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Assigned to lik...@wp.pl by me
Karol Lewandowski
Oct 28, 2021, 5:51:20 AM10/28/21
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Hello everyone,
I am trying to install MoFEM on ARCHIE-WeSt supercomputer using spack with a script. However, it requires loading the correct modules (like compilers), for the installation to proceed successfully. Can anyone share their setup?
ignathanas
Oct 28, 2021, 6:14:55 AM10/28/21
to MoFEM Q&A
Hello Karol,
Here is the bash file I used:
#!/bin/bash
#======================================================
#
# Job script for running MoFEM on a single node
#
#======================================================
#======================================================
# Propogate environment variables to the compute node
#SBATCH --export=ALL
#
# Run in the standard partition (queue)
#SBATCH --partition=standard
#
# Specify project account
#SBATCH --account=kaczmarczyk-fsfnsc
#
# No. of tasks required (max. of 40)
#SBATCH --ntasks=20
#
# Ensure the node is not shared with another job
#SBATCH --exclusive
#
# Specify (hard) runtime (HH:MM:SS)
#SBATCH --time=12:00:00
#
# Job name
#SBATCH --job-name=cn_2
#
# Output file
#SBATCH --output=slurm-%j.out
#======================================================
module purge
# choose which version to load
# module load openfoam/gcc-4.8.5/extend-3.2
# module load openfoam/gcc-4.8.5/extend-4.0
# module load openfoam/intel-2018.2/v1712
module load OpenMPI/3.1.3-GCC-8.2.0-2.31.1
. ~/mofem_install/spack/share/spack/setup-env.sh
# spack load openmpi
#=========================================================
# Prologue script to record job details
# Do not change the line below
#=========================================================
/opt/software/scripts/job_prologue.sh
#----------------------------------------------------------
export EXECUTABLE=path_to_exe
export MESH_FILE=restart_27.h5m
mpirun -np $SLURM_NPROCS $EXECUTABLE -my_file $MESH_FILE 2>&1 | tee -a log
#=========================================================
# Epilogue script to record job endtime and runtime
# Do not change the line below
#=========================================================
/opt/software/scripts/job_epilogue.sh
#----------------------------------------------------------
Lukasz Kaczmraczyk
Oct 28, 2021, 7:46:17 AM10/28/21
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Hello,
You have to load module,
module load OpenMPI/3.1.3-GCC-8.2.0-2.31.1
and you run
spack compiler find
spack external find
However openblas can not ne installed with gcc8.2.0, so I have installed gcc8.3.0 with spack,
spack install gcc _AT_ 8.3.0
spack compiler find
and then you do standard installation
spack install --only dependencies mofem-cephas%gcc _AT_ 8.3.0
spack dev-build -j 4 --source-path $HOME/mofem_install/mofem-cephas \
--keep-prefix \
mofem-cephas _AT_ develop~copy_user_modules%gcc _AT_ 8.3.0
and then users modules as usual.
Karol, would be good to add section to documentation on Doxygen about installation on ARCHIE-WeSt. Sooner or later someone will have the same issue.
Regards,
L.
Karol Lewandowski
Oct 28, 2021, 9:31:00 AM10/28/21
to MoFEM Q&A
When I try to install MoFEM I get:
Error: No compilers with spec gcc _AT_ 8.3.0 found for operating system centos7 and target skylake_avx512.
Lukasz Kaczmraczyk
Oct 28, 2021, 10:08:30 AM10/28/21
to MoFEM Q&A
Oh, replace "_AT_" with "@". This is because of google groups.
Karol Lewandowski
Oct 28, 2021, 10:09:16 AM10/28/21
to MoFEM Q&A
Lukasz, I did it of course
Karol Lewandowski
Oct 28, 2021, 10:09:56 AM10/28/21
to MoFEM Q&A
I put that _AT_ for the same reason you did. :)
Lukasz Kaczmraczyk
Oct 28, 2021, 10:14:52 AM10/28/21
to MoFEM Q&A
What have you done?
spack install gcc _AT_ 8.3.0
spack compiler find
Karol Lewandowski
Oct 28, 2021, 10:16:18 AM10/28/21
to MoFEM Q&A
It did not add this newly installed compiler
Lukasz Kaczmraczyk
Oct 28, 2021, 10:18:31 AM10/28/21
to MoFEM Q&A
Try
spack load gcc _AT_ 8.3.0
spack compiler find
Karol Lewandowski
Oct 28, 2021, 10:21:08 AM10/28/21
to MoFEM Q&A
Ok, now it is installing.
I also forgot about the loading...
Karol Lewandowski
Oct 28, 2021, 7:58:37 PM10/28/21
to MoFEM Q&A
When installing netlib-scalapack-2.1.0
CMake throws the following error:
CMake throws the following error:
>> 17 CMake Error at CMakeLists.txt:17 (if):
18 if given arguments:
19
20 "GNU" "STREQUAL" "GNU" "AND" "CMAKE_Fortran_COMPILER_VERSION" "VERSION_GREATER_EQUAL" "10"
Are we missing something or the script needs to be updated?
Lukasz Kaczmraczyk
Oct 29, 2021, 6:18:15 AM10/29/21
to MoFEM Q&A
Oh, I know this. You have to install newest cmake with spack, and then load cmake.
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