445 512.471.0421 *"No matter where you go - there you are"* -Confucius and/or Buckaroo Bonzai *"Life is really very simply, but we insist on making it complicated"* -Confucius *"To argue with a person who has renounced the use of reason is like administering medicine to the dead."* -Thomas Paine -------------- next part -------------- An HTML attachment was scrubbed... URL: From lhkellogg at ucdavis.edu Tue Mar 6 14:34:06 2018 From: lhkellogg at ucdavis.edu (Louise Kellogg) Date: Tue, 6 Mar 2018 14:34:06 -0800 Subject: [CIG-MC] AGU's new data policy In-Reply-To: <277B34AD-D981-4A95-B8D6-586EF8DB3706@wsu.edu> References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> <277B34AD-D981-4A95-B8D6-586EF8DB3706@wsu.edu> Message-ID: Great minds think alike Katie! We were just discussing this idea at the CIG staff meeting this morning. As it happens, I have a meeting with AGU's Brooks Hanson on a related topic (publication of software), two weeks from now, and I'd be happy to bring this whole topic to the table. As CIG, the organization, we represent a community and I hope we can help influence this direction. Someone else, either here or on the AGU communities discussion of this issue, also raised the issue Matt hints at - barriers to access to publishing in AGU journals for scientists with fewer resources. It's important to ask what the goal of archiving data is, in order to decide what data to archive. Is it reproducibility? or replicability? They are not the same thing, as I was reminded this morning, and the distinction is important. Here is a helpful discussion of the differences, published in a neuroscience journal, but drawing on the work of geophysicist Jon Claerbout: (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778115/). The entire article is interesting, but I'll only quote the following: > > Claerbout defined “reproducing” to mean “running the same software on the > same input data and obtaining the same results” (Rougier et al., 2017), > going so far as to state that “[j]udgement of the reproducibility of > computationally oriented research no longer requires an expert—a clerk can > do it” (Claerbout and Karrenbach, 1992). As a complement, replicating a > published result is then defined to mean “writing and then running new > software based on the description of a computational model or method > provided in the original publication, and obtaining results that are > similar enough …” (Rougier et al., 2017). I will refer to these definitions > of “reproducibility” and “replicability” as Claerbout terminology; they > have also been recommended in social, behavioral and economic sciences > (Bollen et al., 2015). Replicability is the higher standard, and more useful. But it does not necessarily require bit-for-bit conservation of the output of a model. Instead, it may focus on the complete specification of the model and the methods used. That would require input files and perhaps other input information with sufficient metadata to explain what everything is, and it would require archiving of the software in an archive like CIG's, and citation including the specific version number to ensure that the methods are specified completely. Here the work that CIG has been doing on software attribution is relevant. See for example the citation tool: https://geodynamics.org/cig/abc which spells out in detail how to cite software, by version, both in a manuscript and in the references and acknowledgements sections of a paper. These practices are in line with those recommended by library, information, and data scientists. There are instances where a partial or complete preservation of the model may be essential. One example could be be benchmark models. Another example is provided by our geodynamo group, who is using leadership class computers to produce a very limited set of model runs that they intend to mine for knowledge going forward. That model output needs to be preserved as an observational dataset would. Another example: it may be a good idea to preserve additional information on model design, such as the FEM mesh when it is particularly complex. Thanks to Lorraine Hwang for reminding me of the distinction between reproducibility and replicability, for coming up with the FEM mesh preservation example, and for leading the charge on software citation. Best, Louise On Tue, Mar 6, 2018 at 9:28 AM, Cooper, Catherine M wrote: > > I wonder if it wouldn’t be helpful to have a community statement as to > what we consider “data” and what we agree needs to be shared for > reproducibility (which we all agree is important)? But it seems like we > might need to do some outreach on this if there is some misunderstanding > about model output as data amongst AGU and NASA (this has come up in > proposal reviews). > > > On Mar 6, 2018, at 9:01 AM, Juliane Dannberg wrote: > > My experience with this is similar to what Thorsten describes. I also > regularly have TB-sized model output, and usually include the doi of the > version of the code I used in the paper, upload all input files/scripts > etc. I used as supplementary material, and include a sentence that "all > input files necessary to reproduce the model results are included in the > supplementary material". So far, that seemed to be an acceptable solution, > also for AGU journals. > > But I agree that there doesn't seem to be a good way to archive TB-sized > model output over long periods of time... > > Best, > Juliane > > ---------------------------------------------------------------------- > Juliane Dannberg > Postdoctoral Fellow, Colorado State University > http://www.math.colostate.edu/~dannberg/ > > > > > Am 3/6/2018 um 9:39 AM schrieb Thorsten Becker: > > The way I have interpreted AGU's guidelines for geodynamic studies as AGU > editor is to not ask for archiving of model output, but to ask for general > access to all material that would be needed to recreate that output, or > some simpler version of it that is proof of concept. I.e. input data, input > files, and a DOI to version of code, for example, if a community code is > used. > > The general idea is, of course, to make things reproducible, and AGU and > Wiley are among those who realize that this can cause problems, and are > working on solutions with the community. > > One particular issue is that I have not asked for verification that > results are actually reproducible, and taken authors assurances that codes > will be shared at face value (besides when the publications were of > technical nature, and we ask reviewers to actually try to download and run > the software, for example (which usually never works)). I think that part > might change, in that publishers may ask for a code access link and somehow > archive this. > > I can also see some solutions akin to asking for a Docker set up, archived > somewhere, that will allow anyone to rerun the models. There are > interesting challenges involved, but in the end, I think moving to more > openness and reproducibility is a good thing, and the success of CIG shows > how some issues that were raised before we moved into this model resolved > themselves. Things are perfect, but we're making progress. > > My personal experience with publishing numerical stuff in highly visible > journals is that, within a week, there are people actually asking to get > all the code and all the input files to rerun our models, and we've always > shared all of our stuff, of course. I realize that this is a > significant workload (particularly for my grad students who actually put > this stuff together...) and somehow AGU and publishers need to do more to > support people with large data volumes, seismological inversions being > another example. > > > Thorsten Becker - UTIG & DGS, JSG, UT Austin > > > On Tue, Mar 6, 2018 at 7:17 AM, Scott King wrote: > >> >> AGU journals have a new data policy requiring that all the data from the >> work must be in a publicly accessible repository. In general I think this >> is a good thing. They provide several possible solutions. From the >> editor letter… >> >> "*AGU requires that data needed to understand and build upon the >> published research be available in public repositories following **best >> practices >> . >> This includes an explicit statement in the Acknowledgments section on where >> users can access or find the data for this paper. Citations to archived >> data should be included in your reference list and all references, >> including those cited in the supplement, should be included in the main >> reference list. All listed references must be available to the general >> reader by the time of acceptance.*” >> >> They list several possible repositories, none of which seem appropriate >> for 2.9 TB of CicomS results. Set aside the philosophical issue that model >> results are not “data” (they don’t accept that). I have the output used >> in the published figures down to a reasonable size but. I’m curious what >> others are doing. Has anyone else run into this yet? (If not you will.) >> I’m curious if there is a community consensus regarding a repository where >> all geodynamics results would/could end up, as opposed to ending up with >> them scattered across 3-4 (or more) potential repositories. Maybe that’s >> not something to worry about, but since this is new and to me at least I’ve >> had no time to think it through, I’m curious what others are doing. >> >> Thoughts? >> >> Cheers, >> >> Scott >> >> >> >> >> _______________________________________________ >> CIG-MC mailing list >> CIG-MC at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc >> >> > > > > _______________________________________________ > CIG-MC mailing listCIG-MC at geodynamics.orghttp://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc > > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists. > geodynamics.org_cgi-2Dbin_mailman_listinfo_cig-2Dmc&d= > DwIGaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=3iAcC0lqlf3gOx4_ > NidEiA&m=HfT2q7BUNv7lwQ4rNBn6WCxad64-R40vEvd3Ehweq84&s= > XOhKoMDTham1Kxbm10gSj_HK0WwQs7oPVG5RjUctuS0&e= > > > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc > -- ********************************** Louise Kellogg Professor, Department of Earth and Planetary Sciences University of California, Davis *********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljhwang at ucdavis.edu Tue Mar 6 13:30:17 2018 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Tue, 6 Mar 2018 13:30:17 -0800 Subject: [CIG-MC] AGU's new data policy In-Reply-To: <277B34AD-D981-4A95-B8D6-586EF8DB3706@wsu.edu> References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> <277B34AD-D981-4A95-B8D6-586EF8DB3706@wsu.edu> Message-ID: There may also be communities who are interested in model output for reuse as well as reproducibility. Best, -Lorraine ***************************** Lorraine Hwang, Ph.D. Associate Director, CIG 530.752.3656 > On Mar 6, 2018, at 9:28 AM, Cooper, Catherine M wrote: > > > I wonder if it wouldn’t be helpful to have a community statement as to what we consider “data” and what we agree needs to be shared for reproducibility (which we all agree is important)? But it seems like we might need to do some outreach on this if there is some misunderstanding about model output as data amongst AGU and NASA (this has come up in proposal reviews). > > >> On Mar 6, 2018, at 9:01 AM, Juliane Dannberg > wrote: >> >> My experience with this is similar to what Thorsten describes. I also regularly have TB-sized model output, and usually include the doi of the version of the code I used in the paper, upload all input files/scripts etc. I used as supplementary material, and include a sentence that "all input files necessary to reproduce the model results are included in the supplementary material". So far, that seemed to be an acceptable solution, also for AGU journals. >> But I agree that there doesn't seem to be a good way to archive TB-sized model output over long periods of time... >> >> Best, >> Juliane >> >> >> ---------------------------------------------------------------------- >> Juliane Dannberg >> Postdoctoral Fellow, Colorado State University >> http://www.math.colostate.edu/~dannberg/ >> >> >> Am 3/6/2018 um 9:39 AM schrieb Thorsten Becker: >>> The way I have interpreted AGU's guidelines for geodynamic studies as AGU editor is to not ask for archiving of model output, but to ask for general access to all material that would be needed to recreate that output, or some simpler version of it that is proof of concept. I.e. input data, input files, and a DOI to version of code, for example, if a community code is used. >>> >>> The general idea is, of course, to make things reproducible, and AGU and Wiley are among those who realize that this can cause problems, and are working on solutions with the community. >>> >>> One particular issue is that I have not asked for verification that results are actually reproducible, and taken authors assurances that codes will be shared at face value (besides when the publications were of technical nature, and we ask reviewers to actually try to download and run the software, for example (which usually never works)). I think that part might change, in that publishers may ask for a code access link and somehow archive this. >>> >>> I can also see some solutions akin to asking for a Docker set up, archived somewhere, that will allow anyone to rerun the models. There are interesting challenges involved, but in the end, I think moving to more openness and reproducibility is a good thing, and the success of CIG shows how some issues that were raised before we moved into this model resolved themselves. Things are perfect, but we're making progress. >>> >>> My personal experience with publishing numerical stuff in highly visible journals is that, within a week, there are people actually asking to get all the code and all the input files to rerun our models, and we've always shared all of our stuff, of course. I realize that this is a significant workload (particularly for my grad students who actually put this stuff together...) and somehow AGU and publishers need to do more to support people with large data volumes, seismological inversions being another example. >>> >>> >>> Thorsten Becker - UTIG & DGS, JSG, UT Austin >>> On Tue, Mar 6, 2018 at 7:17 AM, Scott King > wrote: >>> >>> AGU journals have a new data policy requiring that all the data from the work must be in a publicly accessible repository. In general I think this is a good thing. They provide several possible solutions. From the editor letter… >>> >>> "AGU requires that data needed to understand and build upon the published research be available in public repositories following best practices . This includes an explicit statement in the Acknowledgments section on where users can access or find the data for this paper. Citations to archived data should be included in your reference list and all references, including