On Sat, Jun 28, 2014 at 8:00 AM, Mark Adams <mfadams@lbl.gov> wrote:

And this is the configure log.

Here is the problem:

Executing: mpixlcxx_r -c -o /tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.o -I/tmp/petsc-ByVZS6/config.compilers -I/tmp/petsc-ByVZS6/config.setCompilers -I/tmp/petsc-ByVZS6/config.functions -I/tmp/petsc-ByVZS6/config.types -I/tmp/petsc-ByVZS6/PETSc.utilities.missing -O5 -qhot=level=0 -qsimd=auto -qmaxmem=-1 -qstrict -qstrict_induction -+ /tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.cc

Possible ERROR while running compiler: exit code 256

stderr:

"/tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.cc", line 4.9: 1540-0848 (S) The macro name "_GNU_SOURCE" is already defined with a different definition.

Source:

#include "confdefs.h"

#include "conffix.h"

#define _BSD_SOURCE

#define _GNU_SOURCE

#ifdef PETSC_HAVE_UNISTD_H

#include <unistd.h>

#endif

#ifdef PETSC_HAVE_NETDB_H

#include <netdb.h>

#endif

int main() {

int (*getdomainname_ptr)(char*,size_t) = getdomainname;

char test[10];

if (getdomainname_ptr(test,10)) return 1;

;

return 0;

}

Compile failed inside link

Jed, what is going on with the _GNU_SOURCE crap?

Matt

Mark

On Sat, Jun 28, 2014 at 4:48 PM, Mark Adams <mfadams@lbl.gov> wrote:

PETSc,

I am trying to build a code with PETSc on Mira and I seem to be getting some conflicting declarations.

I have pulled from dev and reconfigured PETSc today. Any ideas?

Mark

mpixlcxx_r -g -DCH_SPACEDIM=3 -DCH_Linux -DCH_MPI -DMPICH_SKIP_MPICXX -ULAM_WANT_MPI2CPP -DMPI_NO_CPPBIND -DCH_USE_SETVAL -DCH_USE_COMPLEX -DCH_USE_MEMORY_TRACKING -DCH_USE_64 -DCH_USE_DOUBLE -DCH_USE_HDF5 -I/soft/libraries/hdf5/1.8.10/cnk-xl/current/include -DH5_USE_16_API -DCH_USE_PETSC -I/home/adams/petsc_public/include -I/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include -I/gpfs/mira-home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include -I/bgsys/drivers/V1R2M1/ppc64/comm/include -I/bgsys/drivers/V1R2M1/ppc64/comm/lib/xl -I/bgsys/drivers/V1R2M1/ppc64 -I/bgsys/drivers/V1R2M1/ppc64/comm/sys/include -I/bgsys/drivers/V1R2M1/ppc64/spi/include -I/bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk -DCH_FORT_UNDERSCORE -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/AMRTools -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BaseTools -DCH_LANG_CC -c PetscCompGrid.cpp -o o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o

"/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 447.14: 1540-1091 (W) The friend declaration "bdryLo" specifies a default argument expression and is not a definition.

"/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 460.14: 1540-1091 (W) The friend declaration "bdryHi" specifies a default argument expression and is not a definition.

"/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 490.14: 1540-1091 (W) The friend declaration "adjCellLo" specifies a default argument expression and is not a definition.

"/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 521.14: 1540-1091 (W) The friend declaration "adjCellHi" specifies a default argument expression and is not a definition.

"/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 7.5: 1540-0400 (S) "getdomainname(char *, size_t)" has a conflicting declaration.
"/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h", line 916.12: 1540-0424 (I) "getdomainname" is declared on line 916 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h".

"/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 8.8: 1540-0400 (S) "drand48()" has a conflicting declaration.
"/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", line 395.15: 1540-0424 (I) "drand48" is declared on line 395 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h".

"/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 9.8: 1540-0400 (S) "srand48(long)" has a conflicting declaration.
"/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", line 409.13: 1540-0424 (I) "srand48" is declared on line 409 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h".

"/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", line 387.3: 1540-1091 (W) The friend declaration "refine" specifies a default argument expression and is not a definition.

"/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", line 409.3: 1540-1091 (W) The friend declaration "coarsen" specifies a default argument expression and is not a definition.

gmake[2]: *** [o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o] Error 1
gmake[1]: *** [AMRElliptic] Error 2
make: *** [AMRElliptic] Error 2

[adams@miralac1 execBCG]$

--
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