[petsc-dev] problem building on Mira

Sat Jun 28 11:50:46 CDT 2014

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.

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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