[CIG-SHORT] PyLith Installer PETSc Issue
Robert Walker
rlwalker at usc.edu
Fri Sep 14 03:23:17 PDT 2018
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[field];
^
/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
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