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

Thu Feb 12 08:39:32 PST 2015

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:
>
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> 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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> 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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