I mean the output of apt list --installed > TUB22.txt
I will look at it later today and get back to you.
seems like the system path for openmpi differs from ubuntu. Thus, the need to fix openmpi.py.
Can you try the following :
- check whether
mpi.h
is in/usr/include/openmpi
- otherwise, run:
python3 -c 'import distro; print(distro.name().lower())'
and check whether it returns something else thanubuntu
. - edit openmpi.py and add a section about tuxedo.
- rerun the compilation
- if OK, open a pull request
- if not, we will investigate further.
Finally, one can also override CC
with export CC=$(which mpicc)
hello nabil,
thanks for your help.
check whether
mpi.h
is in/usr/include/openmpi
there is no openmpi folder in /usr/include not mpi.h directly in that folder
otherwise, run:
python3 -c 'import distro; print(distro.name().lower())'
and check whether it returns something else thanubuntu
.
I get tuxedo os
, so not sure how salome scrip gets the ubuntu of the folder SALOME-master-native-UB22.04
created during the compilation, does it get it with a different command maybe?
also tested with import platform; platform.linux_distribution()[0].lower()
(got from the python script, but I get an error that platform does not have linux_distribution() property, maybe something to correct? or it does this properties for the rocky/centos/fedora?
so I change line 34 of the python file from:
elif any(distribution in distro.name().lower() for distribution in ["debian", "ubuntu"]) :
to:
elif any(distribution in distro.name().lower() for distribution in ["debian", "ubuntu", "tuxedo os"]) :
the compilation now works, I am not sure how to do the gitpull. would love if instead of doing it for me, you give me a brief explication how to do it so I can do it for any other problems I find in the future.
also:
in the compilation I also observed this (is it normal?):
Compilation of CONFIGURATION … ignored
Compilation of PERSALYS … KO
for openmpi, can you open a pull request on sat_salome following this description ?
concerning PERSALYS, can you share the log file - please check also this thread concerning latex
hello nabil,
I had the time to re tested today, I am having issues that several things are asking for a user logging (to https://codev-tuleap.cea.fr) during the compilation such as paravis
PARAVIS: GIT:https://github.com/SalomePlatform/paravis.git tag:master ..... Username for 'https://codev-tuleap.cea.fr':
Password for 'https://codev-tuleap.cea.fr':
Username for 'https://codev-tuleap.cea.fr':
Password for 'https://codev-tuleap.cea.fr':
WARNING: <KO> launch command rc=1 cwd=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES:
set -x
git clone --recurse-submodules https://github.com/SalomePlatform/paravis.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS
res=$?
if [ $res -eq 0 ]; then
touch -d "$(git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS/.git log -1 --format="%ai")" /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS
fi
exit $res
WARNING: <KO> result command stdout&stderr:
b"+ git clone --recurse-submodules https://github.com/SalomePlatform/paravis.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS\nCloning into '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS'...\nSubmodule 'src/Plugins/MEDReader' (https://codev-tuleap.cea.fr/plugins/git/salome/medreader) registered for path 'src/Plugins/MEDReader'\nCloning into '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS/src/Plugins/MEDReader'...\nfatal: Authentication failed for 'https://codev-tuleap.cea.fr/plugins/git/salome/medreader/'\nfatal: clone of 'https://codev-tuleap.cea.fr/plugins/git/salome/medreader' into submodule path '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS/src/Plugins/MEDReader' failed\nFailed to clone 'src/Plugins/MEDReader'. Retry scheduled\nCloning into '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS/src/Plugins/MEDReader'...\nfatal: Authentication failed for 'https://codev-tuleap.cea.fr/plugins/git/salome/medreader/'\nfatal: clone of 'https://codev-tuleap.cea.fr/plugins/git/salome/medreader' into submodule path '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS/src/Plugins/MEDReader' failed\nFailed to clone 'src/Plugins/MEDReader' a second time, aborting\n+ res=1\n+ [ 1 -eq 0 ]\n+ exit 1\n"
git command failed! Wait 30 seconds and give an other try (2/3)
WARNING: <KO> launch command rc=128 cwd=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES:
set -x
git clone --recurse-submodules https://github.com/SalomePlatform/paravis.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS
res=$?
