<div dir="ltr">Hello Barry, <div><br></div><div>Thank you for your answer. And sorry I forgot those important details ... </div><div><br></div><div>Here is the complete error message for a DMView :</div><div><br></div><div>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: ------------------------------------------------------------------------</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: or see <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind">https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: or try <a href="http://valgrind.org">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: likely location of problem given in stack below</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: ---------------------<span class="gmail-Apple-converted-space"> </span>Stack Frames ------------------------------------</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: The EXACT line numbers in the error traceback are not available.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: instead the line number of the start of the function is given.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #1 H5Dcreate2() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:690</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #2 VecView_MPI_HDF5() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:594</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #3 VecView_MPI() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:787</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #4 VecView() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/interface/vector.c:576</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #5 DMPlexCoordinatesView_HDF5_Internal() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plexhdf5.c:560</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #6 DMPlexView_HDF5_Internal() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plexhdf5.c:802</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #7 DMView_Plex() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plex.c:1366</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #8 DMView() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/interface/dm.c:954</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Signal received</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: See <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html">https://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Petsc Development GIT revision: v3.15.1-558-g07f732cb94<span class="gmail-Apple-converted-space"> </span>GIT Date: 2021-07-04 15:58:55 +0000</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: /ccc/work/cont001/ocre/bridelbert/EULERIAN2D/bin/eulerian2D on a<span class="gmail-Apple-converted-space"> </span>named r1login by bridelbert Mon Jul<span class="gmail-Apple-converted-space"> </span>5 18:45:41 2021</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Configure options --with-clean=1 --prefix=/ccc/work/cont001/ocre/bridelbert/05-PETSC/build_uns3D_inti --with-make-np=8 --with-windows-graphics=0 --with-debugging=1 --download-mpich-shared=0 --with-x=0 --with-pthread=0 --with-valgrind=0 --PETSC_ARCH=INTI_UNS3D --with-fc=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpifort --with-cc=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpicc --with-cxx=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpicxx --with-openmp=0 --download-sowing=/ccc/work/cont001/ocre/bridelbert/v1.1.26-p2.tar.gz --download-metis=/ccc/work/cont001/ocre/bridelbert/git.metis.tar.gz --download-parmetis=/ccc/work/cont001/ocre/bridelbert/git.parmetis.tar.gz --download-fblaslapack=/ccc/work/cont001/ocre/bridelbert/git.fblaslapack.tar.gz --with-cmake-dir=/ccc/products/cmake-3.13.3/system/default --download-hdf5=/ccc/work/cont001/ocre/bridelbert/hdf5-1.12.0.tar.bz2 --download-netcdf=/ccc/work/cont001/ocre/bridelbert/netcdf-4.5.0.tar.gz --download-pnetcdf=/ccc/work/cont001/ocre/bridelbert/pnetcdf-1.12.1.tar.gz --download-exodusii=/ccc/work/cont001/ocre/bridelbert/v2021-01-20.tar.gz --download-zlib=/ccc/work/cont001/ocre/bridelbert/zlib-1.2.11.tar.gz</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #1 User provided function() at unknown file:0</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Checking the memory for corruption.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">--------------------------------------------------------------------------</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">with errorcode 59.</span></p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207);min-height:13px"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">You may or may not see output from other processes, depending on</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">exactly when Open MPI kills them.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">--------------------------------------------------------------------------</span></p></div><div><br></div><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div><div><div><div><div>Here is the complete message for a VecView :</div><div><br></div><div>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: ------------------------------------------------------------------------</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: or see <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind">https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: or try <a href="http://valgrind.org">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: likely location of problem given in stack below</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: ---------------------<span class="gmail-Apple-converted-space"> </span>Stack Frames ------------------------------------</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: The EXACT line numbers in the error traceback are not available.