[CIG-SHORT] Git Version of PETSc does not compile
Romain Jolivet
jolivetinsar at gmail.com
Fri Feb 13 02:11:55 PST 2015
On 12 Feb 2015, at 21:22, Matthew Knepley <knepley at mcs.anl.gov> wrote:
> On Thu, Feb 12, 2015 at 3:18 PM, Romain Jolivet <jolivetinsar at gmail.com> wrote:
> I have the exact same issue running the pylith-installer on our little cluster (no macports installed there).
> This issue shows up for configuring petsc and pylith.
> On the cluster, we are running git 1.9.1
> On my mac, I am running git 1.7.12.4 (Apple Git-37)
>
> You are cloning without pulling any tags. You can fix it using
>
> git fetch —tags
I have tried what you suggested. Now, git describe returns something, but ./configure still does not understands it.
Here is what I get:
pikaru 10:08:33 ~/MYBIN/PyLith/pylith-build/petsc-pylith > ./configure --prefix=/Users/rjolivet/MYBIN/PyLith/pylith-2 --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-debugging=0 --with-shared-libraries=1 --download-chaco=1 --download-ml=1 --download-fblaslapack=1 --with-hdf5=1 --with-hdf5-include=/opt/local/include --with-hdf5-lib=/opt/local/lib/libhdf5.dylib --LIBS=-lz CPPFLAGS="-I/Users/rjolivet/MYBIN/pylith/pylith-2/include " LDFLAGS="-L/Users/rjolivet/MYBIN/pylith/pylith-2/lib " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS="-g -O2" PETSC_DIR=/Users/rjolivet/MYBIN/PyLith/pylith-build/petsc-pylith PETSC_ARCH=arch-pylith
===============================================================================
Configuring PETSc to compile on your system
===============================================================================
TESTING: configureInstallationMethod from PETSc.options.petscclone(config/PETSc/options/petscclone.py:15) fatal: No tags can describe '04fcc16b6fc1fef768ea84f574fa77a92547ade2'.
Try --always, or create some tags.
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
-------------------------------------------------------------------------------
Your petsc source tree is broken. Use "git status" to check, or remove the entire directory and start all over again
*******************************************************************************
Because I need to move forward with my project, I will add —always in petscclone.py where git is called, but there might be a better way.
Any suggestions?
R
>
> Thanks,
>
> Matt
>
> R
>
>
> Romain Jolivet
> Cambridge, UK
> jolivetinsar at gmail.com
> UK: +44 7 596 703 148
> France: +33 6 52 91 76 39
> US: +1 (626) 560 6356
>
> On Feb 12, 2015, at 21: 08, Brad Aagaard wrote:
>
>> Romain,
>>
>> Having to remove the .git directory is very, very suspicious. This seems to indicate conflicts from already installed software or inconsistent environment settings.
>>
>> If you are using something like Macports, then be very careful about managing what gets installed. You may have incompatibilities coming from stuff installed there.
>>
>> As Matt mentioned, in order to diagnose problems like these we almost always need detailed explanations of what you are doing and all the output.
>>
>> Brad
>>
>> On 02/12/2015 12:32 PM, Romain Jolivet wrote:
>>> I will check if there is an older version of petsc in the directory where I put the executable.
>>>
>>> In the mean time, ./configure crashes when I have the .git repository. I would be glad not to remove this guy, but, if I don't, I cannot compile.
>>> What would be the reason for "git describe" to not send back any meaningful informations?
>>> One other way is to add --always in the configure script, where git is called. Should I do that?
>>>
>>> R
>>>
>>>
>>> Romain Jolivet
>>> Cambridge, UK
>>> jolivetinsar at gmail.com
>>> UK: +44 7 596 703 148
>>> France: +33 6 52 91 76 39
>>> US: +1 (626) 560 6356
>>>
>>> On Feb 12, 2015, at 20: 00, cig-short-request at geodynamics.org wrote:
>>>
>>>> Send CIG-SHORT mailing list submissions to
>>>> cig-short at geodynamics.org
>>>>
>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>> or, via email, send a message with subject or body 'help' to
>>>> cig-short-request at geodynamics.org
>>>>
>>>> You can reach the person managing the list at
>>>> cig-short-owner at geodynamics.org
>>>>
>>>> When replying, please edit your Subject line so it is more specific
>>>> than "Re: Contents of CIG-SHORT digest..."
