Just sent credentials. I am also trying on stampede.
Regards Yaakoub El Khamra On Tue, Dec 31, 2013 at 11:44 AM, Matthew Knepley <[email protected]> wrote: > 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 /usr/include/openmpi-x86_64/mpi.h:1506): MPI_Keyval_create is superseded by 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 /usr/include/openmpi-x86_64/mpi.h:1201): MPI_Attr_get is superseded by 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 /usr/include/openmpi-x86_64/mpi.h:1203): MPI_Attr_put is superseded by 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 >