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: instead the line number of the start of the function is given.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #1 H5Dcreate2() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:690</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #2 VecView_MPI_HDF5() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:594</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #3 VecView_MPI() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:787</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #4 VecView_Plex_Local_HDF5_Internal() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plexhdf5.c:132</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #5 VecView_Plex_HDF5_Internal() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plexhdf5.c:247</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #6 VecView_Plex() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plex.c:391</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #7 VecView() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/interface/vector.c:576</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #8 ourmonitor() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/ts/interface/ftn-custom/ztsf.c:129</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #9 TSMonitor() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/ts/interface/tsmon.c:31</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #10 TSSolve() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/ts/interface/ts.c:3858</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Signal received</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: See <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html">https://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Petsc Development GIT revision: v3.15.1-558-g07f732cb94<span class="gmail-Apple-converted-space"> </span>GIT Date: 2021-07-04 15:58:55 +0000</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: /ccc/work/cont001/ocre/bridelbert/EULERIAN2D/bin/eulerian2D on a<span class="gmail-Apple-converted-space"> </span>named r1login by bridelbert Tue Jul<span class="gmail-Apple-converted-space"> </span>6 08:46:43 2021</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Configure options --with-clean=1 --prefix=/ccc/work/cont001/ocre/bridelbert/05-PETSC/build_uns3D_inti --with-make-np=8 --with-windows-graphics=0 --with-debugging=1 --download-mpich-shared=0 --with-x=0 --with-pthread=0 --with-valgrind=0 --PETSC_ARCH=INTI_UNS3D --with-fc=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpifort --with-cc=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpicc --with-cxx=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpicxx --with-openmp=0 --download-sowing=/ccc/work/cont001/ocre/bridelbert/v1.1.26-p2.tar.gz --download-metis=/ccc/work/cont001/ocre/bridelbert/git.metis.tar.gz --download-parmetis=/ccc/work/cont001/ocre/bridelbert/git.parmetis.tar.gz --download-fblaslapack=/ccc/work/cont001/ocre/bridelbert/git.fblaslapack.tar.gz --with-cmake-dir=/ccc/products/cmake-3.13.3/system/default --download-hdf5=/ccc/work/cont001/ocre/bridelbert/hdf5-1.12.0.tar.bz2 --download-netcdf=/ccc/work/cont001/ocre/bridelbert/netcdf-4.5.0.tar.gz --download-pnetcdf=/ccc/work/cont001/ocre/bridelbert/pnetcdf-1.12.1.tar.gz --download-exodusii=/ccc/work/cont001/ocre/bridelbert/v2021-01-20.tar.gz --download-zlib=/ccc/work/cont001/ocre/bridelbert/zlib-1.2.11.tar.gz</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #1 User provided function() at unknown file:0</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Checking the memory for corruption.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">--------------------------------------------------------------------------</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">with errorcode 59.</span></p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207);min-height:13px"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">You may or may not see output from other processes, depending on</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">exactly when Open MPI kills them.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">--------------------------------------------------------------------------</span></p></div><div><br></div><div>I am currently on the "main" branch, my HEAD being at commit id. <span class="gmail-Apple-converted-space" style="font-variant-ligatures:no-common-ligatures;background-color:rgb(252,238,207);color:rgb(149,151,21);font-family:Menlo;font-size:11px"> </span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(252,238,207);color:rgb(149,151,21);font-family:Menlo;font-size:11px">07f732cb949ae259de817d126d140b8fa08e2d25</span></div><div>I have the same issue with the "master" branch actually, that's why I went with the "main", hoping something might have been fixed meanwhile.