[CIG-SHORT] Git Version of PETSc does not compile
Romain Jolivet
jolivetinsar at gmail.com
Thu Feb 12 13:08:24 PST 2015
Alright, here is the bug:
pikaru 21:05:11 ~/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 names found, cannot describe anything.
*******************************************************************************
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
*******************************************************************************
Please find the configure.log file attached.
Also, it does exactly the same thing with the git version of pylith
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: 46, Matthew Knepley wrote:
> On Thu, Feb 12, 2015 at 2:32 PM, Romain Jolivet <jolivetinsar at gmail.com> 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?
>
> If something crashes, you HAVE to send it in, or we will never be able to fix it.
>
> 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 20: 00, cig-short-request at geodynamics.org wrote:
>
>> Send CIG-SHORT mailing list submissions to
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>> 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
>>>
>>>
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>>>
>>> ------------------------------
>>>
>>> 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
>>>
>>>
>>>
>>> _______________________________________________
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>>>
>>>
>>>
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>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead.
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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
> 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
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