Difference between revisions of "HOWTO use MCWrapper on AlmaLinux9 nodes"
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How to use MCWrapper on an interactive AlmaLinux9 node. Both submitting and running the jobs currently has to be done in a CentOS7 container. | How to use MCWrapper on an interactive AlmaLinux9 node. Both submitting and running the jobs currently has to be done in a CentOS7 container. | ||
| + | |||
| + | '''WORK IN PROGRESS''' | ||
= PREREQUISTE = | = PREREQUISTE = | ||
| Line 10: | Line 12: | ||
2. Check if swif2 and singularity commands exist if not add in your | 2. Check if swif2 and singularity commands exist if not add in your | ||
| − | .bashrc (if echo $SHELL give bash), export PATH=/ | + | .bashrc (if echo $SHELL give bash), export PATH=/usr/local:$PATH |
or | or | ||
| − | .cshrc (if echo $SHELL give tcsh), setenv PATH / | + | .cshrc (if echo $SHELL give tcsh), setenv PATH /usr/local:$PATH |
| − | + | ||
| − | + | ||
= RUN MCWrapper interactiveley = | = RUN MCWrapper interactiveley = | ||
1. Open your favorite $SHELL in the CentOS7 container: | 1. Open your favorite $SHELL in the CentOS7 container: | ||
| − | singularity exec --bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld /cvmfs/singularity.opensciencegrid.org/jeffersonlab/gluex_prod:v1 bash | + | singularity exec --bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld,/group/halld/Software,/work/osgpool/halld /cvmfs/singularity.opensciencegrid.org/jeffersonlab/gluex_prod:v1 bash |
or | or | ||
| − | singularity exec --bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld /cvmfs/singularity.opensciencegrid.org/jeffersonlab/gluex_prod:v1 tcsh | + | singularity exec --bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld,/group/halld/Software,/work/osgpool/halld /cvmfs/singularity.opensciencegrid.org/jeffersonlab/gluex_prod:v1 tcsh |
2. Set up gxenv: | 2. Set up gxenv: | ||
source /group/halld/Software/build_scripts/gluex_env_boot_jlab.sh | source /group/halld/Software/build_scripts/gluex_env_boot_jlab.sh | ||
| + | or | ||
| + | source /group/halld/Software/build_scripts/gluex_env_boot_jlab.csh | ||
3. Set up the environment with the last official xml file based on ccdb v1: | 3. Set up the environment with the last official xml file based on ccdb v1: | ||
gxenv /group/halld/www/halldweb/html/halld_versions/version_5.17.0.xml | gxenv /group/halld/www/halldweb/html/halld_versions/version_5.17.0.xml | ||
| + | |||
| + | 4. When you are in the container, check if you can access all your files, if not add the corresponding path - [my stuff path] - to "--bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld,/group/halld/Software,/work/osgpool/halld,[my stuff path]" | ||
= Run MCWrapper to register jobs = | = Run MCWrapper to register jobs = | ||
1. To go in the OS7 container and favorite $SHELL | 1. To go in the OS7 container and favorite $SHELL | ||
| − | singularity exec --bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld /cvmfs/singularity.opensciencegrid.org/jeffersonlab/gluex_prod:v1 bash | + | singularity exec --bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld,/group/halld/Software,/work/osgpool/halld /cvmfs/singularity.opensciencegrid.org/jeffersonlab/gluex_prod:v1 bash |
or | or | ||
| − | singularity exec --bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld /cvmfs/singularity.opensciencegrid.org/jeffersonlab/gluex_prod:v1 tcsh | + | singularity exec --bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld,/group/halld/Software,/work/osgpool/halld /cvmfs/singularity.opensciencegrid.org/jeffersonlab/gluex_prod:v1 tcsh |
2. | 2. | ||
source /group/halld/Software/build_scripts/gluex_env_boot_jlab.sh | source /group/halld/Software/build_scripts/gluex_env_boot_jlab.sh | ||
| − | or | + | or |
source /group/halld/Software/build_scripts/gluex_env_jlab.csh | source /group/halld/Software/build_scripts/gluex_env_jlab.csh | ||
| Line 44: | Line 48: | ||
gxenv /group/halld/www/halldweb/html/halld_versions/version_5.17.0.xml | gxenv /group/halld/www/halldweb/html/halld_versions/version_5.17.0.xml | ||
| − | 4. Set MCWRAPPER_CENTRAL to your local version | + | 4. When you are in the container, check if you can access all your files, if not add the corresponding path - [my stuff path] - to "--bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld,/group/halld/Software,/work/osgpool/halld,[my stuff path]" |
| + | |||
| + | 5. Set MCWRAPPER_CENTRAL to your local version | ||
git clone https://github.com/JeffersonLab/gluex_MCwrapper | git clone https://github.com/JeffersonLab/gluex_MCwrapper | ||
Latest revision as of 11:59, 13 August 2024
Contents
Introduction
How to use MCWrapper on an interactive AlmaLinux9 node. Both submitting and running the jobs currently has to be done in a CentOS7 container.