>>>>
>>>>
>>>> Today's Topics:
>>>>
>>>> 1. Re: Git Version of PETSc does not compile (Matthew Knepley)
>>>>
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Message: 1
>>>> Date: Thu, 12 Feb 2015 10:39:32 -0600
>>>> From: Matthew Knepley <knepley at mcs.anl.gov>
>>>> To: "cig-short at geodynamics.org" <cig-short at geodynamics.org>
>>>> Subject: Re: [CIG-SHORT] Git Version of PETSc does not compile
>>>> Message-ID:
>>>> <CAMYG4G=yAZ9hNL8uqaH+8aC2ybsgKXm7oNe4dUuakKg2ZOJ5Xg at mail.gmail.com>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> On Thu, Feb 12, 2015 at 10:28 AM, Romain Jolivet <jolivetinsar at gmail.com>
>>>> wrote:
>>>>
>>>>> In order to do that, I had to configure, so I ran:
>>>>>
>>>>>>> ./configure --prefix=/Users/rjolivet/MYBIN/PyLith/pylith-2
>>>>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>>>>> --with-debugging=0 --with-shared-libraries=1 --download-chaco=1
>>>>> --download-ml=1 --download-fblaslapack=1 --with-hdf5=1
>>>>> --with-hdf5-include=/opt/local/include
>>>>> --with-hdf5-lib=/opt/local/lib/libhdf5.dylib --LIBS=-lz
>>>>> CPPFLAGS="-I/Users/rjolivet/MYBIN/pylith/pylith-2/include "
>>>>> LDFLAGS="-L/Users/rjolivet/MYBIN/pylith/pylith-2/lib " CFLAGS="-g -O2"
>>>>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS="-g -O2"
>>>>> PETSC_DIR=/Users/rjolivet/MYBIN/PyLith/pylith-build/petsc-pylith
>>>>> PETSC_ARCH=arch-pylith
>>>>>
>>>>> A (minor) thing is that, on my mac, I have to remove the .git directory in
>>>>> order to do that. I don’t know why but when I do:
>>>>>
>>>>>>> git describe
>>>>> fatal: No names found, cannot describe anything.
>>>>>
>>>>
>>>> You have destroyed the repository, since all history is kept under the .git
>>>> directory. I would start over.
>>>> You definitely do not have to remove it to build.
>>>>
>>>>
>>>>> So I removed the .git directory and it configures fine.
>>>>>
>>>>> I then type
>>>>>>> make V=1 -f ./gmakefile
>>>>>
>>>>> Please find the output attached.
>>>>>
>>>>
>>>> So you have extraneous include directories:
>>>>
>>>> mpicc -c -g -O2 -fPIC -I/Users/rjolivet/MYBIN/pylith/pylith-2/include
>>>> -I/Users/rjolivet/MYBIN/PyLith/pylith-build/petsc-pylith/include
>>>> -I/Users/rjolivet/MYBIN/PyLith/pylith-build/petsc-pylith/arch-pylith/include
>>>> -I/Users/rjolivet/MYBIN/PyLith/pylith-2/include -I/opt/local/include
>>>> -I/opt/local/include/openmpi-gcc49
>>>> -I/Users/rjolivet/MYBIN/pylith/pylith-2/include -MMD -MP
>>>> /Users/rjolivet/MYBIN/PyLith/pylith-build/petsc-pylith/src/mat/interface/dlregismat.c
>>>> -o arch-pylith/obj/src/mat/interface/dlregismat.o
>>>>
>>>> which are probably coming in from you defining CFLAGS or passing them to
>>>> PETSc somehow. It sounds like
>>>> one of those has an old PETSc version.
>>>>
>>>> Thanks,
>>>>
>>>> Matt
>>>>
>>>>
>>>>> R
>>>>>
>>>>>
>>>>>
>>>>> Romain Jolivet
>>>>> Cambridge, UK
>>>>> jolivetinsar at gmail.com
>>>>> UK: +44 7596 703 148
>>>>> France: +33 6 52 91 76 39
>>>>> USA: +1 (626) 560 6356
>>>>>
>>>>> On 12 Feb 2015, at 16:13, cig-short-request at geodynamics.org wrote:
>>>>>
>>>>> Send CIG-SHORT mailing list submissions to
>>>>> cig-short at geodynamics.org
>>>>>
>>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>> or, via email, send a message with subject or body 'help' to
>>>>> cig-short-request at geodynamics.org
>>>>>
>>>>> You can reach the person managing the list at
>>>>> cig-short-owner at geodynamics.org
>>>>>
>>>>> When replying, please edit your Subject line so it is more specific
>>>>> than "Re: Contents of CIG-SHORT digest..."
