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

Brad Aagaard baagaard at usgs.gov
Thu Feb 12 13:08:04 PST 2015 

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
>>> -------------- next part --------------
>>> An HTML attachment was scrubbed...
>>> URL: <
>>> http://lists.geodynamics.org/pipermail/cig-short/attachments/20150212/d7532d3b/attachment.html
>>>>
>>>
>>> ------------------------------
>>>
>>> Subject: Digest Footer
>>>
>>> _______________________________________________
>>> CIG-SHORT mailing list
>>> CIG-SHORT at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>
>>> ------------------------------
>>>
>>> End of CIG-SHORT Digest, Vol 101, Issue 12
>>> ******************************************
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <http://lists.geodynamics.org/pipermail/cig-short/attachments/20150212/3598b455/attachment-0001.html>
>>
>> ------------------------------
>>
>> Subject: Digest Footer
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>> ------------------------------
>>
>> End of CIG-SHORT Digest, Vol 101, Issue 14
>> ******************************************
>
>
>
> N�n�r����)em�h�yhiם�w^��
>

More information about the CIG-SHORT mailing list