if [ $res -eq 0 ]; then
touch -d "$(git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS/.git log -1 --format="%ai")" /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS
fi
exit $res
WARNING: <KO> result command stdout&stderr:
b"+ git clone --recurse-submodules https://github.com/SalomePlatform/paravis.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS\nfatal: destination path '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS' already exists and is not an empty directory.\n+ res=128\n+ [ 128 -eq 0 ]\n+ exit 128\n"
git command failed! Wait 30 seconds and give an other try (3/3)
WARNING: <KO> launch command rc=128 cwd=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES:
set -x
git clone --recurse-submodules https://github.com/SalomePlatform/paravis.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS
res=$?
if [ $res -eq 0 ]; then
touch -d "$(git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS/.git log -1 --format="%ai")" /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS
fi
exit $res
WARNING: <KO> result command stdout&stderr:
b"+ git clone --recurse-submodules https://github.com/SalomePlatform/paravis.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS\nfatal: destination path '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/PARAVIS' already exists and is not an empty directory.\n+ res=128\n+ [ 128 -eq 0 ]\n+ exit 128\n"
KO
Hi Franco,
it is a known issue which is being about to be fixed
hello nabil,
I tested in my pc to recompile from zero using the script with the following lines:
SALOME_WORKSPACE=$PWD
export SALOME_WORKSPACE=$PWD
git clone https://github.com/SalomePlatform/sat.git SAT
git clone https://github.com/SalomePlatform/sat_salome.git SAT_SALOME
systemTux='tuxedo os'
sed -i "s|, \"ubuntu\"|, \"ubuntu\", \"$systemTux\"|" $SALOME_WORKSPACE/SAT_SALOME/products/env_scripts/scotch.py
cd $SALOME_WORKSPACE
SAT/sat init --add_project $PWD/SAT_SALOME/salome.pyconf
the sed changes correctly the file as it can be seen in the resulting line here:
elif any(distribution in distro.name().lower() for distribution in ["debian", "ubuntu", "tuxedo os"]) :
but during the compilation scotch still fails.
I checked that
prereq_inc='/usr/include/scotch-long'
prereq_lib='/usr/lib/x86_64-linux-gnu/scotch-long'
are correctly there and there are.
same error:
In file included from dummysizes.c:94:
common.h:125:21: fatal error: mpi.h: No such file or directory
125 | #include <mpi.h>
| ^~~~~~~
compilation terminated.
make[2]: *** [Makefile:3104: ptdummysizes] Error 1
make[2]: *** Waiting for unfinished jobs…
make[2]: Leaving directory ‘/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/BUILD/scotch/src/libscotch’
make[1]: *** [Makefile:72: ptscotch] Error 2
make[1]: Leaving directory ‘/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/BUILD/scotch/src/libscotch’
make: *** [Makefile:103: libptscotch] Error 2
ERROR on make
now with sat I am getting KO for CAS and mmgpluging:
CAS: GIT:http://git.dev.opencascade.org/repos/occt.git tag:CR780-SALOME-PATCH . WARNING: <KO> launch command rc=1 cwd=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES:
set -x
git clone http://git.dev.opencascade.org/repos/occt.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS
if [ $? -ne 0 ]; then
exit 1
fi
git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS/.git --work-tree=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS checkout CR780-SALOME-PATCH
if [ $? -ne 0 ]; then
exit 1
fi
git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS/.git status | grep HEAD
if [ $? -ne 0 ]; then
exit 1
fi
touch -d "$(git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS/.git log -1 --format="%ai")" /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS
if [ $? -ne 0 ]; then
exit 1
fi
exit 0
WARNING: <KO> result command stdout&stderr:
b"+ git clone http://git.dev.opencascade.org/repos/occt.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS\nCloning into '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS'...\nUpdating files: 86% (31230/36063)\rUpdating files: 87% (31375/36063)\rUpdating files: 88% (31736/36063)\rUpdating files: 89% (32097/36063)\rUpdating files: 90% (32457/36063)\rUpdating files: 91% (32818/36063)\rUpdating files: 92% (33178/36063)\rUpdating files: 93% (33539/36063)\rUpdating files: 94% (33900/36063)\rUpdating files: 95% (34260/36063)\rUpdating files: 96% (34621/36063)\rUpdating files: 97% (34982/36063)\rUpdating files: 98% (35342/36063)\rUpdating files: 99% (35703/36063)\rUpdating files: 100% (36063/36063)\rUpdating files: 100% (36063/36063), done.\n+ [ 0 -ne 0 ]\n+ git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS/.git --work-tree=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS checkout CR780-SALOME-PATCH\nSwitched to a new branch 'CR780-SALOME-PATCH'\nBranch 'CR780-SALOME-PATCH' set up to track remote branch 'CR780-SALOME-PATCH' from 'origin'.\n+ [ 0 -ne 0 ]\n+ git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS/.git status\n+ grep HEAD\n+ [ 1 -ne 0 ]\n+ exit 1\n"
