[petsc-dev] problem building on Mira

[Matthew Knepley]

On Sat, Jun 28, 2014 at 8:00 AM, Mark Adams <mfadams at 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 at 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 at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20140628/876c885b/attachment.html>