>>>>>
>>>>>
>>>>> Today's Topics:
>>>>>
>>>>> 1. Re: Git Version of PETSc does not compile (Romain Jolivet)
>>>>> 2. Re: Git Version of PETSc does not compile (Matthew Knepley)
>>>>>
>>>>>
>>>>> ----------------------------------------------------------------------
>>>>>
>>>>> Message: 1
>>>>> Date: Thu, 12 Feb 2015 15:57:40 +0000
>>>>> From: Romain Jolivet <jolivetinsar at gmail.com>
>>>>> To: cig-short at geodynamics.org
>>>>> Subject: Re: [CIG-SHORT] Git Version of PETSc does not compile
>>>>> Message-ID: <61E15CC8-6107-404D-A00E-2275FEBA2EBA at gmail.com>
>>>>> Content-Type: text/plain; charset="windows-1252"
>>>>>
>>>>> I have that line in matimpl.h.
>>>>> I just pulled a couple of hours ago by doing:
>>>>>
>>>>> git clone --depth 1 -b knepley/pylith
>>>>> https://bitbucket.org/petsc/petsc.git petsc-pylith
>>>>>
>>>>>
>>>>> When I do git log, I see:
>>>>>
>>>>> git log
>>>>>
>>>>> commit 04fcc16b6fc1fef768ea84f574fa77a92547ade2
>>>>> Author: Matthew G. Knepley <knepley at gmail.com>
>>>>> Date: Tue Feb 10 07:14:54 2015 -0600
>>>>>
>>>>> Merge branch 'knepley/fix-veclock-fftw' into knepley/pylith
>>>>>
>>>>> * knepley/fix-veclock-fftw:
>>>>> DM: Fix more Vec lock issues
>>>>> FFTW: Updated for vector locking
>>>>>
>>>>> So I guess we are on the same version…
>>>>> R
>>>>>
>>>>>
>>>>> Romain Jolivet
>>>>> Cambridge, UK
>>>>> jolivetinsar at gmail.com
>>>>> UK: +44 7596 703 148
>>>>> France: +33 6 52 91 76 39
>>>>> USA: +1 (626) 560 6356
>>>>>
>>>>> On 12 Feb 2015, at 15:51, cig-short-request at geodynamics.org wrote:
>>>>>
>>>>> Message: 1
>>>>> Date: Thu, 12 Feb 2015 09:35:54 -0600
>>>>> From: Matthew Knepley <knepley at mcs.anl.gov>
>>>>> To: "cig-short at geodynamics.org" <cig-short at geodynamics.org>
>>>>> Subject: Re: [CIG-SHORT] Git Version of PETSc does not compile
>>>>> Message-ID:
>>>>> <CAMYG4Gn_7_G5ZVP_RnrsJAvD9+Je5mzt1mCgJLHB2rZ=DpxaTg at mail.gmail.com>
>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>
>>>>> On Thu, Feb 12, 2015 at 8:27 AM, Romain Jolivet <jolivetinsar at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> As I tried to compile the newest version of PETSc from the git repository,
>>>>> I ran into some compiling problems.
>>>>> It says that MAT_GetSubMatrix (which was not present in the previous
>>>>> versions of pets I was using) is undeclared when compiling
>>>>> src/mat/interface/dlregismat.c
>>>>> I checked and it seems to be declared the same way MAT_GetSubMatrices is.
>>>>> Any thoughts? Please find attached the make and configure log files.
>>>>>
>>>>>
>>>>> The declaration of that value is here:
>>>>>
>>>>>
>>>>>
>>>>> https://bitbucket.org/petsc/petsc/src/04fcc16b6fc1fef768ea84f574fa77a92547ade2/include/petsc-private/matimpl.h?at=knepley%2Fpylith#cl-1534
>>>>>
>>>>> where you can see I am on the knepley/pylth branch. What branch are you on?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>> -------------- next part --------------
>>>>> An HTML attachment was scrubbed...
>>>>> URL: <
>>>>> http://lists.geodynamics.org/pipermail/cig-short/attachments/20150212/1d11d491/attachment-0001.html
>>>>>>
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> Message: 2
>>>>> Date: Thu, 12 Feb 2015 10:12:34 -0600
>>>>> From: Matthew Knepley <knepley at mcs.anl.gov>
>>>>> To: "cig-short at geodynamics.org" <cig-short at geodynamics.org>
>>>>> Subject: Re: [CIG-SHORT] Git Version of PETSc does not compile
>>>>> Message-ID:
>>>>> <CAMYG4GmXVw3qVK8e2_8Jeiz0VO6autQje25E+6nsx=DGTDaFFg at mail.gmail.com>
>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>
>>>>> On Thu, Feb 12, 2015 at 9:57 AM, Romain Jolivet <jolivetinsar at gmail.com>
>>>>> wrote:
>>>>>
>>>>> I have that line in matimpl.h.