git command failed! Wait 30 seconds and give an other try (2/3)
WARNING: <KO> launch command rc=1 cwd=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES:
set -x
git clone http://git.dev.opencascade.org/repos/occt.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS
if [ $? -ne 0 ]; then
exit 1
fi
git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS/.git --work-tree=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS checkout CR780-SALOME-PATCH
if [ $? -ne 0 ]; then
exit 1
fi
git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS/.git status | grep HEAD
if [ $? -ne 0 ]; then
exit 1
fi
touch -d "$(git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS/.git log -1 --format="%ai")" /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS
if [ $? -ne 0 ]; then
exit 1
fi
exit 0
WARNING: <KO> result command stdout&stderr:
b"+ git clone http://git.dev.opencascade.org/repos/occt.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS\nfatal: destination path '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS' already exists and is not an empty directory.\n+ [ 128 -ne 0 ]\n+ exit 1\n"
git command failed! Wait 30 seconds and give an other try (3/3)
WARNING: <KO> launch command rc=1 cwd=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES:
set -x
git clone http://git.dev.opencascade.org/repos/occt.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS
if [ $? -ne 0 ]; then
exit 1
fi
git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS/.git --work-tree=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS checkout CR780-SALOME-PATCH
if [ $? -ne 0 ]; then
exit 1
fi
git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS/.git status | grep HEAD
if [ $? -ne 0 ]; then
exit 1
fi
touch -d "$(git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS/.git log -1 --format="%ai")" /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS
if [ $? -ne 0 ]; then
exit 1
fi
exit 0
WARNING: <KO> result command stdout&stderr:
b"+ git clone http://git.dev.opencascade.org/repos/occt.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS\nfatal: destination path '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/CAS' already exists and is not an empty directory.\n+ [ 128 -ne 0 ]\n+ exit 1\n"
KO
mmgplugin: GIT:https://github.com/SalomePlatform/mmgplugin.git tag:main ....... WARNING: <KO> launch command rc=1 cwd=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES:
set -x
git clone https://github.com/SalomePlatform/mmgplugin.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin
if [ $? -ne 0 ]; then
exit 1
fi
git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin/.git --work-tree=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin checkout main
if [ $? -ne 0 ]; then
exit 1
fi
git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin/.git status | grep HEAD
if [ $? -ne 0 ]; then
exit 1
fi
touch -d "$(git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin/.git log -1 --format="%ai")" /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin
if [ $? -ne 0 ]; then
exit 1
fi
exit 0
WARNING: <KO> result command stdout&stderr:
b"+ git clone https://github.com/SalomePlatform/mmgplugin.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin\nCloning into '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin'...\n+ [ 0 -ne 0 ]\n+ git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin/.git --work-tree=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin checkout main\nAlready on 'main'\nYour branch is up to date with 'origin/main'.\n+ [ 0 -ne 0 ]\n+ git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin/.git status\n+ grep HEAD\n+ [ 1 -ne 0 ]\n+ exit 1\n"
git command failed! Wait 30 seconds and give an other try (2/3)
WARNING: <KO> launch command rc=1 cwd=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES:
set -x
