[CIG-SHORT] PyLith Installer PETSc Issue
Robert Walker
rlwalker at usc.edu
Tue Sep 18 22:43:30 PDT 2018
I tried on a local machine, and on a virgin cluster install, the
same....here is the result from the local machine.
${PETSC_DIR} is not set, period. Might this be the issue?
Robert
Robert L. Walker
PhD Candidate Petroleum Engineering
Mork Family Department of Chemicals and Materials Sciences
University of Southern California
----------------------------------------------
Mobile US: +1 (213) - 290 -7101
Mobile EU: +34 62 274 66 40
rlwalker at usc.edu
On Tue, Sep 18, 2018 at 4:07 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
> Robert,
>
> Do you have another PETSc installed on your machine or PETSC_DIR set in
> your environment to another location?
>
> Can you verify that the PETSc source has this hash
> c3d7e8a3961e2564b0ee47a7f7034285c2c0f620 with the most recent commit on
> Aug 29?
>
> Brad
>
>
> On 09/18/2018 03:53 PM, Robert Walker wrote:
>
>> Brad,
>>
>> I tried again, the installer indicated that it pulled the knepley/pylith
>> branch, still I get the exact same error.
>>
>> Robert
>>
>> Robert L. Walker
>> PhD Candidate Petroleum Engineering
>> Mork Family Department of Chemicals and Materials Sciences
>> University of Southern California
>> ----------------------------------------------
>> Mobile US: +1 (213) - 290 -7101
>> Mobile EU: +34 62 274 66 40
>> rlwalker at usc.edu <mailto:rlwalker at usc.edu>
>>
>>
>> On Tue, Sep 18, 2018 at 9:40 AM, Brad Aagaard <baagaard at usgs.gov <mailto:
>> baagaard at usgs.gov>> wrote:
>>
>> My original reply didn't go to the cig-short list, so I am sending
>> it again.
>>
>> It sounds like your build issue is the branch of PETSc being used.
>> You need the knepley/pylith branch of PETSc, not the master branch.
>> Matt sometimes adds new features in the knepley/pylith branch before
>> they get merged into master. Likewise, he controls when master gets
>> merged into the knepley/pylith branch so that we know when to expect
>> PETSc updates to break things in PyLith.
>>
>> Matt also mentioned that there was a short time period last week
>> when he broke the knepley/pylith PETSc branch. This is fixed now.
>>
>> Brad
>>
>>
>> On 9/14/18 3:23 AM, Robert Walker wrote:
>>
>> Hello,
>>
>> Not sure if this is the right place to ask this, or it would be
>> better to kick it over to petsc-users.
>> I am trying to use the installer to build PyLith from source,
>> and I am encountering the following error when trying to make
>> pylith-petsc, using the configure settings that are stock for
>> the installer script, but listed below anyway:
>>
>> ./configure --prefix=/home/rcf-40/rlwalker/pylith \
>> --with-c2html=0 --with-x=0 \
>> --with-clanguage=C \
>> --with-mpicompilers=1 \
>> --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 \
>> --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1
>> --with-hdf5=1 --with-hdf5-dir=/home/rcf-40/rlwalker/pylith
>> --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0
>> CPPFLAGS="-I/home/rcf-40/rlwalker/pylith/include
>> -I/home/rcf-40/rlwalker/pylith/include "
>> LDFLAGS="-L/home/rcf-40/rlwalker/pylith/lib
>> -L/home/rcf-40/rlwalker/pylith/lib64
>> -L/home/rcf-40/rlwalker/pylith/lib
>> -L/home/rcf-40/rlwalker/pylith/lib64 " CFLAGS="-fPIC"
>> CXXFLAGS="-fPIC -DMPICH_IGNORE_CXX_SEEK" FCFLAGS="" \
>> PETSC_DIR=/home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith
>> PETSC_ARCH=arch-pylith && \
>>
>>
>> /*
>> ============================================================
>> ======
>> */
>> /* ( End PETSc Config....Next is the error) */
>> /*
>> ============================================================
>> ======
>> */
>>
>>
>>
>> In file included from
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmpleximpl.h:8:0,
>> from
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/petscfeimpl.h:7,
>> from
>> /auto/rcf-proj/rlw1/build/pylith/petsc-pylith/src/dm/field/
>> impls/ds/dmfieldds.c:2:
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:
>> In function ‘DMGetLocalOffset_Private’:
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:335:15:
>> error: dereferencing pointer to incomplete type
>> *start = s->atlasOff[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:335:35:
>> error: dereferencing pointer to incomplete type
>> *start = s->atlasOff[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:336:24:
>> error: dereferencing pointer to incomplete type
>> *end = *start + s->atlasDof[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:336:44:
>> error: dereferencing pointer to incomplete type
>> *end = *start + s->atlasDof[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:
>> In function ‘DMGetLocalFieldOffset_Private’:
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:357:46:
>> error: dereferencing pointer to incomplete type
>> const PetscSection s = dm->defaultSection->field[field];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:358:15:
>> error: dereferencing pointer to incomplete type
>> *start = s->atlasOff[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:358:35:
>> error: dereferencing pointer to incomplete type
>> *start = s->atlasOff[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:359:24:
>> error: dereferencing pointer to incomplete type
>> *end = *start + s->atlasDof[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:359:44:
>> error: dereferencing pointer to incomplete type