>>>>> I just pulled a couple of hours ago by doing:
>>>>>
>>>>> git clone --depth 1 -b knepley/pylith
>>>>>
>>>>> https://bitbucket.org/petsc/petsc.git petsc-pylith
>>>>>
>>>>> When I do git log, I see:
>>>>>
>>>>> git log
>>>>>
>>>>> commit 04fcc16b6fc1fef768ea84f574fa77a92547ade2
>>>>> Author: Matthew G. Knepley <knepley at gmail.com>
>>>>> Date: Tue Feb 10 07:14:54 2015 -0600
>>>>>
>>>>> Merge branch 'knepley/fix-veclock-fftw' into knepley/pylith
>>>>>
>>>>>
>>>>> * knepley/fix-veclock-fftw:
>>>>> DM: Fix more Vec lock issues
>>>>> FFTW: Updated for vector locking
>>>>>
>>>>> So I guess we are on the same version…
>>>>>
>>>>>
>>>>> Next lets check that you are not picking up some old version of PETSc
>>>>> somewhere else on
>>>>> your machine through include paths.
>>>>>
>>>>> make V=1 -f ./gmakefile
>>>>>
>>>>> and send all output
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>> R
>>>>>
>>>>>
>>>>> Romain Jolivet
>>>>> Cambridge, UK
>>>>> jolivetinsar at gmail.com
>>>>> UK: +44 7596 703 148
>>>>> France: +33 6 52 91 76 39
>>>>> USA: +1 (626) 560 6356
>>>>>
>>>>> On 12 Feb 2015, at 15:51, cig-short-request at geodynamics.org wrote:
>>>>>
>>>>> Message: 1
>>>>> Date: Thu, 12 Feb 2015 09:35:54 -0600
>>>>> From: Matthew Knepley <knepley at mcs.anl.gov>
>>>>> To: "cig-short at geodynamics.org" <cig-short at geodynamics.org>
>>>>> Subject: Re: [CIG-SHORT] Git Version of PETSc does not compile
>>>>> Message-ID:
>>>>> <CAMYG4Gn_7_G5ZVP_RnrsJAvD9+Je5mzt1mCgJLHB2rZ=DpxaTg at mail.gmail.com>
>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>
>>>>> On Thu, Feb 12, 2015 at 8:27 AM, Romain Jolivet <jolivetinsar at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> As I tried to compile the newest version of PETSc from the git repository,
>>>>> I ran into some compiling problems.
>>>>> It says that MAT_GetSubMatrix (which was not present in the previous
>>>>> versions of pets I was using) is undeclared when compiling
>>>>> src/mat/interface/dlregismat.c
>>>>> I checked and it seems to be declared the same way MAT_GetSubMatrices is.
>>>>> Any thoughts? Please find attached the make and configure log files.
>>>>>
>>>>>
>>>>> The declaration of that value is here:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> https://bitbucket.org/petsc/petsc/src/04fcc16b6fc1fef768ea84f574fa77a92547ade2/include/petsc-private/matimpl.h?at=knepley%2Fpylith#cl-1534
>>>>>
>>>>> where you can see I am on the knepley/pylth branch. What branch are you on?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> CIG-SHORT mailing list
>>>>> CIG-SHORT at geodynamics.org
>>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> What most experimenters take for granted before they begin their
>>>>> experiments is infinitely more interesting than any results to which their
>>>>> experiments lead.
>>>>> -- Norbert Wiener
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>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> CIG-SHORT mailing list
>>>>> CIG-SHORT at geodynamics.org
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>>>>
>>>>
>>>>
>>>> --
>>>> What most experimenters take for granted before they begin their
>>>> experiments is infinitely more interesting than any results to which their
>>>> experiments lead.
>>>> -- Norbert Wiener
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>>>> CIG-SHORT mailing list
>>>> CIG-SHORT at geodynamics.org
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>>>> End of CIG-SHORT Digest, Vol 101, Issue 14
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>>>
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>>>
>>> N �n�r����)em�h�yhiם�w^��
>>>
>>
>> _______________________________________________
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> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
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>
>
> --
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
> -- Norbert Wiener
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
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