those cited in the supplement, should be included in the main reference list. All listed references must be available to the general reader by the time of acceptance.” >>> >>> They list several possible repositories, none of which seem appropriate for 2.9 TB of CicomS results. Set aside the philosophical issue that model results are not “data” (they don’t accept that). I have the output used in the published figures down to a reasonable size but. I’m curious what others are doing. Has anyone else run into this yet? (If not you will.) I’m curious if there is a community consensus regarding a repository where all geodynamics results would/could end up, as opposed to ending up with them scattered across 3-4 (or more) potential repositories. Maybe that’s not something to worry about, but since this is new and to me at least I’ve had no time to think it through, I’m curious what others are doing. >>> >>> Thoughts? >>> >>> Cheers, >>> >>> Scott >>> >>> >>> >>> >>> _______________________________________________ >>> CIG-MC mailing list >>> CIG-MC at geodynamics.org >>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc >>> >>> >>> >>> _______________________________________________ >>> CIG-MC mailing list >>> CIG-MC at geodynamics.org >>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc >> _______________________________________________ >> CIG-MC mailing list >> CIG-MC at geodynamics.org >> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_cig-2Dmc&d=DwIGaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=3iAcC0lqlf3gOx4_NidEiA&m=HfT2q7BUNv7lwQ4rNBn6WCxad64-R40vEvd3Ehweq84&s=XOhKoMDTham1Kxbm10gSj_HK0WwQs7oPVG5RjUctuS0&e= > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc -------------- next part -------------- An HTML attachment was scrubbed... URL: From sking07 at vt.edu Tue Mar 6 17:48:57 2018 From: sking07 at vt.edu (Scott King) Date: Tue, 6 Mar 2018 20:48:57 -0500 Subject: [CIG-MC] AGU's new data policy In-Reply-To: References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> <277B34AD-D981-4A95-B8D6-586EF8DB3706@wsu.edu> Message-ID: <5AF3E3A9-E515-43E6-9CB5-0BA50BCCD995@vt.edu> True. Others might want our data. That is worth thinking about. Maybe I’m a frustrated economist at heart. Mr google tells me that the cost of enterprise storage is between $2,500 and $10,000 a year. That money is coming out of the total funding available for science somehow. My 3 TB for this one paper would cost the scientific community something like 0.25 to 1.0 GRA per year. Food for thought. Sent from my iPhone > On Mar 6, 2018, at 4:30 PM, Lorraine Hwang wrote: > > There may also be communities who are interested in model output for reuse as well as reproducibility. > > Best, > -Lorraine > > ***************************** > Lorraine Hwang, Ph.D. > Associate Director, CIG > 530.752.3656 > > > >> On Mar 6, 2018, at 9:28 AM, Cooper, Catherine M wrote: >> >> >> I wonder if it wouldn’t be helpful to have a community statement as to what we consider “data” and what we agree needs to be shared for reproducibility (which we all agree is important)? But it seems like we might need to do some outreach on this if there is some misunderstanding about model output as data amongst AGU and NASA (this has come up in proposal reviews). >> >> >>> On Mar 6, 2018, at 9:01 AM, Juliane Dannberg wrote: >>> >>> My experience with this is similar to what Thorsten describes. I also regularly have TB-sized model output, and usually include the doi of the version of the code I used in the paper, upload all input files/scripts etc. I used as supplementary material, and include a sentence that "all input files necessary to reproduce the model results are included in the supplementary material". So far, that seemed to be an acceptable solution, also for AGU journals. >>> But I agree that there doesn't seem to be a good way to archive TB-sized model output over long periods of time... >>> >>> Best, >>> Juliane >>> >>> >>> ---------------------------------------------------------------------- >>> Juliane Dannberg >>> Postdoctoral Fellow, Colorado State University >>> http://www.math.colostate.edu/~dannberg/ >>> >>> >>>> Am 3/6/2018 um 9:39 AM schrieb Thorsten Becker: >>>> The way I have interpreted AGU's guidelines for geodynamic studies as AGU editor is to not ask for archiving of model output, but to ask for general access to all material that would be needed to recreate that output, or some simpler version of it that is proof of concept. I.e. input data, input files, and a DOI to version of code, for example, if a community code is used. >>>> >>>> The general idea is, of course, to make things reproducible, and AGU and Wiley are among those who realize that this can cause problems, and are working on solutions with the community. >>>> >>>> One particular issue is that I have not asked for verification that results are actually reproducible, and taken authors assurances that codes will be shared at face value (besides when the publications were of technical nature, and we ask reviewers to actually try to download and run the software, for example (which usually never works)). I think that part might change, in that publishers may ask for a code access link and somehow archive this. >>>> >>>> I can also see some solutions akin to asking for a Docker set up, archived somewhere, that will allow anyone to rerun the models. There are interesting challenges involved, but in the end, I think moving to more openness and reproducibility is a good thing, and the success of CIG shows how some issues that were raised before we moved into this model resolved themselves. Things are perfect, but we're making progress. >>>> >>>> My personal experience with publishing numerical stuff in highly visible journals is that, within a week, there are people actually asking to get all the code and all the input files to rerun our models, and we've always shared all of our stuff, of course. I realize that this is a significant workload (particularly for my grad students who actually put this stuff together...) and somehow AGU and publishers need to do more to support people with large data volumes, seismological inversions being another example. >>>> >>>> >>>> Thorsten Becker - UTIG & DGS, JSG, UT Austin >>>> >>>>> On Tue, Mar 6, 2018 at 7:17 AM, Scott King wrote: >>>>> >>>>> AGU journals have a new data policy requiring that all the data from the work must be in a publicly accessible repository. In general I think this is a good thing. They provide several possible solutions. From the editor letter… >>>>> >>>>> "AGU requires that data needed to understand and build upon the published research be available in public repositories following best practices. This includes an explicit statement in the Acknowledgments section on where users can access or find the data for this paper. Citations to archived data should be included in your reference list and all references, including those cited in the supplement, should be included in the main reference list. All listed references must be available to the general reader by the time of acceptance.” >>>>> >>>>> They list several possible repositories, none of which seem appropriate for 2.9 TB of CicomS results. Set aside the philosophical issue that model results are not “data” (they don’t accept that). I have the output used in the published figures down to a reasonable size but. I’m curious what others are doing. Has anyone else run into this yet? (If not you will.) I’m