[petsc-users] Problem about optimized version
Matthew Knepley
knepley at gmail.com
Wed Aug 31 08:55:05 CDT 2022
On Wed, Aug 31, 2022 at 9:40 AM wangxq2020--- via petsc-users <
petsc-users at mcs.anl.gov> wrote:
> Hi
> 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 ./configure
> --download-hypre=/public3/home/scg6368/packages_dir/hypre-2.24.0.tar.gz
> --with-mpich-dir="/public3/soft/mpich/mpich-3.4.2"
> . The result as below
>
>
> =============================================================================================
> Configuring PETSc to compile on your system
>
>
> =============================================================================================
> =============================================================================================
> ***** 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:
>
>
> 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
> Version: gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
> 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
> Version: g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
> 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
> Version: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
> Linkers:
> 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
> 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
> Libraries linked against: -lquadmath -lstdc++ -ldl
> BlasLapack:
> Library: -llapack -lblas
> Unknown if this uses OpenMP (try export OMP_NUM_THREADS=<1-4>
> yourprogram -log_view)
> uses 4 byte integers
> MPI:
> Version: 3
> Includes: -I/public3/soft/mpich/mpich-3.4.2/include
> mpiexec: /public3/soft/mpich/mpich-3.4.2/bin/mpiexec
> Implementation: mpich3
> MPICH_NUMVERSION: 30402300
> X:
> Library: -lX11
> pthread:
> Library: -lpthread
> cmake:
> Version: 2.8.12
> /usr/bin/cmake
> hypre:
> Version: 2.24.0
> Includes:
> -I/public3/home/scg6368/petsc-3.17.2-opt/arch-linux-c-debug/include
> 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
> regex:
> Language used to compile PETSc: C
> PETSc:
> PETSC_ARCH: arch-linux-c-debug
> PETSC_DIR: /public3/home/scg6368/petsc-3.17.2-opt
> Prefix: <inplace installation>
> Scalar type: real
> Precision: double
> Support for __float128
> Integer size: 4 bytes
> Single library: yes
> Shared libraries: yes
> Memory alignment from malloc(): 16 bytes
> Using GNU make: /usr/bin/gmake
>
> xxx=========================================================================xxx
> Configure stage complete. Now build PETSc libraries with:
> make PETSC_DIR=/public3/home/scg6368/petsc-3.17.2-opt
> PETSC_ARCH=arch-linux-c-debug all
>
> xxx=========================================================================xxx
> [scg6368 at ln1:~/petsc-3.17.2-opt]$ make
> PETSC_DIR=/public3/home/scg6368/petsc-3.17.2-opt
> PETSC_ARCH=arch-linux-c-debug all
>
> 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
>
This usually means that you have run with an mpiexec from a different MPI
installation than the one you compiled PETSc with.
Thanks,
Matt
> INITIALIZATION TO COMPUTE INITIAL PRESSURE TO CREATE FRACTURE WITH
> INITIAL VOLUME AT INJECTION RATE = 0.000000e+00 ......
> snesU converged in 0 iterations 2.
> snesV converged in 0 iterations 2.
> V min / max: 1.000000e+00 1.000000e+00
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind
> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple MacOS
> 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 https://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.17.2, Jun 02, 2022
> [0]PETSC ERROR: ./test37 on a arch-linux-c-opt named ln1.para.bscc by
> scg6368 Wed Aug 31 21:27:26 2022
> [0]PETSC ERROR: Configure options --with-debugging=no
> [0]PETSC ERROR: #1 User provided function() at unknown file:0
> [0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is
> causing the crash.
> Abort(59) on node 0 (rank 0 in comm 0): application called
> MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> snesU converged in 0 iterations 2.
> --------------------------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> --------------------------------------------------------------------------
> snesV converged in 0 iterations 2.
> V min / max: 1.000000e+00 1.000000e+00
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind
> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple MacOS
> 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 https://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.17.2, Jun 02, 2022
>
> 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。
>
> #!/bin/sh
> #An example for MPI job.
> #SBATCH -J PFM_frac53
> #SBATCH -o job_37-1-%j.log
> #SBATCH -e job_37-1-%j.err
> #SBATCH -N 1
> #SBATCH -n 20
> #SBATCH --partition=amd_512
> echo Time is `date`
> echo Directory is $PWD
> echo This job runs on the following nodes:
> echo $SLURM_JOB_NODELIST
> echo This job has allocated $SLURM_JOB_CPUS_PER_NODE cpu cores.
> #module load intelmpi/2018.update4
> #module load intelmpi/2019.update5
> #module load intelmpi/2020
> #module load hpcx/2.9.0/hpcx-intel-2019.update5
> module load mpi/openmpi/4.1.1-gcc7.3.0
> module load mpich/3.4.2
> #module load openmpi/4.0.2/gcc/4.8.5
> #module load openmpi/3.0.5/gcc/9.2.0
> #module load gcc/9.2.0
> #MPIRUN=mpirun #Intel mpi and Open MPI
> MPIRUN=mpiexec #MPICH
> #MPIOPT="-env I_MPI_FABRICS shm:ofi" #Intel MPI 2018 ofa, 2019 and 2020 ofi
> #MPIOPT="--mca btl self,sm,openib --mca btl_openib_cpc_include rdmacm
> --mca btl_openib_if_include mlx5_0:1" #Open MPI
> MPIOPT="-iface ib0" #MPICH3
> #MPIOPT=
> #$MPIRUN $MPIOPT ./mpiring
> $MPIRUN ./test37 -options_file options/test37.opts -p runtest37-1
>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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