On Tue, Dec 31, 2013 at 11:38 AM, Yaakoub El Khamra <[email protected] > wrote:
> > snes ex12 also hangs. Then I started trying all other examples, all MPI > examples hang. Basic MPI code and benchmarks appear to compile and run > fine. I recompiled PETSc and went carefully over the output, there are a > lot of warnings (even from a stable build) > > If I compile petsc with openmpi 1.7.3 and gcc 4.8.2 and the configure line: > > /configure --with-mpi-compilers=yes --download-metis --download-parmetis > --download-fiat --with-fortran=yes --download-scientificpython > --download-f-blas-lapack=1 --download-triangle --download-chaco > --download-exodusii --download-netcdf --download-hdf5 > > I get a lot of warnings from MPI that might significant. I can provide > access to the fedora 20 box where I am working. > Either send login info to [email protected], or get a stack trace of the hang using gdb. Thanks, Matt > /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:159:5: warning: > ‘MPI_Keyval_create’ is deprecated (declared at > /usr/include/openmpi-x86_64/mpi.h:1506): MPI_Keyval_create is superseded by > MPI_Comm_create_keyval in MPI-2.0 [-Wdeprecated-declarations] > ierr = > MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelTmpShared,&Petsc_Tmp_keyval,0);CHKERRQ(ierr); > ^ > /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:159:5: warning: > ‘OMPI_C_MPI_NULL_COPY_FN’ is deprecated (declared at > /usr/include/openmpi-x86_64/mpi.h:828): MPI_NULL_COPY_FN is deprecated in > MPI-2.0 [-Wdeprecated-declarations] > /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:162:3: warning: > ‘MPI_Attr_get’ is deprecated (declared at > /usr/include/openmpi-x86_64/mpi.h:1201): MPI_Attr_get is superseded by > MPI_Comm_get_attr in MPI-2.0 [-Wdeprecated-declarations] > ierr = > MPI_Attr_get(comm,Petsc_Tmp_keyval,(void**)&tagvalp,(int*)&iflg);CHKERRQ(ierr); > ^ > /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:168:5: warning: > ‘MPI_Attr_put’ is deprecated (declared at > /usr/include/openmpi-x86_64/mpi.h:1203): MPI_Attr_put is superseded by > MPI_Comm_set_attr in MPI-2.0 [-Wdeprecated-declarations] > ierr = MPI_Attr_put(comm,Petsc_Tmp_keyval,tagvalp);CHKERRQ(ierr); > ^ > /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c: In function > ‘PetscSharedWorkingDirectory’: > /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:282:5: warning: > ‘MPI_Keyval_create’ is deprecated (declared at > /usr/include/openmpi-x86_64/mpi.h:1506): MPI_Keyval_create is superseded by > MPI_Comm_create_keyval in MPI-2.0 [-Wdeprecated-declarations] > ierr = > MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelTmpShared,&Petsc_WD_keyval,0);CHKERRQ(ierr); > ^ > /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:282:5: warning: > ‘OMPI_C_MPI_NULL_COPY_FN’ is deprecated (declared at > /usr/include/openmpi-x86_64/mpi.h:828): MPI_NULL_COPY_FN is deprecated in > MPI-2.0 [-Wdeprecated-declarations] > /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:285:3: warning: > ‘MPI_Attr_get’ is deprecated (declared at > /usr/include/openmpi-x86_64/mpi.h:1201): MPI_Attr_get is superseded by > MPI_Comm_get_attr in MPI-2.0 [-Wdeprecated-declarations] > ierr = > MPI_Attr_get(comm,Petsc_WD_keyval,(void**)&tagvalp,(int*)&iflg);CHKERRQ(ierr); > ^ > /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:291:5: warning: > ‘MPI_Attr_put’ is deprecated (declared at > /usr/include/openmpi-x86_64/mpi.h:1203): MPI_Attr_put is superseded by > MPI_Comm_set_attr in MPI-2.0 [-Wdeprecated-declarations] > ierr = MPI_Attr_put(comm,Petsc_WD_keyval,tagvalp);CHKERRQ(ierr); > > > > Regards > Yaakoub El Khamra > > > On Mon, Dec 30, 2013 at 10:58 PM, Matthew Knepley <[email protected]>wrote: > >> On Mon, Dec 30, 2013 at 7:34 PM, Yaakoub El Khamra < >> [email protected]> wrote: >> >>> >>> If I create a dm with DMPlexCreateBoxMesh and immediately attempt to >>> distribute it with DMPlexDistribute, the call to DMPlexDistribute never >>> returns. I am working with a development checkout and the code looks as >>> follows: >>> >>> call DMPlexCreateBoxMesh(PETSC_COMM_WORLD, 2, PETSC_TRUE, dm, >>> $ ierr) >>> CHKERRQ(ierr) >>> >>> call DMPlexDistribute(dm, "chaco", 0, >>> $ PETSC_NULL_OBJECT, distributedMesh, ierr) >>> CHKERRQ(ierr) >>> >>> Any thoughts? >>> >> >> Can you run SNES ex12? It does exactly this and gets run in the nightly >> tests. I can run it in parallel >> with no problems. My guess is that something is going wrong with the >> Fortran binding. Can you >> get a stack trace for the hang? If not, can you send a full Fortran >> program which exhibits your problem? >> >> Matt >> >> >>> Regards >>> Yaakoub El Khamra >>> >> >> >> >> -- >> 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 >> > > -- 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