curious if there is a community consensus regarding a repository where all geodynamics results would/could end up, as opposed to ending up with them scattered across 3-4 (or more) potential repositories. Maybe that’s not something to worry about, but since this is new and to me at least I’ve had no time to think it through, I’m curious what others are doing. >>>>> >>>>> Thoughts? >>>>> >>>>> Cheers, >>>>> >>>>> Scott >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> CIG-MC mailing list >>>>> CIG-MC at geodynamics.org >>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc >>>> >>>> >>>> >>>> _______________________________________________ >>>> CIG-MC mailing list >>>> CIG-MC at geodynamics.org >>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc >>> >>> _______________________________________________ >>> CIG-MC mailing list >>> CIG-MC at geodynamics.org >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_cig-2Dmc&d=DwIGaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=3iAcC0lqlf3gOx4_NidEiA&m=HfT2q7BUNv7lwQ4rNBn6WCxad64-R40vEvd3Ehweq84&s=XOhKoMDTham1Kxbm10gSj_HK0WwQs7oPVG5RjUctuS0&e= >> >> _______________________________________________ >> CIG-MC mailing list >> CIG-MC at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc -------------- next part -------------- An HTML attachment was scrubbed... URL: From lhkellogg at ucdavis.edu Tue Mar 6 18:37:38 2018 From: lhkellogg at ucdavis.edu (Louise Kellogg) Date: Tue, 6 Mar 2018 18:37:38 -0800 Subject: [CIG-MC] AGU's new data policy In-Reply-To: <5AF3E3A9-E515-43E6-9CB5-0BA50BCCD995@vt.edu> References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> <277B34AD-D981-4A95-B8D6-586EF8DB3706@wsu.edu> <5AF3E3A9-E515-43E6-9CB5-0BA50BCCD995@vt.edu> Message-ID: <3685A214-3AFC-438C-B556-C8C7DE1FFC0A@ucdavis.edu> Hi Scott, I have similar concerns about the cost-benefit. Among other things, the cost of *reproducing* a calculation presumably generally drops over time, making me question the value of storing the model output vs. regenerating it. The geodynamo calculations are an exception because they were so expensive to generate. This is different for the seismic and geodetic observations stored by IRIS and UNAVCO, which are not reproducible since they are observations of the natural system. I also have a concern about discoverability. If you store your model outputs on a system provided by VT and I store mine on a UC system, would anyone really be able to find them? We as a community have not agreed on metadata or other relevant information for finding data. So I fear we may end up with a pricy “write once, read never” system. Best, Louise > On Mar 6, 2018, at 5:48 PM, Scott King wrote: > > True. Others might want our data. That is worth thinking about. > > Maybe I’m a frustrated economist at heart. Mr google tells me that the cost of enterprise storage is between $2,500 and $10,000 a year. That money is coming out of the total funding available for science somehow. My 3 TB for this one paper would cost the scientific community something like 0.25 to 1.0 GRA per year. Food for thought. > > Sent from my iPhone > > On Mar 6, 2018, at 4:30 PM, Lorraine Hwang > wrote: > >> There may also be communities who are interested in model output for reuse as well as reproducibility. >> >> Best, >> -Lorraine >> >> ***************************** >> Lorraine Hwang, Ph.D. >> Associate Director, CIG >> 530.752.3656 >> >> >> >>> On Mar 6, 2018, at 9:28 AM, Cooper, Catherine M > wrote: >>> >>> >>> I wonder if it wouldn’t be helpful to have a community statement as to what we consider “data” and what we agree needs to be shared for reproducibility (which we all agree is important)? But it seems like we might need to do some outreach on this if there is some misunderstanding about model output as data amongst AGU and NASA (this has come up in proposal reviews). >>> >>> >>>> On Mar 6, 2018, at 9:01 AM, Juliane Dannberg > wrote: >>>> >>>> My experience with this is similar to what Thorsten describes. I also regularly have TB-sized model output, and usually include the doi of the version of the code I used in the paper, upload all input files/scripts etc. I used as supplementary material, and include a sentence that "all input files necessary to reproduce the model results are included in the supplementary material". So far, that seemed to be an acceptable solution, also for AGU journals. >>>> But I agree that there doesn't seem to be a good way to archive TB-sized model output over long periods of time... >>>> >>>> Best, >>>> Juliane >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> Juliane Dannberg >>>> Postdoctoral Fellow, Colorado State University >>>> http://www.math.colostate.edu/~dannberg/ >>>> >>>> >>>> Am 3/6/2018 um 9:39 AM schrieb Thorsten Becker: >>>>> The way I have interpreted AGU's guidelines for geodynamic studies as AGU editor is to not ask for archiving of model output, but to ask for general access to all material that would be needed to recreate that output, or some simpler version of it that is proof of concept. I.e. input data, input files, and a DOI to version of code, for example, if a community code is used. >>>>> >>>>> The general idea is, of course, to make things reproducible, and AGU and Wiley are among those who realize that this can cause problems, and are working on solutions with the community. >>>>> >>>>> One particular issue is that I have not asked for verification that results are actually reproducible, and taken authors assurances that codes will be shared at face value (besides when the publications were of technical nature, and we ask reviewers to actually try to download and run the software, for example (which usually never works)). I think that part might change, in that publishers may ask for a code access link and somehow archive this. >>>>> >>>>> I can also see some solutions akin to asking for a Docker set up, archived somewhere, that will allow anyone to rerun the models. There are interesting challenges involved, but in the end, I think moving to more openness and reproducibility is a good thing, and the success of CIG shows how some issues that were raised before we moved into this model resolved themselves. Things are perfect, but we're making progress. >>>>> >>>>> My personal experience with publishing numerical stuff in highly visible journals is that, within a week, there are people actually asking to get all the code and all the input files to rerun our models, and we've always shared all of our stuff, of course. I realize that this is a significant workload (particularly for my grad students who actually put this stuff together...) and somehow AGU and publishers need to do more to support people with large data volumes, seismological inversions being another example. >>>>> >>>>> >>>>> Thorsten Becker - UTIG & DGS, JSG, UT Austin >>>>> On Tue, Mar 6, 2018 at 7:17 AM, Scott King > wrote: >>>>> >>>>> AGU journals have a new data policy requiring that all the data from the work must be in a publicly accessible repository. In general I think this is a good thing. They provide several possible solutions. From the editor letter… >>>>> >>>>> "AGU requires that data needed to understand and build upon the published research be available in public repositories following best practices . This includes an explicit statement in the Acknowledgments section on where users can access or find the data for this paper. Citations to archived data should be included in