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Hi,
<div class=""><br class="">
</div>
<div class="">Are you sure that you are using the same version of petsc in your batch script? Can you echo $PETSC_DIR and $PETSC_ARCH?
<div class=""><br class="">
</div>
<div class="">Also, it looks like you are using my hydraulic fracturing code VPFHF. That's great and I am glad to see that somebody is continuing to use it. We have not touched the code since a bit after Chukwudi graduated and you must have had to do a few
changes to compile it with petsc 3.17. WOuld you mind contributing your changes back to the main repository? A pull request would be greatly appreciated.</div>
<div class=""><br class="">
</div>
<div class="">Regards,</div>
<div class="">Blaise Bourdin<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Aug 31, 2022, at 9:39 AM, wangxq2020--- via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" class="">petsc-users@mcs.anl.gov</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Hi
<div class=""><span style="white-space:pre" class=""></span>I run the program on the debuged version of PETSC successfuly. Then I want using the optimized version. And configure by ./configure --with-debugging=no --with-packages-download-dir=~/packages_dir
--with-mpich-dir="/public3/soft/mpich/mpich-3.4.2". Then I installed the Hypre package by
<span style="font-size: 14px;" class="">./configure --download-hypre=/public3/home/scg6368/packages_dir/hypre-2.24.0.tar.gz --with-mpich-dir="/public3/soft/mpich/mpich-3.4.2"</span></div>
<div class="">. The result as below</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""><span style="font-size: 14px;" class="">=============================================================================================</span></div>
<div class=""><span style="font-size: 14px;" class=""> Configuring PETSc to compile on your system </span></div>
<div class=""><span style="font-size: 14px;" class="">=============================================================================================</span></div>
<div class=""><span style="font-size: 14px;" class="">============================================================================================= ***** WARNING: You have a version of GNU make older than 4.0. It will
work, but may not support all the parallel testing options. You can install the latest GNU make with your package manager, such as brew or macports,
or use the --download-make option to get the latest GNU make ***** =============================================================================================
============================================================================================= Running configure on HYPRE; this may take several minutes
============================================================================================= =============================================================================================
Running make on HYPRE; this may take several minutes =============================================================================================
============================================================================================= Running make install on HYPRE; this may take several minutes
============================================================================================= Compilers:
</span></div>
<div class=""><span style="font-size: 14px;" class=""> C Compiler: /public3/soft/mpich/mpich-3.4.2/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -g3 -O0 </span></div>
<div class=""><span style="font-size: 14px;" class=""> Version: gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)</span></div>
<div class=""><span style="font-size: 14px;" class=""> C++ Compiler: /public3/soft/mpich/mpich-3.4.2/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -g -O0 -std=gnu++11
-fPIC </span></div>
<div class=""><span style="font-size: 14px;" class=""> Version: g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)</span></div>
<div class=""><span style="font-size: 14px;" class=""> Fortran Compiler: /public3/soft/mpich/mpich-3.4.2/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -g -O0 </span></div>
<div class=""><span style="font-size: 14px;" class=""> Version: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)</span></div>
<div class=""><span style="font-size: 14px;" class="">Linkers:</span></div>
