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

Thu Feb 12 13:22:36 PST 2015

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

  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:
>
>
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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
>
>
>
>
> _______________________________________________
>
> 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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>
> --
>
> 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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