[petsc-users] PDSLin hybrid solver performance with PETSc
Afrah Najib
afrah.nacib at gmail.com
Mon Apr 30 06:20:32 CDT 2018
Hi all,
I am testing PDSLin hybrid solver performance with PETSc krylov method on a
SPD matrix called audik_1 matrix(format is ijv full matrix ordered by rows)
https://sparse.tamu.edu/GHS_psdef/audikw_1
I am also running on cluster with Intel(R) Xeon(R) CPU E5-2680 v4 @
2.40GHz processor and 28 core , 128 ; 512GB per node
but it takes a lot of time for Schur complement factorization.
Compiler Subdomains processors Precond TmatrixPartition TmatrixDist
Tfactorise TcompApproSchur TprepApproSchur Tfactoschur Tprecond_Total Tsolve
gcc 8 128 Sparse 23.49532 0.6009915 6.059546 212.8243 0.04027608 38.74885
257.6796 13.69609
gcc 8 16 Sparse 11.864 0.4385703 27.23499 1390.153 0.5523289 55.20706
1473.207 4.213825
gcc 8 32 Sparse 9.912792 0.2592737 16.79125 934.3571 0.2372452 49.39175
1000.813 37.2029
gcc 8 64 Sparse 12.61929 0.2336042 8.2316 632.839 0.1113939 52.21551
693.4153 13.94034
My PETSc in stallation configuration is like this:
export PETSC_DIR=/X/petsc
export PETSC_ARCH=arch-real
./configure PETSC_DIR=/X/petsc \
prefix=/X/petsc/petsc-install \
PETSC_ARCH=arch-real \
--with-debugging=0 \
--with-cc=/Y/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc \
--with-cxx=/Y/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicxx \
--with-fc=/Y/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90 \
--with-valgrind=1 \
--with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0 \
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9 \
--with-blas-lapack-dir=/Y/progs/intel/compilers_and_libraries_2017.0.098/linux/mkl/lib/intel64.
*My slurm scrpt content is like this:*
#!/bin/bash -l
#SBATCH -J "Paudik16"
#SBATCH -A X
#SBATCH -p X
#SBATCH --exclusive
#SBATCH -o Paudik_8_2_16.%j.out
#SBATCH -e Paudik_8_2_16.%j.err
#SBATCH -N 8
#SBATCH --ntasks-per-node=2
#SBATCH --cpus-per-task=1
export KMP_AFFINITY=verbose,disabled
export MKL_NUM_THREADS=${SLURM_CPUS_PER_TASK}
export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
module purge
module load gcc/7.1.0
module load mpi/openmpi-3.0.0-gcc-7.1.0
module load intel/mkl_2017.0.098
file=input.in
matrixFile=~/dataDir/ijv/audikw_1.ijv
mpirun -np $SLURM_NTASKS ./dtest_pdslin $file $matrixFile
*I attached an output of one file along with the input configuration of
PDSLin.*
Any idea of how to enhance these results.
Note in PDSLin, I tried with parallel Schur permutation but I got the
following error :
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 8 FPE: Floating Point
E/Xception,probably divide by zero
[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[1]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[1]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[1]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[1]PETSC ERROR: to get more information on the crash.
[1]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 59.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
e/Xactly when Open MPI kills them.
--------------------------------------------------------------------------
[13]PETSC ERROR:
------------------------------------------------------------------------
[13]PETSC ERROR: Caught signal number 8 FPE: Floating Point
E/Xception,probably divide by zero
[13]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[13]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[13]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[13]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[13]PETSC ERROR: to get more information on the crash.
[11]PETSC ERROR:
------------------------------------------------------------------------
[11]PETSC ERROR: Caught signal number 8 FPE: Floating Point
E/Xception,probably divide by zero
[11]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[11]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[11]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[11]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[11]PETSC ERROR: to get more information on the crash.
[3]PETSC ERROR:
------------------------------------------------------------------------
[3]PETSC ERROR: Caught signal number 8 FPE: Floating Point
E/Xception,probably divide by zero
[3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[3]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[3]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[3]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[3]PETSC ERROR: to get more information on the crash.