<div class=""><span style="font-size: 14px;" class=""> Shared linker: /public3/soft/mpich/mpich-3.4.2/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -g3 -O0</span></div>
<div class=""><span style="font-size: 14px;" class=""> Dynamic linker: /public3/soft/mpich/mpich-3.4.2/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -g3 -O0</span></div>
<div class=""><span style="font-size: 14px;" class=""> Libraries linked against: -lquadmath -lstdc++ -ldl </span></div>
<div class=""><span style="font-size: 14px;" class="">BlasLapack:</span></div>
<div class=""><span style="font-size: 14px;" class=""> Library: -llapack -lblas</span></div>
<div class=""><span style="font-size: 14px;" class=""> Unknown if this uses OpenMP (try export OMP_NUM_THREADS=<1-4> yourprogram -log_view) </span></div>
<div class=""><span style="font-size: 14px;" class=""> uses 4 byte integers</span></div>
<div class=""><span style="font-size: 14px;" class="">MPI:</span></div>
<div class=""><span style="font-size: 14px;" class=""> Version: 3</span></div>
<div class=""><span style="font-size: 14px;" class=""> Includes: -I/public3/soft/mpich/mpich-3.4.2/include</span></div>
<div class=""><span style="font-size: 14px;" class=""> mpiexec: /public3/soft/mpich/mpich-3.4.2/bin/mpiexec</span></div>
<div class=""><span style="font-size: 14px;" class=""> Implementation: mpich3</span></div>
<div class=""><span style="font-size: 14px;" class=""> MPICH_NUMVERSION: 30402300</span></div>
<div class=""><span style="font-size: 14px;" class="">X:</span></div>
<div class=""><span style="font-size: 14px;" class=""> Library: -lX11</span></div>
<div class=""><span style="font-size: 14px;" class="">pthread:</span></div>
<div class=""><span style="font-size: 14px;" class=""> Library: -lpthread</span></div>
<div class=""><span style="font-size: 14px;" class="">cmake:</span></div>
<div class=""><span style="font-size: 14px;" class=""> Version: 2.8.12</span></div>
<div class=""><span style="font-size: 14px;" class=""> /usr/bin/cmake</span></div>
<div class=""><span style="font-size: 14px;" class="">hypre:</span></div>
<div class=""><span style="font-size: 14px;" class=""> Version: 2.24.0</span></div>
<div class=""><span style="font-size: 14px;" class=""> Includes: -I/public3/home/scg6368/petsc-3.17.2-opt/arch-linux-c-debug/include</span></div>
<div class=""><span style="font-size: 14px;" class=""> Library: -Wl,-rpath,/public3/home/scg6368/petsc-3.17.2-opt/arch-linux-c-debug/lib -L/public3/home/scg6368/petsc-3.17.2-opt/arch-linux-c-debug/lib -lHYPRE</span></div>
<div class=""><span style="font-size: 14px;" class="">regex:</span></div>
<div class=""><span style="font-size: 14px;" class=""> Language used to compile PETSc: C</span></div>
<div class=""><span style="font-size: 14px;" class="">PETSc:</span></div>
<div class=""><span style="font-size: 14px;" class=""> PETSC_ARCH: arch-linux-c-debug</span></div>
<div class=""><span style="font-size: 14px;" class=""> PETSC_DIR: /public3/home/scg6368/petsc-3.17.2-opt</span></div>
<div class=""><span style="font-size: 14px;" class=""> Prefix: <inplace installation></span></div>
<div class=""><span style="font-size: 14px;" class=""> Scalar type: real</span></div>
<div class=""><span style="font-size: 14px;" class=""> Precision: double</span></div>
<div class=""><span style="font-size: 14px;" class=""> Support for __float128</span></div>
<div class=""><span style="font-size: 14px;" class=""> Integer size: 4 bytes</span></div>
<div class=""><span style="font-size: 14px;" class=""> Single library: yes</span></div>
<div class=""><span style="font-size: 14px;" class=""> Shared libraries: yes</span></div>
<div class=""><span style="font-size: 14px;" class=""> Memory alignment from malloc(): 16 bytes</span></div>
<div class=""><span style="font-size: 14px;" class=""> Using GNU make: /usr/bin/gmake</span></div>
<div class=""><span style="font-size: 14px;" class="">xxx=========================================================================xxx</span></div>
<div class=""><span style="font-size: 14px;" class=""> Configure stage complete. Now build PETSc libraries with:</span></div>
<div class=""><span style="font-size: 14px;" class=""> make PETSC_DIR=/public3/home/scg6368/petsc-3.17.2-opt PETSC_ARCH=arch-linux-c-debug all</span></div>
<div class=""><span style="font-size: 14px;" class="">xxx=========================================================================xxx</span></div>
