[CIG-SHORT] Git Version of PETSc does not compile

Thu Feb 12 12:32:06 PST 2015

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:

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> Today's Topics:
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>   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
>> 
>> 
>> 
>> _______________________________________________
>> 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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> 
> -- 
> 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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