<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Tue, Dec 31, 2013 at 11:38 AM, Yaakoub El Khamra <span dir="ltr"><<a href="mailto:yaakoub@tacc.utexas.edu" target="_blank">yaakoub@tacc.utexas.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div>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)</div>
<div><br></div><div>If I compile petsc with openmpi 1.7.3 and gcc 4.8.2 and the configure line:</div><div><br></div><div>/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<br>
</div><div><br></div><div>I get a lot of warnings from MPI that might significant. I can provide access to the fedora 20 box where I am working. </div></div></blockquote><div><br></div><div>Either send login info to <a href="mailto:petsc-maint@mcs.anl.gov">petsc-maint@mcs.anl.gov</a>, or get a stack trace of the hang using gdb.</div>
<div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>/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warning: ‘MPI_Keyval_create’ is deprecated (declared at /usr/include/openmpi-x86_64/mpi.h:1506): MPI_Keyval_create is superseded by MPI_Comm_create_keyval in MPI-2.0 [-Wdeprecated-declarations]</div>
<div> ierr = MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelTmpShared,&Petsc_Tmp_keyval,0);CHKERRQ(ierr);</div><div> ^</div><div>/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]</div>
<div>/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warning: ‘MPI_Attr_get’ is deprecated (declared at /usr/include/openmpi-x86_64/mpi.h:1201): MPI_Attr_get is superseded by MPI_Comm_get_attr in MPI-2.0 [-Wdeprecated-declarations]</div>
<div> ierr = MPI_Attr_get(comm,Petsc_Tmp_keyval,(void**)&tagvalp,(int*)&iflg);CHKERRQ(ierr);</div><div> ^</div><div>/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]</div>
<div> ierr = MPI_Attr_put(comm,Petsc_Tmp_keyval,tagvalp);CHKERRQ(ierr);</div><div> ^</div><div>/home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c: In function ‘PetscSharedWorkingDirectory’:</div><div>/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]</div>
<div> ierr = MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelTmpShared,&Petsc_WD_keyval,0);CHKERRQ(ierr);</div><div> ^</div><div>/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]</div>
<div>/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]</div>
<div> ierr = MPI_Attr_get(comm,Petsc_WD_keyval,(void**)&tagvalp,(int*)&iflg);CHKERRQ(ierr);</div><div> ^</div><div>/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]</div>
<div> ierr = MPI_Attr_put(comm,Petsc_WD_keyval,tagvalp);CHKERRQ(ierr);</div></div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><br>Regards<br>Yaakoub El Khamra<br></div>
<br><br><div class="gmail_quote">On Mon, Dec 30, 2013 at 10:58 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div><div>On Mon, Dec 30, 2013 at 7:34 PM, Yaakoub El Khamra <span dir="ltr"><<a href="mailto:yaakoub@tacc.utexas.edu" target="_blank">yaakoub@tacc.utexas.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><br></div>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:<div>
<br></div><div><div> call DMPlexCreateBoxMesh(PETSC_COMM_WORLD, 2, PETSC_TRUE, dm,</div><div> $ ierr)</div><div> CHKERRQ(ierr)</div><div><br></div><div> call DMPlexDistribute(dm, "chaco", 0, </div>
<div> $ PETSC_NULL_OBJECT, distributedMesh, ierr)</div><div> CHKERRQ(ierr)</div><div><br></div><div>Any thoughts? </div></div></div></blockquote><div><br></div></div></div><div>Can you run SNES ex12? It does exactly this and gets run in the nightly tests. I can run it in parallel</div>
<div>with no problems. My guess is that something is going wrong with the Fortran binding. Can you</div><div>get a stack trace for the hang? If not, can you send a full Fortran program which exhibits your problem?</div><div>
<br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Regards<span><font color="#888888"><br>
Yaakoub El Khamra<span><font color="#888888"><br></font></span></font></span></div><span><font color="#888888">
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</font></span></div></div></div><span><font color="#888888">
</font></span></blockquote></div><span><font color="#888888"><br><br clear="all"><span class="HOEnZb"><font color="#888888"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
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</blockquote></div><br></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
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