your reference list and all references, including those cited in the supplement, should be included in the main reference list. All listed references must be available to the general reader by the time of acceptance.” >>>>> >>>>> They list several possible repositories, none of which seem appropriate for 2.9 TB of CicomS results. Set aside the philosophical issue that model results are not “data” (they don’t accept that). I have the output used in the published figures down to a reasonable size but. I’m curious what others are doing. Has anyone else run into this yet? (If not you will.) I’m curious if there is a community consensus regarding a repository where all geodynamics results would/could end up, as opposed to ending up with them scattered across 3-4 (or more) potential repositories. Maybe that’s not something to worry about, but since this is new and to me at least I’ve had no time to think it through, I’m curious what others are doing. >>>>> >>>>> Thoughts? >>>>> >>>>> Cheers, >>>>> >>>>> Scott >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> CIG-MC mailing list >>>>> CIG-MC at geodynamics.org >>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> CIG-MC mailing list >>>>> CIG-MC at geodynamics.org >>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc >>>> _______________________________________________ >>>> CIG-MC mailing list >>>> CIG-MC at geodynamics.org >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_cig-2Dmc&d=DwIGaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=3iAcC0lqlf3gOx4_NidEiA&m=HfT2q7BUNv7lwQ4rNBn6WCxad64-R40vEvd3Ehweq84&s=XOhKoMDTham1Kxbm10gSj_HK0WwQs7oPVG5RjUctuS0&e= >>> _______________________________________________ >>> CIG-MC mailing list >>> CIG-MC at geodynamics.org >>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc >> _______________________________________________ >> CIG-MC mailing list >> CIG-MC at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdk at vt.edu Wed Mar 7 16:17:02 2018 From: sdk at vt.edu (Scott King) Date: Wed, 7 Mar 2018 19:17:02 -0500 Subject: [CIG-MC] AGU's new data policy In-Reply-To: <3685A214-3AFC-438C-B556-C8C7DE1FFC0A@ucdavis.edu> References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> <277B34AD-D981-4A95-B8D6-586EF8DB3706@wsu.edu> <5AF3E3A9-E515-43E6-9CB5-0BA50BCCD995@vt.edu> <3685A214-3AFC-438C-B556-C8C7DE1FFC0A@ucdavis.edu> Message-ID: <08A7E42B-D8F5-4CEB-94D3-8A0855E07A59@vt.edu> Well said! > On Mar 6, 2018, at 9:37 PM, Louise Kellogg wrote: > > I have similar concerns about the cost-benefit. Among other things, the cost of *reproducing* a calculation presumably generally drops over time, making me question the value of storing the model output vs. regenerating it. The geodynamo calculations are an exception because they were so expensive to generate. > > This is different for the seismic and geodetic observations stored by IRIS and UNAVCO, which are not reproducible since they are observations of the natural system. > > I also have a concern about discoverability. If you store your model outputs on a system provided by VT and I store mine on a UC system, would anyone really be able to find them? We as a community have not agreed on metadata or other relevant information for finding data. So I fear we may end up with a pricy “write once, read never” system. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljhwang at ucdavis.edu Fri Mar 9 10:27:04 2018 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Fri, 9 Mar 2018 10:27:04 -0800 Subject: [CIG-MC] CIG Event Deadlines: PyLith & ASPECT Hacks, CGU Abstracts Message-ID: <9260D67F-2D29-4BF1-A288-6AF76F684EB8@ucdavis.edu> Hi Before you head off for Spring Break, don’t forget to make your summer plans to attend CIG events. Deadlines to apply are rapidly approaching. 2018 CGU CIG Joint Meeting - Mantle Convection and Lithosphere Workshop. June 10-14, Niagara Falls, Ontario. Abstract deadline: March 16. Travel Support deadline March 31. ASPECT Hackathon . June 19-30, Big Bear Lake, California. Registration closes March 31 PyLith Hackathon . June 18-24, Big Bear lake, California.Registration closes March 31 We hope to see you at these events! Best, -Lorraine ***************************** Lorraine Hwang, Ph.D. Associate Director, CIG 530.752.3656 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mibillen at ucdavis.edu Tue Mar 13 01:40:55 2018 From: mibillen at ucdavis.edu (Magali Billen) Date: Tue, 13 Mar 2018 09:40:55 +0100 Subject: [CIG-MC] AGU's new data policy In-Reply-To: <08A7E42B-D8F5-4CEB-94D3-8A0855E07A59@vt.edu> References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> <277B34AD-D981-4A95-B8D6-586EF8DB3706@wsu.edu> <5AF3E3A9-E515-43E6-9CB5-0BA50BCCD995@vt.edu> <3685A214-3AFC-438C-B556-C8C7DE1FFC0A@ucdavis.edu> <08A7E42B-D8F5-4CEB-94D3-8A0855E07A59@vt.edu> Message-ID: One other thought about the AGU’s new data policy. What are people’s thoughts about using movies of simulation output as a way of archiving the model results? These have to put together well to document the model results, but together with the ability to rerun a model, they are a much smaller way to archive results. I also find that in reviewing papers that have time-dependent models, its nice to see movies that document the full dynamics beyond what can be shown in snap-shots. Often what we put in the paper depends on what we are focused on in that particular manuscript, but there is often a lot more that could later be “mined” from model results. Making the movies allows others to see the data mining potential of the model results, for questions that we might not have consider ourselves. This of course is more difficult for 3D simulations, but I still think it could be a good way of making the model results more transparent and useful. Thoughts - should movies be part of a CIG recommendation for how to archive results for manuscripts? Magali > On Mar 8, 2018, at 1:17 AM, Scott King wrote: > > > Well said! > >> On Mar 6, 2018, at 9:37 PM, Louise Kellogg > wrote: >> >> I have similar concerns about the cost-benefit. Among other things, the cost of *reproducing* a calculation presumably generally drops over time, making me question the value of storing the model output vs. regenerating it. The geodynamo calculations are an exception because they were so expensive to generate. >> >> This is different for the seismic and geodetic observations stored by IRIS and UNAVCO, which are not reproducible since they are observations of the natural system. >> >> I also have a concern about discoverability. If you store your model outputs on a system provided by VT and I store mine on a UC system, would anyone really be able to find them? We as a community have not agreed on metadata or other relevant information for finding data. So I fear we may end up with a pricy “write once, read never” system. > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc ____________________________________________________________ Professor of Geophysics Earth & Planetary Sciences Dept., UC Davis Davis, CA 95616 2129 Earth & Physical Sciences Bldg. Office Phone: (530) 752-4169 http://magalibillen.faculty.ucdavis.edu Currently on Sabbatical at Munich University (LMU) Department of Geophysics (PST + 9 hr) Avoid implicit bias - check before you submit: http://www.tomforth.co.uk/genderbias/ ___________________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Thomas.Ruedas at dlr.de Tue Mar 13 03:01:28 2018 From: Thomas.Ruedas at dlr.de (Thomas