[CIG-SHORT] PyLith Installer PETSc Issue
Robert Walker
rlwalker at usc.edu
Tue Sep 18 22:49:28 PDT 2018
Trying again, and hard setting PETSC_DIR, no that is not the issue.
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 10:43 PM, Robert Walker <rlwalker at usc.edu> wrote:
> 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/i
>>> mpls/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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