<div class=""><span style="font-size: 14px;" class="">[scg6368@ln1:~/petsc-3.17.2-opt]$ make PETSC_DIR=/public3/home/scg6368/petsc-3.17.2-opt PETSC_ARCH=arch-linux-c-debug all </span></div>
<div class=""><span style="font-size: 14px;" class=""><br class="">
</span></div>
<div class=""><span style="font-size: 14px;" class="">But after I compiled the C file, run the program on the login node by mpiexec -n 2 ./test37. It appears that the program is processed by two cores serially, not in parallel. The result is </span></div>
</div>
<div class="">
<div style="" class=""><span style="font-size: 14px;" class=""> INITIALIZATION TO COMPUTE INITIAL PRESSURE TO CREATE FRACTURE WITH INITIAL VOLUME AT INJECTION RATE = 0.000000e+00 ......</span></div>
<div style="" class=""><span style="font-size: 14px;" class=""> snesU converged in 0 iterations 2.</span></div>
<div style="" class=""><span style="font-size: 14px;" class=""> snesV converged in 0 iterations 2.</span></div>
<div style="" class=""><span style="font-size: 14px;" class=""> V min / max: 1.000000e+00 1.000000e+00</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: ------------------------------------------------------------------------</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: or see
<a href="https://petsc.org/release/faq/#valgrind" class="">https://petsc.org/release/faq/#valgrind</a></span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: or try
<a href="http://valgrind.org" class="">http://valgrind.org</a> on GNU/linux and Apple MacOS to find memory corruption errors</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run </span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: to get more information on the crash.</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: Signal received</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: See
<a href="https://petsc.org/release/faq/" class="">https://petsc.org/release/faq/</a> for trouble shooting.</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: Petsc Release Version 3.17.2, Jun 02, 2022 </span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: ./test37 on a arch-linux-c-opt named ln1.para.bscc by scg6368 Wed Aug 31 21:27:26 2022</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: Configure options --with-debugging=no</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: #1 User provided function() at unknown file:0</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">Abort(59) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0</span></div>
<div style="" class=""><span style="font-size: 14px;" class=""> snesU converged in 0 iterations 2.</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">--------------------------------------------------------------------------</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">Primary job terminated normally, but 1 process returned</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">a non-zero exit code. Per user-direction, the job has been aborted.</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">--------------------------------------------------------------------------</span></div>
<div style="" class=""><span style="font-size: 14px;" class=""> snesV converged in 0 iterations 2.</span></div>
<div style="" class=""><span style="font-size: 14px;" class=""> V min / max: 1.000000e+00 1.000000e+00</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: ------------------------------------------------------------------------</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: or see
<a href="https://petsc.org/release/faq/#valgrind" class="">https://petsc.org/release/faq/#valgrind</a></span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: or try
<a href="http://valgrind.org" class="">http://valgrind.org</a> on GNU/linux and Apple MacOS to find memory corruption errors</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run </span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: to get more information on the crash.</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: Signal received</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: See
<a href="https://petsc.org/release/faq/" class="">https://petsc.org/release/faq/</a> for trouble shooting.</span></div>
<div style="" class=""><span style="font-size: 14px;" class="">[0]PETSC ERROR: Petsc Release Version 3.17.2, Jun 02, 2022 </span></div>
<div style="font-size: 14px;" class=""><br class="">
</div>
</div>