Ruedas) Date: Tue, 13 Mar 2018 11:01:28 +0100 Subject: [CIG-MC] AGU's new data policy In-Reply-To: References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> <277B34AD-D981-4A95-B8D6-586EF8DB3706@wsu.edu> <5AF3E3A9-E515-43E6-9CB5-0BA50BCCD995@vt.edu> <3685A214-3AFC-438C-B556-C8C7DE1FFC0A@ucdavis.edu> <08A7E42B-D8F5-4CEB-94D3-8A0855E07A59@vt.edu> Message-ID: I agree that movies are often useful for providing insights into results that may not have been included in a paper, but they cannot be more than a convenient supplement for a data archive, because they do not provide the quantitative information in a format that can be reused by others. Providing the actual datasets, by contrast, would allow others to generate movies if they want. A more practical solution for producing a "small" archive is probably the use of lossy compression formats. I recall a paper in G3 by Afonso et al. (2015) (http://onlinelibrary.wiley.com/doi/10.1002/2015GC006031/abstract) in which a method was presented that allows the efficient compression of multidimensional datasets. Although the paper had phase diagrams in mind, this or a similar method could probably be used for storing modeling results without any substantial modifications at a lower cost than the storage of the raw, uncompressed data. Such an archive would not store the original raw data, but it would provide a dataset that should allow the reproduction and, more importantly, the replication of the published results. The advantage of replicability over reproducibility was brought up by Louise Kellogg earlier in this thread, and I concur with her that this is what AGU should aim for. Maybe it would be good if the community could settle on a data compression standard and provide tools for it. Best, Thomas Am 13.03.18 um 09:40 schrieb Magali Billen: > What are people’s thoughts about using movies of simulation output as a > way of archiving the model results? > > These have to put together well to document the model results, but > together with the ability to rerun a model, they are a much smaller way > to archive results.  I also find that in reviewing papers that have > time-dependent models, its nice to see movies that document the full > dynamics  beyond what can be shown > in snap-shots. Often what we put in the paper depends on what we are > focused on in that particular manuscript, but there is often a lot more > that could later be “mined” from model results. Making the > movies allows others to see the data mining potential of the model > results, for questions that we might > not have consider ourselves. This of course is more difficult for 3D > simulations, but I still think it could > be a good way of making the model results more transparent and useful. > > Thoughts - should movies be part of a CIG recommendation for how to > archive results for manuscripts? -- orcid.org/0000-0002-7739-1412 From sdk at vt.edu Tue Mar 13 05:53:51 2018 From: sdk at vt.edu (Scott King) Date: Tue, 13 Mar 2018 08:53:51 -0400 Subject: [CIG-MC] AGU's new data policy In-Reply-To: References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> <277B34AD-D981-4A95-B8D6-586EF8DB3706@wsu.edu> <5AF3E3A9-E515-43E6-9CB5-0BA50BCCD995@vt.edu> <3685A214-3AFC-438C-B556-C8C7DE1FFC0A@ucdavis.edu> <08A7E42B-D8F5-4CEB-94D3-8A0855E07A59@vt.edu> Message-ID: <0D163403-BA82-4848-BE27-1B952969A0EC@vt.edu> Hi also agree that movies can be useful, although in some cases not so interesting as one might think (strongly internally heated models can be a "nothing burger” in isotherms but you can find large-scale structure that develops looking at the geoid or dynamic topography. I’m unfamiliar with the Afonso et al. paper so I will need to look at it. Sounds interesting, thanks for pointing it out. My concern (without having read it) is that sometimes in time-dependent fluid simulations, to be reproducible you need the smallest bits because that is where instabilities grow from (think chaos). In that regard, I’m not even sure we have a good definition of what “reproducible” really means. Are we sure that the same code on a vastly different compiler with different versions of the libraries will produce the same result? Circa 10 years ago this was not clear with some NWS codes. They were certified with specific compiler versions. The computer science community is wrestling with some of these issues in regard to large simulations (i.e. what Louise calls leadership class) because there are groups that are pursuing the idea that you want an algorithm that can continue on “successfully" even if/when one node fails. Understand that this new policy is broader than AGU. The policy is called FAIR and stands for Finable, Accessible, Interoperable, and Reusable. I think the ideas are excellent and worthy and we as a community should get behind them and in many cases, this is a good idea. There is an article and links to more information here so people can actually see what the policy (which seems to be evolving) really is... https://eos.org/agu-news/enabling-fair-data-across-the-earth-and-space-sciences > On Mar 13, 2018, at 6:01 AM, Thomas Ruedas wrote: > > I agree that movies are often useful for providing insights into results that may not have been included in a paper, but they cannot be more than a convenient supplement for a data archive, because they do not provide the quantitative information in a format that can be reused by others. Providing the actual datasets, by contrast, would allow others to generate movies if they want. > A more practical solution for producing a "small" archive is probably the use of lossy compression formats. I recall a paper in G3 by Afonso et al. (2015) (http://onlinelibrary.wiley.com/doi/10.1002/2015GC006031/abstract) in which a method was presented that allows the efficient compression of multidimensional datasets. Although the paper had phase diagrams in mind, this or a similar method could probably be used for storing modeling results without any substantial modifications at a lower cost than the storage of the raw, uncompressed data. Such an archive would not store the original raw data, but it would provide a dataset that should allow the reproduction and, more importantly, the replication of the published results. The advantage of replicability over reproducibility was brought up by Louise Kellogg earlier in this thread, and I concur with her that this is what AGU should aim for. Maybe it would be good if the community could settle on a data compression standard and provide tools for it. > > Best, > Thomas > > Am 13.03.18 um 09:40 schrieb Magali Billen: >> What are people’s thoughts about using movies of simulation output as a way of archiving the model results? >> These have to put together well to document the model results, but together with the ability to rerun a model, they are a much smaller way to archive results. I also find that in reviewing papers that have time-dependent models, its nice to see movies that document the full dynamics beyond what can be shown >> in snap-shots. Often what we put in the paper depends on what we are focused on in that particular manuscript, but there is often a lot more that could later be “mined” from model results. Making the >> movies allows others to see the data mining potential of the model results, for questions that we might >> not have consider ourselves. This of course is more difficult for 3D simulations, but I still think it could >> be a good way of making the model