[CIG-SHORT] PyLith configure script cannot find PETSc

Fri Feb 13 07:54:43 PST 2015

On Fri, Feb 13, 2015 at 9:47 AM, Romain Jolivet <jolivetinsar at gmail.com>
wrote:

> The configure.log file is attached.
>
> In the build directory of PETSc, I could find this arch-pylith directory,
> indeed, but not where PETSc has been installed (with all the other pylith
> stuffs like nemesis, spatialdata etc).
> When I build pylith, I point to the directory where petsc has been
> installed, not built. Should I do that?
>

Ah, this is the difference between installing in a custom place (usually
now called $PETSC_DIR)
and using the default installation in $PETSC_DIR/$PETSC_ARCH. The
recommended PyLith
thing was to use the default, so our tools were not checking the other
option.

Brad, we can check for an installation in $PETSC_DIR if we look for

  $PETSC_DIR/include/petscconf.h

or

  $PETSC_DIR/lib/petsc-conf/petscrules

Otherwise we use the default form. This is a clash between two different
styles of Linux
installation, and it is a pain.

  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 13 Feb 2015, at 15:43, Matthew Knepley <knepley at mcs.anl.gov> wrote:
>
> On Fri, Feb 13, 2015 at 9:34 AM, Romain Jolivet <jolivetinsar at gmail.com>
> wrote:
>
>> I don’t have  $PETSC_DIR/$PETSC_ARCH/lib/petsc-conf
>> It is the one being checked for in configure.
>> What I have is only $PETSC_DIR/lib/petsc-conf
>> That is both on our linux cluster and on my iMac.
>>
>
> The build process creates them. If they are not there, PETSc was not
> built. The
> configure log has a record of created files. Can you send it for the
> configuration
> that you cannot find this directory for?
>
>   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 13 Feb 2015, at 15:28, Matthew Knepley <knepley at mcs.anl.gov> wrote:
>>
>> On Fri, Feb 13, 2015 at 9:22 AM, Romain Jolivet <jolivetinsar at gmail.com>
>> wrote:
>>
>>> I got it to work, but not with the m4 file you provided.
>>> In your file, you test for $PETSC_DIR/$PETSC_ARCH/lib/petsc-conf
>>>
>> While the architecture I have is $PETSC_DIR/lib/petsc-conf
>>> The variable PETSC_ARCH is not used in the destination directory when I
>>> install petsc…
>>> Is that normal?
>>>
>>
>> Both of these directories exist. What is being checked for?
>>
>>   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 13 Feb 2015, at 14:54, Brad Aagaard <baagaard at usgs.gov> wrote:
>>>
>>> Romain and Matt,
>>>
>>> This is already fixed. Romain needs to pull the m4 dir or reclone pylith.
>>>
>>> In the top level pylith dir,
>>>
>>> cd m4
>>> git pull origin master
>>>
>>> Brad
>>>
>>>
>>>
>>> On Feb 13, 2015, at 3:54 AM, Romain Jolivet <jolivetinsar at gmail.com>
>>> wrote:
>>>
>>> Oh, sorry, here it is.
>>> R
>>>
>>> <cit_petsc.m4>
>>>
>>>
>>> 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 13 Feb 2015, at 11:52, Matthew Knepley <knepley at mcs.anl.gov> wrote:
>>>
>>> On Fri, Feb 13, 2015 at 5:45 AM, Romain Jolivet <jolivetinsar at gmail.com>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> After compiling manually petsc from the git repository, I noticed the
>>>> architecture of the file directories that are copied into the —prefix
>>>> argument are different from why I was used to.
>>>> As a consequence, the configure in pylith cannot find the petsc
>>>> libraries.
>>>> I looked into the m4/cit_petsc.m4 file used by autoreconf, and I do not
>>>> see the case for the architecture I have.
>>>>
>>>> I could modify it to adapt to my system, but, there should be a better
>>>> way.
>>>> Attached is the modified cit_petsc.m4 I modified to compile pylith.
>>>> Any suggestions?
>>>>
>>>
>>> There is nothing attached. The PyLith master branch tracks PETSc
>>> knepley/pylith, so all fixes
>>> should be there.
>>>
>>>   Thanks,
>>>
>>>     Matt
>>>
>>>
>>>>
>>>> R
>>>>
>>>>
>>>> —————————————————————————————————————
>>>> —————————————————————————————————————
>>>> Romain Jolivet
>>>> Postdoctoral Fellow
>>>>
>>>> University of Cambridge
>>>> Department of Earth Sciences
>>>> Bullard Labs
>>>> Madingley Rise
>>>> Madingley Road
>>>> Cambridge CB3 0EZ
>>>> United Kingdom
>>>>
>>>> email: rpj29 at cam.ac.uk
>>>> Phone: +44 1223 748 938
>>>> Mobile: +44 7596 703 148
>>>>
>>>> France: +33 6 52 91 76 39
>>>> US: +1 (626) 560 6356
>>>> —————————————————————————————————————
>>>> —————————————————————————————————————
>>>>
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>>>
>>>
>>>
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>>> What most experimenters take for granted before they begin their
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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
>>  _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>>
>>
>> _______________________________________________
>> 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
>  _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
>
>
> _______________________________________________
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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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