git clone https://github.com/SalomePlatform/mmgplugin.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin
if [ $? -ne 0 ]; then
exit 1
fi
git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin/.git --work-tree=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin checkout main
if [ $? -ne 0 ]; then
exit 1
fi
git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin/.git status | grep HEAD
if [ $? -ne 0 ]; then
exit 1
fi
touch -d "$(git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin/.git log -1 --format="%ai")" /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin
if [ $? -ne 0 ]; then
exit 1
fi
exit 0
WARNING: <KO> result command stdout&stderr:
b"+ git clone https://github.com/SalomePlatform/mmgplugin.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin\nfatal: destination path '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin' already exists and is not an empty directory.\n+ [ 128 -ne 0 ]\n+ exit 1\n"
git command failed! Wait 30 seconds and give an other try (3/3)
WARNING: <KO> launch command rc=1 cwd=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES:
set -x
git clone https://github.com/SalomePlatform/mmgplugin.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin
if [ $? -ne 0 ]; then
exit 1
fi
git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin/.git --work-tree=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin checkout main
if [ $? -ne 0 ]; then
exit 1
fi
git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin/.git status | grep HEAD
if [ $? -ne 0 ]; then
exit 1
fi
touch -d "$(git --git-dir=/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin/.git log -1 --format="%ai")" /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin
if [ $? -ne 0 ]; then
exit 1
fi
exit 0
WARNING: <KO> result command stdout&stderr:
b"+ git clone https://github.com/SalomePlatform/mmgplugin.git /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin\nfatal: destination path '/home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/SOURCES/mmgplugin' already exists and is not an empty directory.\n+ [ 128 -ne 0 ]\n+ exit 1\n"
KO
sorry for the inconvenience. I should have tested non SALOME modules as well. commit is reverted until more robust implementation regarding the non salome modules.
reported issue about git should in principle be fixed now - checked on my side on various git versions as well as on windows & linux.
can confirm that all deps are correctly graved by SAT tool (y)
Hi Franco,
thanks for your valuable feedback. Can you tell whether the issue about scotch compilation is still present ?
Indeed, note that one can “force” usage of mpicc
and mpicxx
wrappers by:
export CC=$(which mpicc)
export CXX=$(which mpicxx)
hello nabil,
well, scotch compiled correctly (i did a sed
to modify the python file you mentioned previously) but paravis does not compile.
INSTALL directory = /home/franco/Downloads/salomeTest/SALOME-master-native-UB22.04/INSTALL/FIELDS
Compilation of PARAVIS ....................... KO CONFIGURE
I did not see a folder for paravis in the logs. so I can not give you much info about…
Can you share file LOGS/PARAVIS/cmake or the output of:
# retrieve sources
SAT/sat -o "APPLICATION.properties.git_server='github'" prepare SALOME-master-native -p PARAVIS
# compile
SAT/sat -t -o "APPLICATION.properties.git_server='github'" compile SALOME-master-native -p PARAVIS --clean_all 2>&1 |tee paravis.log
namely file paravis.log
?
Regards.
hello nabil , in my other pc I just tested pyFMI does not work in sat
script.txt (118,4 KB)
also I tested (in my work PC) and now it compiles everything. including paravis, I am not sure if there was any modification of the sat repo as I pull it again before trying to compile.
so in one PC works in the other one no. they have different processors and graphic cards and same OS.
concerning paravis, is t ok now ?
Regarding the second issue, you need to share the installed packages on your ub22 node. in principle, pyfmi is patched by sat to be compatible with cython
hello nabil,
yes I saw but cython is installed in my PC…
for paravis it is ok (at least in the PC where pyFMI compiles)
for the other PC here is the output of apt list --installed > TUB22.txt
TUB22.txt (221,8 KB)
(the cython is the same as in the previous output in the pc that is working so it might be something else.)
also, worth noticing that SAT/sat config SALOME-master-native --check_system
outputs that everything is OK
regards