results more transparent and useful. >> Thoughts - should movies be part of a CIG recommendation for how to archive results for manuscripts? > > > -- > orcid.org/0000-0002-7739-1412 > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc From ljhwang at ucdavis.edu Tue Mar 13 15:28:58 2018 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Tue, 13 Mar 2018 15:28:58 -0700 Subject: [CIG-MC] AGU's new data policy In-Reply-To: <0D163403-BA82-4848-BE27-1B952969A0EC@vt.edu> References: <975B089E-2E3A-439E-BA70-B5182109D221@vt.edu> <8bdf1efd-db7b-cba1-aca9-4c3e577af0b4@gmail.com> <277B34AD-D981-4A95-B8D6-586EF8DB3706@wsu.edu> <5AF3E3A9-E515-43E6-9CB5-0BA50BCCD995@vt.edu> <3685A214-3AFC-438C-B556-C8C7DE1FFC0A@ucdavis.edu> <08A7E42B-D8F5-4CEB-94D3-8A0855E07A59@vt.edu> <0D163403-BA82-4848-BE27-1B952969A0EC@vt.edu> Message-ID: At the risk of heresy and seeing a future in which we are overtaken by our data (too many sci fi shows), are there questions we should ask ourselves when publishing about intent - reuse vs. reproducibility vs. replicability. These all have different standards associated with it. Do we make the blanket statement that is seemingly the directive coming from publishers that all “data” must be archived? Is this reasonable and necessary? Maybe a carrot is better than a stick. Can we “certify” papers meet FAIR standards and reward those who want to meet those standards with a “badge” (these were trendy a few years back :) )? Another form of a carrot would be a DOI. Researchers should understand how by meeting these standards they will receive credit for the reuse of their data. Without viable solutions and only a directive, I can see where AGU policy is prohibitive for scientists without access to institutional repositories and funds to pay for a 3rd party solution. Best, -Lorraine ***************************** Lorraine Hwang, Ph.D. Associate Director, CIG 530.752.3656 > On Mar 13, 2018, at 5:53 AM, Scott King wrote: > > > Hi also agree that movies can be useful, although in some cases not so interesting as one might think (strongly internally heated models can be a "nothing burger” in isotherms but you can find large-scale structure that develops looking at the geoid or dynamic topography. I’m unfamiliar with the Afonso et al. paper so I will need to look at it. Sounds interesting, thanks for pointing it out. My concern (without having read it) is that sometimes in time-dependent fluid simulations, to be reproducible you need the smallest bits because that is where instabilities grow from (think chaos). In that regard, I’m not even sure we have a good definition of what “reproducible” really means. Are we sure that the same code on a vastly different compiler with different versions of the libraries will produce the same result? Circa 10 years ago this was not clear with some NWS codes. They were certified with specific compiler versions. The computer science community is wrestling with some of these issues in regard to large simulations (i.e. what Louise calls leadership class) because there are groups that are pursuing the idea that you want an algorithm that can continue on “successfully" even if/when one node fails. Understand that this new policy is broader than AGU. The policy is called FAIR and stands for Finable, Accessible, Interoperable, and Reusable. I think the ideas are excellent and worthy and we as a community should get behind them and in many cases, this is a good idea. There is an article and links to more information here so people can actually see what the policy (which seems to be evolving) really is... > > https://eos.org/agu-news/enabling-fair-data-across-the-earth-and-space-sciences > > >> On Mar 13, 2018, at 6:01 AM, Thomas Ruedas wrote: >> >> I agree that movies are often useful for providing insights into results that may not have been included in a paper, but they cannot be more than a convenient supplement for a data archive, because they do not provide the quantitative information in a format that can be reused by others. Providing the actual datasets, by contrast, would allow others to generate movies if they want. >> A more practical solution for producing a "small" archive is probably the use of lossy compression formats. I recall a paper in G3 by Afonso et al. (2015) (http://onlinelibrary.wiley.com/doi/10.1002/2015GC006031/abstract) in which a method was presented that allows the efficient compression of multidimensional datasets. Although the paper had phase diagrams in mind, this or a similar method could probably be used for storing modeling results without any substantial modifications at a lower cost than the storage of the raw, uncompressed data. Such an archive would not store the original raw data, but it would provide a dataset that should allow the reproduction and, more importantly, the replication of the published results. The advantage of replicability over reproducibility was brought up by Louise Kellogg earlier in this thread, and I concur with her that this is what AGU should aim for. Maybe it would be good if the community could settle on a data compression standard and provide tools for it. >> >> Best, >> Thomas >> >> Am 13.03.18 um 09:40 schrieb Magali Billen: >>> What are people’s thoughts about using movies of simulation output as a way of archiving the model results? >>> These have to put together well to document the model results, but together with the ability to rerun a model, they are a much smaller way to archive results. I also find that in reviewing papers that have time-dependent models, its nice to see movies that document the full dynamics beyond what can be shown >>> in snap-shots. Often what we put in the paper depends on what we are focused on in that particular manuscript, but there is often a lot more that could later be “mined” from model results. Making the >>> movies allows others to see the data mining potential of the model results, for questions that we might >>> not have consider ourselves. This of course is more difficult for 3D simulations, but I still think it could >>> be a good way of making the model results more transparent and useful. >>> Thoughts - should movies be part of a CIG recommendation for how to archive results for manuscripts? >> >> >> -- >> orcid.org/0000-0002-7739-1412 >> _______________________________________________ >> CIG-MC mailing list >> CIG-MC at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc -------------- next part -------------- An HTML attachment was scrubbed... URL: From rhcui at asch.whigg.ac.cn Tue Mar 13 18:47:09 2018 From: rhcui at asch.whigg.ac.cn (=?UTF-8?B?5bSU6I2j6Iqx?