<div style="font-size: 14px;" class="">Then I run the program on the compute nodes by sbatch scipt. It appears that there is no hypre. The content of the script is as follows，the job error file is attached. I don't know where the problem is and would like your
help. Thank you very much。</div>
<div style="font-size: 14px;" class=""><br class="">
</div>
<div style="font-size: 14px;" class="">
<div style="font-family: Consolas, "Courier New", monospace; font-size: 15px; line-height: 20px; white-space: pre;" class="">
<div class=""><span style="color: #008000;" class="">#!/bin/sh</span></div>
<div class=""><span style="color: #008000;" class="">#An example for MPI job.</span></div>
<div class=""><span style="color: #008000;" class="">#SBATCH -J PFM_frac53</span></div>
<div class=""><span style="color: #008000;" class="">#SBATCH -o job_37-1-%j.log</span></div>
<div class=""><span style="color: #008000;" class="">#SBATCH -e job_37-1-%j.err</span></div>
<div class=""><span style="color: #008000;" class="">#SBATCH -N 1</span></div>
<div class=""><span style="color: #008000;" class="">#SBATCH -n 20</span></div>
<div class=""><span style="color: #008000;" class="">#SBATCH --partition=amd_512</span></div>
<div class=""><span style="color: #795e26;" class="">echo</span> Time is <span style="color: #a31515;" class="">
`date`</span></div>
<div class=""><span style="color: #795e26;" class="">echo</span> Directory is <span style="color: #001080;" class="">
$PWD</span></div>
<div class=""><span style="color: #795e26;" class="">echo</span> This job runs on the following nodes:</div>
<div class=""><span style="color: #795e26;" class="">echo</span> <span style="color: #001080;" class="">
$SLURM_JOB_NODELIST</span></div>
<div class=""><span style="color: #795e26;" class="">echo</span> This job has allocated
<span style="color: #001080;" class="">$SLURM_JOB_CPUS_PER_NODE</span> cpu cores.</div>
<div class=""><span style="color: #008000;" class="">#module load intelmpi/2018.update4</span></div>
<div class=""><span style="color: #008000;" class="">#module load intelmpi/2019.update5</span></div>
<div class=""><span style="color: #008000;" class="">#module load intelmpi/2020</span></div>
<div class=""><span style="color: #008000;" class="">#module load hpcx/2.9.0/hpcx-intel-2019.update5</span></div>
<div class="">module load mpi/openmpi/4.1.1-gcc7.3.0</div>
<div class="">module load mpich/3.4.2</div>
<div class=""><span style="color: #008000;" class="">#module load openmpi/4.0.2/gcc/4.8.5</span></div>
<div class=""><span style="color: #008000;" class="">#module load openmpi/3.0.5/gcc/9.2.0</span></div>
<div class=""><span style="color: #008000;" class="">#module load gcc/9.2.0</span></div>
<div class=""><span style="color: #008000;" class="">#MPIRUN=mpirun #Intel mpi and Open MPI</span></div>
<div class="">MPIRUN=mpiexec <span style="color: #008000;" class="">#MPICH</span></div>
<div class=""><span style="color: #008000;" class="">#MPIOPT="-env I_MPI_FABRICS shm:ofi" #Intel MPI 2018 ofa, 2019 and 2020 ofi</span></div>
<div class=""><span style="color: #008000;" class="">#MPIOPT="--mca btl self,sm,openib --mca btl_openib_cpc_include rdmacm --mca btl_openib_if_include mlx5_0:1" #Open MPI</span></div>
<div class="">MPIOPT=<span style="color: #a31515;" class="">"-iface ib0"</span> <span style="color: #008000;" class="">
#MPICH3</span></div>
<div class=""><span style="color: #008000;" class="">#MPIOPT=</span></div>
<div class=""><span style="color: #008000;" class="">#$MPIRUN $MPIOPT ./mpiring</span></div>
<div class=""><span style="color: #001080;" class="">$MPIRUN</span> ./test37 -options_file options/test37.opts -p runtest37-1</div>
</div>
</div>
<div class=""><span style="font-size: 14px;" class=""><br class="">
</span></div>
<span id="cid:69681C9C-AEE1-4012-A272-6DFCA6F2C473"><job_37-1-1233983.err></span></div>
</blockquote>
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<div>— <br class="">
Tier 1 Canada Research Chair in Mathematical and Computational Aspects of Solid Mechanics</div>
<div>Professor, Department of Mathematics & Statistics<br class="">
Hamilton Hall room 409A, McMaster University<br class="">
1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada <br class="">
<a href="https://www.math.mcmaster.ca/bourdin" class="">https://www.math.mcmaster.ca/bourdin</a> | +1 (905) 525 9140 ext. 27243</div>
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