[3]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[3]PETSC ERROR: Signal received
[3]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[3]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[3]PETSC ERROR: [9]PETSC ERROR:
------------------------------------------------------------------------
[9]PETSC ERROR: Caught signal number 8 FPE: Floating Point
E/Xception,probably divide by zero
[9]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[9]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[9]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[9]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[9]PETSC ERROR: to get more information on the crash.
[7]PETSC ERROR:
------------------------------------------------------------------------
[7]PETSC ERROR: Caught signal number 8 FPE: Floating Point
E/Xception,probably divide by zero
[7]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[7]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[7]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[7]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[7]PETSC ERROR: to get more information on the crash.
[5]PETSC ERROR:
------------------------------------------------------------------------
[5]PETSC ERROR: Caught signal number 8 FPE: Floating Point
E/Xception,probably divide by zero
[5]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[5]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[5]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[5]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[5]PETSC ERROR: to get more information on the crash.
[5]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[5]PETSC ERROR: Signal received
[5]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[5]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[5]PETSC ERROR: [15]PETSC ERROR:
------------------------------------------------------------------------
[15]PETSC ERROR: Caught signal number 8 FPE: Floating Point
E/Xception,probably divide by zero
[15]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[15]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[15]PETSC ERROR: [13]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[13]PETSC ERROR: Signal received
[13]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
for trouble shooting.
[13]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[13]PETSC ERROR: ./dtest_pdslin on a named s060 by afarea Mon Apr 30
05:29:53 2018
[13]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[11]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[11]PETSC ERROR: Signal received
[11]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
for trouble shooting.
[11]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[11]PETSC ERROR: ./dtest_pdslin on a named s054 by afarea Mon Apr 30
05:29:53 2018
[11]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
./dtest_pdslin on a named s034 by afarea Mon Apr 30 05:29:53 2018
[3]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[3]PETSC ERROR: #1 User provided function() line 0 in unknown file
[9]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[9]PETSC ERROR: Signal received
[9]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[9]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[9]PETSC ERROR: ./dtest_pdslin on a named s044 by afarea Mon Apr 30
05:29:53 2018
[9]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[7]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[7]PETSC ERROR: Signal received
[7]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[7]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[7]PETSC ERROR: ./dtest_pdslin on a named s036 by afarea Mon Apr 30
05:29:53 2018
[7]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[7]PETSC ERROR: #1 User provided function() line 0 in unknown file
./dtest_pdslin on a named s035 by afarea Mon Apr 30 05:29:53 2018
[5]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[5]PETSC ERROR: #1 User provided function() line 0 in unknown file
configure using --with-debugging=yes, recompile, link, and run
[15]PETSC ERROR: to get more information on the crash.
[15]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[15]PETSC ERROR: Signal received
[15]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
for trouble shooting.
[15]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[15]PETSC ERROR: ./dtest_pdslin on a named s071 by afarea Mon Apr 30
05:29:53 2018
[13]PETSC ERROR: #1 User provided function() line 0 in unknown file
[11]PETSC ERROR: #1 User provided function() line 0 in unknown file
[9]PETSC ERROR: #1 User provided function() line 0 in unknown file
[15]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[15]PETSC ERROR: #1 User provided function() line 0 in unknown file
[1]PETSC ERROR: Signal received
[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[1]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[1]PETSC ERROR: ./dtest_pdslin on a named f002 by afarea Mon Apr 30
05:29:53 2018
[1]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[1]PETSC ERROR: #1 User provided function() line 0 in unknown file
[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[1]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[1]PETSC ERROR: ./dtest_pdslin on a named f002 by afarea Mon Apr 30
05:29:53 2018
[1]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[1]PETSC ERROR: #1 User provided function() line 0 in unknown file
[6]PETSC ERROR:
------------------------------------------------------------------------
[6]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch system) has told this process to end
[6]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[6]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[6]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[6]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[6]PETSC ERROR: to get more information on the crash.
[6]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[6]PETSC ERROR: Signal received
[6]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[6]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[6]PETSC ERROR: ./dtest_pdslin on a named s036 by afarea Mon Apr 30
05:29:53 2018
[6]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[6]PETSC ERROR: #1 User provided function() line 0 in unknown file
[4]PETSC ERROR:
------------------------------------------------------------------------
[4]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch system) has told this process to end
[4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[4]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[4]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[4]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[4]PETSC ERROR: to get more information on the crash.