</div><div><br></div><div>I cannot provide you with a MWE yet unfortunately because it's part of a bigger solver and I have to extract the workflow from it. I'll work on it so you have everything you need.</div><div><br></div><div>Thanks !!</div><div><br></div><div>Thibault</div></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le mar. 6 juil. 2021 à 01:08, Barry Smith <<a href="mailto:bsmith@petsc.dev">bsmith@petsc.dev</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;"><div><br></div> Please send the error message that is printed to the screen. <div><br></div><div> Also please send the exact PETSc version you are using. If possible also a code that reproduces the problem. </div><div><br></div><div> Can you view other simpler things with HDF5? Like say just a vector? </div><div><br></div><div> Barry</div><div><br></div><div><br><div><div><br><blockquote type="cite"><div>On Jul 5, 2021, at 11:50 AM, Thibault Bridel-Bertomeu <<a href="mailto:thibault.bridelbertomeu@gmail.com" target="_blank">thibault.bridelbertomeu@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Dear all,<div><br></div><div>I keep having this error on one of the supercomputers I have access to :</div><div><br></div><div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: The EXACT line numbers in the error traceback are not available.</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: instead the line number of the start of the function is given.</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #1 H5Dcreate2() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:690</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #2 VecView_MPI_HDF5() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:594</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #3 VecView_MPI() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:787</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #4 VecView() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/interface/vector.c:576</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #5 DMPlexCoordinatesView_HDF5_Internal() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plexhdf5.c:560</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #6 DMPlexView_HDF5_Internal() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plexhdf5.c:802</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #7 DMView_Plex() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plex.c:1366</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: #8 DMView() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/interface/dm.c:954</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</span></div></div><div><br></div><div>The configure options are as follow :</div><div><br></div><div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[1]PETSC ERROR: Configure options --with-clean=1 --prefix=/ccc/work/cont001/ocre/bridelbert/05-PETSC/build_uns3D_inti --with-make-np=8 --with-windows-graphics=0 --with-debugging=1 --download-mpich-shared=0 --with-x=0 --with-pthread=0 --with-valgrind=0 --PETSC_ARCH=INTI_UNS3D --with-fc=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpifort --with-cc=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpicc --with-cxx=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpicxx --with-openmp=0 --download-sowing=/ccc/work/cont001/ocre/bridelbert/v1.1.26-p2.tar.gz --download-metis=/ccc/work/cont001/ocre/bridelbert/git.metis.tar.gz --download-parmetis=/ccc/work/cont001/ocre/bridelbert/git.parmetis.tar.gz --download-fblaslapack=/ccc/work/cont001/ocre/bridelbert/git.fblaslapack.tar.gz --with-cmake-dir=/ccc/products/cmake-3.13.3/system/default --download-hdf5=/ccc/work/cont001/ocre/bridelbert/hdf5-1.12.0.tar.bz2 --download-netcdf=/ccc/work/cont001/ocre/bridelbert/netcdf-4.5.0.tar.gz --download-pnetcdf=/ccc/work/cont001/ocre/bridelbert/pnetcdf-1.12.1.tar.gz --download-exodusii=/ccc/work/cont001/ocre/bridelbert/v2021-01-20.tar.gz --download-zlib=/ccc/work/cont001/ocre/bridelbert/zlib-1.2.11.tar.gz</span></div></div><div><br></div><div>The piece of code that is responsible is that one :</div><div><br></div><div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures"><span> </span>call PetscViewerHDF5Open(PETSC_COMM_WORLD, "debug_initmesh.h5", FILE_MODE_WRITE, hdf5Viewer, ierr); CHKERRA(ierr)</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures"><span> </span>call PetscViewerPushFormat(hdf5Viewer, PETSC_VIEWER_HDF5_XDMF, ierr); CHKERRA(ierr)</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures"><span> </span>call DMView(dm, hdf5Viewer, ierr); CHKERRA(ierr)</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures"><span> </span>call PetscViewerPopFormat(hdf5Viewer, ierr); CHKERRA(ierr)</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures"><span> </span>call PetscViewerDestroy(hdf5Viewer, ierr); CHKERRA(ierr)</span></div></div><div><br></div><div>I tried with gcc, intel compiler, openmpi 2.x.x or openmpi 4.x.x ... same problems ... can anyone please advise ? It's starting to make me quite crazy ... x(</div><div><br></div><div>Thank you !!!</div><div><br clear="all"><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div><div><div><div><div>Thibault</div></div></div></div></div></div></div></div></div></div></div></div></div>
</div></blockquote></div><br></div></div></div></blockquote></div>