=) Date: Wed, 14 Mar 2018 09:47:09 +0800 (GMT+08:00) Subject: [CIG-MC] an error about using CitcomS Message-ID: <7ebaaf7.ca9a.16222308a89.Coremail.rhcui@asch.whigg.ac.cn> Hi all, I am Ronghua Cui, i am now using CitcomS to make instantaneous mantle flow with ggrd mode. When i use the viscosity ratio of upper_mantle/lower_mantle as 1/60, it works good. But if i change the ratio to 1/80, it comes out the error like this: gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/0/vtk_v.70.0.gz' gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/0/visc.29.0.gz' gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/vtk_ecor.68.gz' gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/vtk_ecor.66.gz' gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/vtk_ecor.38.gz' gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/vtk_ecor.2.gz' gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/vtk_ecor.42.gz' ... Does anybody know what's the reason of this problem and how to solve it? Thanks. With regards, Ronghua -------------- next part -------------- An HTML attachment was scrubbed... URL: From tan2tan2 at gmail.com Tue Mar 13 19:17:11 2018 From: tan2tan2 at gmail.com (tan2) Date: Wed, 14 Mar 2018 10:17:11 +0800 Subject: [CIG-MC] an error about using CitcomS In-Reply-To: <7ebaaf7.ca9a.16222308a89.Coremail.rhcui@asch.whigg.ac.cn> References: <7ebaaf7.ca9a.16222308a89.Coremail.rhcui@asch.whigg.ac.cn> Message-ID: Hi Ronghua, Changing the viscosity would not affect how CitcomS reads the ggrd files. Your error message looks like a local file system issue to me. It is likely that the computing node that CitcomS was running on cannot access the file system mounted on /public1. You will need to report this problem to your sysadmin. Cheers, On Wed, Mar 14, 2018 at 9:47 AM, 崔荣花 wrote: > Hi all, > > I am Ronghua Cui, i am now using CitcomS to make instantaneous mantle flow > with ggrd mode. When i use the viscosity ratio of upper_mantle/lower_mantle > as 1/60, it works good. But if i change the ratio to 1/80, it comes out the > error like this: > > gzdir: cannot open file '/public1/cuirh/gypsum/0313/ > output_gypsum_layer4-0313-1/0/vtk_v.70.0.gz' > gzdir: cannot open file '/public1/cuirh/gypsum/0313/ > output_gypsum_layer4-0313-1/0/visc.29.0.gz' > gzdir: cannot open file '/public1/cuirh/gypsum/0313/ > output_gypsum_layer4-0313-1/vtk_ecor.68.gz' > gzdir: cannot open file '/public1/cuirh/gypsum/0313/ > output_gypsum_layer4-0313-1/vtk_ecor.66.gz' > gzdir: cannot open file '/public1/cuirh/gypsum/0313/ > output_gypsum_layer4-0313-1/vtk_ecor.38.gz' > gzdir: cannot open file '/public1/cuirh/gypsum/0313/ > output_gypsum_layer4-0313-1/vtk_ecor.2.gz' > gzdir: cannot open file '/public1/cuirh/gypsum/0313/ > output_gypsum_layer4-0313-1/vtk_ecor.42.gz' > > ... > > Does anybody know what's the reason of this problem and how to solve it? > > Thanks. > > > With regards, > > Ronghua > > > > > _______________________________________________ > CIG-MC mailing list > CIG-MC at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rhcui at asch.whigg.ac.cn Tue Mar 13 23:07:54 2018 From: rhcui at asch.whigg.ac.cn (=?UTF-8?B?5bSU6I2j6Iqx?=) Date: Wed, 14 Mar 2018 14:07:54 +0800 (GMT+08:00) Subject: [CIG-MC] an error about using CitcomS In-Reply-To: References: <7ebaaf7.ca9a.16222308a89.Coremail.rhcui@asch.whigg.ac.cn> Message-ID: <15c88238.dc3f.162231f449f.Coremail.rhcui@asch.whigg.ac.cn> Thanks. I have know the reason. it's about the storage space. o(*￣︶￣*)o Cheers, -----原始邮件----- 发件人:tan2 发送时间:2018-03-14 10:17:11 (星期三) 收件人: cig-mc at geodynamics.org 抄送: 主题: Re: [CIG-MC] an error about using CitcomS Hi Ronghua, Changing the viscosity would not affect how CitcomS reads the ggrd files. Your error message looks like a local file system issue to me. It is likely that the computing node that CitcomS was running on cannot access the file system mounted on /public1. You will need to report this problem to your sysadmin. Cheers, On Wed, Mar 14, 2018 at 9:47 AM, 崔荣花 wrote: Hi all, I am Ronghua Cui, i am now using CitcomS to make instantaneous mantle flow with ggrd mode. When i use the viscosity ratio of upper_mantle/lower_mantle as 1/60, it works good. But if i change the ratio to 1/80, it comes out the error like this: gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/0/vtk_v.70.0.gz' gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/0/visc.29.0.gz' gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/vtk_ecor.68.gz' gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/vtk_ecor.66.gz' gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/vtk_ecor.38.gz' gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/vtk_ecor.2.gz' gzdir: cannot open file '/public1/cuirh/gypsum/0313/output_gypsum_layer4-0313-1/vtk_ecor.42.gz' ... Does anybody know what's the reason of this problem and how to solve it? Thanks. With regards, Ronghua _______________________________________________ CIG-MC mailing list CIG-MC at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljhwang at ucdavis.edu Thu Mar 15 11:10:23 2018 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Thu, 15 Mar 2018 11:10:23 -0700 Subject: [CIG-MC] CGU-CIG Abstracts Deadline - 1 1/2 days remaining Message-ID: ****** DEADLINE March 16, 2018 at 11:59 pm EASTERN TIME **** Don’t forget - tomorrow midnight ET is your deadline to submit your abstracts for the joint CIG CGU meeting in Niagara Falls Canada June 10-14. Submit Abstracts: https://meeting2018.cgu-ugc.ca/program/ Join CGU as an Associate Member for the best rates and select CGU as your affiliation when submitting an abstract: http://cgu-ugc.ca/aboutcgu/membership/join-cgu/ Travel support is available through CIG. Deadline for full consideration is March 31: https://geodynamics.org/cig/events/calendar/2018-cgu-cig/?eID=1338 Best, -Lorraine ***************************** Lorraine Hwang, Ph.D. Associate Director, CIG 530.752.3656 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljhwang at ucdavis.edu Tue Mar 27 09:29:36 2018 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Tue, 27 Mar 2018 09:29:36 -0700 Subject: [CIG-MC] 2018 CGU CIG Joint Meeting: Mantle Convection and Lithosphere Workshop. June 10-14, Niagara Falls, Ontario. Message-ID: <35C8E3F5-E4C1-4D5E-8B62-8D7D8265FB81@ucdavis.edu> Registration for the 2018 Joint Meeting is now available online and can be accessed here: https://meeting2018.cgu-ugc.ca/registration/ Note that "early bird" fees apply through April 27. We encourage you to book your housing via the links on the meeting website (https://meeting2018.cgu-ugc.ca/accommodation/ ) early so as not to be disappointed about later availability. Our discounted hotel options are open to attendees through May 10. Travel information regarding flight options and transport from airports to the conference will be posted on the meeting website shortly. We look forward to seeing you in Niagara Falls in June. Sincerely, The 2018 Joint Meeting Local Organizing and Scientific Programming Committees -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljhwang at ucdavis.edu Tue Mar 27 09:26:42 2018 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Tue, 27 Mar 2018 09:26:42 -0700 Subject: [CIG-MC] CIG Event Deadlines and Updates; PyLith & ASPECT Hacks, CGU Abstracts Message-ID: <9CE4CFA5-CA09-41AA-9044-A8155E68E9D8@ucdavis.edu> HI Application for travel support and registration for CIG sponsored events CLOSES this Saturday March 31. Please note the following updates: ASPECT and PyLith Hackthons The location of this event has been MOVED. In addition, the dates of the ASPECT Hackathon will be adjusted. We anticipate starting a day earlier and hence, ending earlier. We will update all applicants on the new West Coast location and dates when they are confirmed. The event website will be updated as more information becomes available. ASPECT Hackathon > PyLith Hackathon > Joint CGU & CIG Meeting, Niagara Falls, Ontario Please see separate email on registration and housing for this event. To be fully considered for travel support, apply before the March 31 deadline. Early bird registration fees apply through April 27 2018 CGU CIG Joint Meeting > Best, -Lorraine ***************************** Lorraine Hwang, Ph.D. Associate Director, CIG 530.752.3656 -------------- next part -------------- An HTML attachment was scrubbed... URL: