[petsc-dev] problem building on Mira

[Barry Smith]

On Jun 28, 2014, at 11:50 AM, Brian Van Straalen <bvstraalen at lbl.gov> wrote:

> the warnings for Chombo has to do with the C++11 standard and that the trunk is not compliant with a very specific and amazingly annoying new aspect of the language.  I fixed this in the 3.2 release but haven’t back ported these changes to the development trunk.  I will work on that this week, but that is not what’s stopping you.
> 
> The PETSc Syntax error seems to be related to 
> 
>> petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h
> 
> where there are new definitions for things that live inside the C standard libraries.  My guess is that PETSc’s configure was run with a different compiler than you are compiling with.

   The quick fix is to edit the petscfix.h file and remove the extra definitions. Then run the make again.

   Barry

  On some very obscure systems these definitions need to be added, we are not sure why configure has added them for the BlueGene and will track down why and fix it.
> 
> 
> 
> 
> On Jun 28, 2014, at 7:48 AM, 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]$ 
> 
> Brian Van Straalen         Lawrence Berkeley Lab
> BVStraalen at lbl.gov         Computational Research
> (510) 486-4976             Division (crd.lbl.gov)
> 
> 
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>