WORK IN PROGRESS
PREREQUISTE
1. Check what is your SHELL by doing echo $SHELL
2. Check if swif2 and singularity commands exist if not add in your
.bashrc (if echo $SHELL give bash), export PATH=/usr/local:$PATH
or
.cshrc (if echo $SHELL give tcsh), setenv PATH /usr/local:$PATH
RUN MCWrapper interactiveley
1. Open your favorite $SHELL in the CentOS7 container:
singularity exec --bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld,/group/halld/Software,/work/osgpool/halld /cvmfs/singularity.opensciencegrid.org/jeffersonlab/gluex_prod:v1 bash
or
singularity exec --bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld,/group/halld/Software,/work/osgpool/halld /cvmfs/singularity.opensciencegrid.org/jeffersonlab/gluex_prod:v1 tcsh
2. Set up gxenv:
source /group/halld/Software/build_scripts/gluex_env_boot_jlab.sh
or
source /group/halld/Software/build_scripts/gluex_env_boot_jlab.csh
3. Set up the environment with the last official xml file based on ccdb v1:
gxenv /group/halld/www/halldweb/html/halld_versions/version_5.17.0.xml
4. When you are in the container, check if you can access all your files, if not add the corresponding path - [my stuff path] - to "--bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld,/group/halld/Software,/work/osgpool/halld,[my stuff path]"
Run MCWrapper to register jobs
1. To go in the OS7 container and favorite $SHELL
singularity exec --bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld,/group/halld/Software,/work/osgpool/halld /cvmfs/singularity.opensciencegrid.org/jeffersonlab/gluex_prod:v1 bash
or
singularity exec --bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld,/group/halld/Software,/work/osgpool/halld /cvmfs/singularity.opensciencegrid.org/jeffersonlab/gluex_prod:v1 tcsh
2.
source /group/halld/Software/build_scripts/gluex_env_boot_jlab.sh
or
source /group/halld/Software/build_scripts/gluex_env_jlab.csh
3.
gxenv /group/halld/www/halldweb/html/halld_versions/version_5.17.0.xml
4. When you are in the container, check if you can access all your files, if not add the corresponding path - [my stuff path] - to "--bind /cvmfs/oasis.opensciencegrid.org/gluex/group/halld:/group/halld,/scratch,/u/home,/usr/local,/work/halld,/group/halld/Software,/work/osgpool/halld,[my stuff path]"
5. Set MCWRAPPER_CENTRAL to your local version
git clone https://github.com/JeffersonLab/gluex_MCwrapper
by default the MakeMC.sh/MakeMC.csh/gluex_MC.py are not executable, so do not forget to do chmod +x MakeMC.sh;chmod +x MakeMC.csh;chmod +x gluex_MC.py
setenv MCWRAPPER_CENTRAL path to your local version
or
export MCWRAPPER_CENTRAL=path to your local version
if it is not working copy this python steering file here: /work/halld/home/ijaegle/public/FromBoToMe/my_gluex_MC.py
5. In your MC.cfg, use
BATCH_SYSTEM=swif2cont
and
OS=el9