>> *end = *start + s->atlasDof[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:
>> In function ‘DMGetGlobalOffset_Private’:
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:383:32:
>> error: dereferencing pointer to incomplete type
>> const PetscInt dof = s->atlasDof[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:383:52:
>> error: dereferencing pointer to incomplete type
>> const PetscInt dof = s->atlasDof[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:384:32:
>> error: dereferencing pointer to incomplete type
>> const PetscInt cdof = s->bc ? s->bc->atlasDof[point -
>> s->bc->pStart] : 0;
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:384:40:
>> error: dereferencing pointer to incomplete type
>> const PetscInt cdof = s->bc ? s->bc->atlasDof[point -
>> s->bc->pStart] : 0;
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:384:64:
>> error: dereferencing pointer to incomplete type
>> const PetscInt cdof = s->bc ? s->bc->atlasDof[point -
>> s->bc->pStart] : 0;
>>
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:385:15:
>> error: dereferencing pointer to incomplete type
>> *start = s->atlasOff[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:385:35:
>> error: dereferencing pointer to incomplete type
>> *start = s->atlasOff[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:
>> In function ‘DMGetGlobalFieldOffset_Private’:
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:417:50:
>> error: dereferencing pointer to incomplete type
>> const PetscSection fs = dm->defaultSection->field[fiel
>> d];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:419:33:
>> error: dereferencing pointer to incomplete type
>> const PetscInt loff = s->atlasOff[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:419:53:
>> error: dereferencing pointer to incomplete type
>> const PetscInt loff = s->atlasOff[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:420:34:
>> error: dereferencing pointer to incomplete type
>> const PetscInt goff = gs->atlasOff[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:420:54:
>> error: dereferencing pointer to incomplete type
>> const PetscInt goff = gs->atlasOff[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:421:34:
>> error: dereferencing pointer to incomplete type
>> const PetscInt lfoff = fs->atlasOff[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:421:54:
>> error: dereferencing pointer to incomplete type
>> const PetscInt lfoff = fs->atlasOff[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:422:34:
>> error: dereferencing pointer to incomplete type
>> const PetscInt fdof = fs->atlasDof[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:422:54:
>> error: dereferencing pointer to incomplete type
>> const PetscInt fdof = fs->atlasDof[point - s->pStart];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:423:34:
>> error: dereferencing pointer to incomplete type
>> const PetscInt fcdof = fs->bc ?
>> fs->bc->atlasDof[point - fs->bc->pStart] : 0;
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:423:43:
>> error: dereferencing pointer to incomplete type
>> const PetscInt fcdof = fs->bc ?
>> fs->bc->atlasDof[point - fs->bc->pStart] : 0;
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:423:68:
>> error: dereferencing pointer to incomplete type
>> const PetscInt fcdof = fs->bc ?
>> fs->bc->atlasDof[point - fs->bc->pStart] : 0;
>>
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:427:50:
>> error: dereferencing pointer to incomplete type
>> const PetscSection ffs = dm->defaultSection->field[f];
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:428:20:
>> error: dereferencing pointer to incomplete type
>> ffcdof += ffs->bc ? ffs->bc->atlasDof[point -
>> ffs->bc->pStart] : 0;
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:428:30:
>> error: dereferencing pointer to incomplete type
>> ffcdof += ffs->bc ? ffs->bc->atlasDof[point -
>> ffs->bc->pStart] : 0;
>> ^
>> /home/rcf-40/rlwalker/NTS/build/pylith/petsc-pylith/include/
>> petsc/private/dmimpl.h:428:56:
>> error: dereferencing pointer to incomplete type
>> ffcdof += ffs->bc ? ffs->bc->atlasDof[point -
>> ffs->bc->pStart] : 0;
>> ^
>> make[3]: *** [arch-pylith/obj/dm/field/impls/ds/dmfieldds.o]
>> Error 1
>> make[3]: Leaving directory
>> `/auto/rcf-proj/rlw1/build/pylith/petsc-pylith'
>> make[2]: *** [petsc] Error 2
>> make[2]: Leaving directory `/auto/rcf-proj/rlw1/build/pylith'
>> make[1]: *** [installed_petsc] Error 2
>> make[1]: Leaving directory `/auto/rcf-proj/rlw1/build/pylith'
>> make: *** [installed_pylith] Error 2
>>
>> /* ========================================================== */
>> /* End Error */
>> /* ========================================================== */
>>
>> Looking at ìt my thought is that there is a goof in the
>> interaction between the PetscSection type and the functions
>> outlined in dmimpl.h....it's a private function so maybe a PETSc
>> bug, but again I don't remember what version PETSc that the
>> pylith installer script pulls.
>>
>> Thanks,
>>
>> Robert
>>
>>
>>
>>
>> Robert L. Walker
>> MS Petroleum Engineering
>> Mork Family Department of Chemicals and Materials Sciences
>> University of Southern California
>> ----------------------------------------------
>> Mobile US: +1 (213) - 290 -7101
>> Mobile EU: +34 62 274 66 40
>> rlwalker at usc.edu <mailto:rlwalker at usc.edu>
>> <mailto:rlwalker at usc.edu <mailto:rlwalker at usc.edu>>
>>
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