[4]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[4]PETSC ERROR: Signal received
[4]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[4]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[4]PETSC ERROR: ./dtest_pdslin on a named s035 by afarea Mon Apr 30
05:29:53 2018
[4]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[4]PETSC ERROR: ./dtest_pdslin on a named s035 by afarea Mon Apr 30
05:29:53 2018
[4]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[4]PETSC ERROR: #1 User provided function() line 0 in unknown file
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch system) has told this process to end
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[0]PETSC ERROR: ./dtest_pdslin on a named f002 by afarea Mon Apr 30
05:29:53 2018
[0]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file
[10]PETSC ERROR:
------------------------------------------------------------------------
[10]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch system) has told this process to end
[10]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[10]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[10]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[10]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[10]PETSC ERROR: to get more information on the crash.
[10]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[10]PETSC ERROR: Signal received
[10]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
for trouble shooting.
[10]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[10]PETSC ERROR: ./dtest_pdslin on a named s054 by afarea Mon Apr 30
05:29:53 2018
[8]PETSC ERROR: ./dtest_pdslin on a named s044 by afarea Mon Apr 30
05:29:53 2018
[8]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[8]PETSC ERROR: #1 User provided function() line 0 in unknown file
[14]PETSC ERROR:
------------------------------------------------------------------------
[14]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch system) has told this process to end
[14]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[14]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[14]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[14]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[14]PETSC ERROR: to get more information on the crash.
[14]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[14]PETSC ERROR: Signal received
[14]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
for trouble shooting.
[14]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[14]PETSC ERROR: ./dtest_pdslin on a named s071 by afarea Mon Apr 30
05:29:53 2018
[14]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[14]PETSC ERROR: #1 User provided function() line 0 in unknown file
[15]PETSC ERROR:
------------------------------------------------------------------------
[15]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch system) has told this process to end
[15]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[15]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[15]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[15]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[15]PETSC ERROR: to get more information on the crash.
[15]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[15]PETSC ERROR: Signal received
[15]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
for trouble shooting.
[15]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[15]PETSC ERROR: ./dtest_pdslin on a named s071 by afarea Mon Apr 30
05:29:53 2018
[15]PETSC ERROR: #2 User provided function() line 0 in unknown file
[2]PETSC ERROR:
------------------------------------------------------------------------
[2]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch system) has told this process to end
[2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[2]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[2]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[2]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[2]PETSC ERROR: to get more information on the crash.
[2]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[2]PETSC ERROR: Signal received
[2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[2]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[2]PETSC ERROR: ./dtest_pdslin on a named s034 by afarea Mon Apr 30
05:29:53 2018
[2]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[2]PETSC ERROR: #1 User provided function() line 0 in unknown file
[3]PETSC ERROR:
------------------------------------------------------------------------
[3]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch system) has told this process to end
[3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[3]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[3]PETSC ERROR: or try http://valgrind.org on GNU/linu/X and Apple Mac OS
/X to find memory corruption errors
[3]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[3]PETSC ERROR: to get more information on the crash.
[3]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[3]PETSC ERROR: Signal received
[3]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[3]PETSC ERROR: Petsc Release Version 3.9.0, unknown
[3]PETSC ERROR: ./dtest_pdslin on a named s034 by afarea Mon Apr 30
05:29:53 2018
[3]PETSC ERROR: Configure options PETSC_DIR=/X/petsc
prefi/X=/X/petsc/petsc-install PETSC_ARCH=arch-real --with-debugging=0
--with-cc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpicc
--with-c/X/X=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpic/X/X
--with-fc=/okyanus/progs/openmpi/openmpi-3.0.0-gcc-7.1.0/bin/mpif90
--with-valgrind=1 --with-valgrind-dir=/X/root/usr/local/valgrind-3.13.0
--with-hwloc-dir=/X/root/usr/local/hwloc-1.11.9
--with-blaslapack-dir=/okyanus/progs/intel/compilers_and_libraries_2017.0.098/linu/X/mkl/lib/intel64
[3]PETSC ERROR: #2 User provided function() line 0 in unknown file
[f002:38724] 17 more processes have sent help message help-mpi-api.t/Xt /
mpi-abort
[f002:38724] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages
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