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#1 2022-08-04 20:03:13

moroub
Member
Registered: 2022-08-04
Posts: 2

Can't execute Salome Meca with the singularity container

Hi,

I downloaded the Salome-Meca singularity container at named salome_meca-lgpl-2021.0.0-2-20211014-scibian-9.sif on my laptop and on a remote cluster to use the capability of AsterStudy to launch remote workload. While I can launch Salome-Meca on my laptop without troubles, things get more complicated on the distant server. Here is the terminal output:

[moroub@server Salome-Meca]$ singularity exec ./salome_meca-lgpl-2021.0.0-2-20211014-scibian-9.sif /opt/salome_meca/salome_meca shell
/usr/bin/lua: /usr/share/lmod/lmod/libexec/MT.lua:1333: table index is nil
stack traceback:
    /usr/share/lmod/lmod/libexec/MT.lua:1333: in function 'add'
    /usr/share/lmod/lmod/libexec/Master.lua:570: in function 'reloadAll'
    /usr/share/lmod/lmod/libexec/cmdfuncs.lua:928: in function 'cmd'
    /usr/share/lmod/lmod/libexec/lmod:604: in function 'main'
    /usr/share/lmod/lmod/libexec/lmod:650: in main chunk
    [C]: in ?
/usr/bin/lua: /usr/share/lmod/lmod/libexec/MT.lua:1333: table index is nil
stack traceback:
    /usr/share/lmod/lmod/libexec/MT.lua:1333: in function 'add'
    /usr/share/lmod/lmod/libexec/Master.lua:570: in function 'reloadAll'
    /usr/share/lmod/lmod/libexec/cmdfuncs.lua:928: in function 'cmd'
    /usr/share/lmod/lmod/libexec/lmod:604: in function 'main'
    /usr/share/lmod/lmod/libexec/lmod:650: in main chunk
    [C]: in ?
/usr/bin/lua: /usr/share/lmod/lmod/libexec/MT.lua:1333: table index is nil
stack traceback:
    /usr/share/lmod/lmod/libexec/MT.lua:1333: in function 'add'
    /usr/share/lmod/lmod/libexec/Master.lua:570: in function 'reloadAll'
    /usr/share/lmod/lmod/libexec/cmdfuncs.lua:928: in function 'cmd'
    /usr/share/lmod/lmod/libexec/lmod:604: in function 'main'
    /usr/share/lmod/lmod/libexec/lmod:650: in main chunk
    [C]: in ?
/usr/bin/lua: /usr/share/lmod/lmod/libexec/MT.lua:1333: table index is nil
stack traceback:
    /usr/share/lmod/lmod/libexec/MT.lua:1333: in function 'add'
    /usr/share/lmod/lmod/libexec/Master.lua:570: in function 'reloadAll'
    /usr/share/lmod/lmod/libexec/cmdfuncs.lua:928: in function 'cmd'
    /usr/share/lmod/lmod/libexec/lmod:604: in function 'main'
    /usr/share/lmod/lmod/libexec/lmod:650: in main chunk
    [C]: in ?
Illegal option --
Usage: /usr/bin/which [-a] args
*****************************************************
INFO : Running salome_meca in software rendering mode
*****************************************************
Lmod has detected the following error:  The following module(s) are unknown:
"python3-pyqt/5.15.2" "embree/3.12.2" "numpy/1.15.1" "python/3.6.5" "pv/5.9.0" "opencv/3.2.0"
"python36-psutil/5.5.1" "tbb/2018.u6" "openvkl/0.11.0" "python36-h5py/2.8.0" "rkcommon/1.6.0"
"melissa/0.0.0" "python3-sip/4.19.25" "netcdf-c/4.6.2" "cminpack/1.3.6" "python36-cython3/0.25.2"
"hdf5/1.10.3" "occ/7.5.0" "py36-nlopt/2.4.2" "boost/1.58.0.0" "python3-jinja/2.7.3"
"python36-six/1.12.0" "zeromq/4.3.1" "lapack/3.8.0" "med/4.1serial64" "swig/3.0.12" "qwt-qt5152/6.1.2"
"qt/5.15.2" "python36-lxml/3.4.0" "ospray/2.4.0" "omniorbpy/4.2.2" "libxslt/1.1.28" "gdal/2.4.0"
"python3-scipy/0.19.1" "gl2ps/1.4.0.1" "python3-pygments/2.0.2" "omniorb/4.2.2"
"python3-matplotlib/3.0.3" "python3-docutils/0.12" "openturns/1.16.0"

Please check the spelling or version number. Also try "module spider ..."



ERROR:salome:Failed to load env modules: boost/1.58.0.0 cminpack/1.3.6 embree/3.12.2 gdal/2.4.0 gl2ps/1.4.0.1 hdf5/1.10.3 lapack/3.8.0 libxslt/1.1.28 med/4.1serial64 melissa/0.0.0 netcdf-c/4.6.2 numpy/1.15.1 occ/7.5.0 omniorb/4.2.2 omniorbpy/4.2.2 opencv/3.2.0 openturns/1.16.0 openvkl/0.11.0 ospray/2.4.0 pv/5.9.0 py36-nlopt/2.4.2 python/3.6.5 python3-docutils/0.12 python3-jinja/2.7.3 python3-matplotlib/3.0.3 python3-pygments/2.0.2 python3-pyqt/5.15.2 python3-scipy/0.19.1 python3-sip/4.19.25 python36-cython3/0.25.2 python36-h5py/2.8.0 python36-lxml/3.4.0 python36-psutil/5.5.1 python36-six/1.12.0 qt/5.15.2 qwt-qt5152/6.1.2 rkcommon/1.6.0 swig/3.0.12 tbb/2018.u6 zeromq/4.3.1 ...

[moroub@server Salome-Meca]$ singularity --version
singularity version 3.8.7-1.el8

[moroub@server Salome-Meca]$ cat /etc/os-release
NAME="Rocky Linux"
VERSION="8.5 (Green Obsidian)"
ID="rocky"
ID_LIKE="rhel centos fedora"
VERSION_ID="8.5"
PLATFORM_ID="platform:el8"
PRETTY_NAME="Rocky Linux 8.5 (Green Obsidian)"
ANSI_COLOR="0;32"
CPE_NAME="cpe:/o:rocky:rocky:8:GA"
HOME_URL="https://rockylinux.org/"
BUG_REPORT_URL="https://bugs.rockylinux.org/"
ROCKY_SUPPORT_PRODUCT="Rocky Linux"
ROCKY_SUPPORT_PRODUCT_VERSION="8"

Any hints on what could happen ?

Let me know of you need more info.

Moise

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#2 2022-08-05 16:46:52

moroub
Member
Registered: 2022-08-04
Posts: 2

Re: Can't execute Salome Meca with the singularity container

Hi,

I solved the problem. On the server, Lmod was also installed and singularity container seems to import the server environment when running, creating conflict. I have to launch the container with the argument --cleanenv to solve the issue:

singularity exec --cleanenv ./salome_meca-lgpl-2021.0.0-2-20211014-scibian-9.sif /opt/salome_meca/salome_meca shell

Moise

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