software:himster2
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| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| software:himster2 [2019/09/11 09:46] – himuser | software:himster2 [2022/01/14 18:44] (current) – external edit 127.0.0.1 | ||
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| - | === SSH connection to the git repository | + | === Source code checkout |
| - | Set up the ssh connection to '' | ||
| - | |||
| - | \\ | ||
| - | === Source code checkout === | ||
| < | < | ||
| git clone https:// | git clone https:// | ||
| </ | </ | ||
| - | Alternatively (not preferred), check out from the fileserver | + | Alternatively (not preferred), check out from the fileserver. \\ |
| + | |||
| + | Set up the ssh connection to '' | ||
| + | Then check out: | ||
| < | < | ||
| git clone agmaas@bwec-fileserver:/ | git clone agmaas@bwec-fileserver:/ | ||
| Line 18: | Line 17: | ||
| \\ | \\ | ||
| === Environment setup === | === Environment setup === | ||
| - | load module and set the variable FAIRSOFT_BUILD_DIR: | + | load module and set the variable FAIRSOFT_BUILD_DIR:\\ |
| + | new since Nov 2020: | ||
| < | < | ||
| - | module load fairsoft/ | + | export MODULEPATH=$MODULEPATH:/ |
| - | export FAIRSOFT_BUILD_DIR=/ | + | module load fairsoft/ |
| + | export FAIRSOFT_BUILD_DIR=/ | ||
| </ | </ | ||
| + | |||
| or | or | ||
| < | < | ||
| Line 38: | Line 40: | ||
| In the following a minimum script to run a single job on slurm is given. | In the following a minimum script to run a single job on slurm is given. | ||
| + | To submit your job use | ||
| + | < | ||
| + | $ sbatch myjobscript | ||
| + | </ | ||
| + | |||
| + | |||
| + | Example for myjobscript: | ||
| < | < | ||
| Line 55: | Line 64: | ||
| #SBATCH -A m2_him_exp | #SBATCH -A m2_him_exp | ||
| - | + | ||
| - | + | # A script | |
| - | # Launch the executable | + | # environment settings |
| - | # needed to run the program, as if you would run it just after login on himsterII. | + | # run it just after login on himsterII. Something like |
| - | # Something like | + | # |
| # module load fairsoft/ | # module load fairsoft/ | ||
| # export FAIRSOFT_BUILD_DIR=... | # export FAIRSOFT_BUILD_DIR=... | ||
| + | # | ||
| # should be in there. Think about what you need. | # should be in there. Think about what you need. | ||
| # | # | ||
| - | # The file output.log is where all the shell output of the job will be saved. | ||
| - | srun -o output.log myscript.sh | + | source mysetenv.sh |
| + | |||
| + | # Submit the executable with the needed arguments (it might also be a script) | ||
| + | |||
| + | srun < | ||
| </ | </ | ||
| Line 72: | Line 85: | ||
| An example script is given here to run a train of jobs with different '' | An example script is given here to run a train of jobs with different '' | ||
| - | It is broken down in pieces with comments | + | It is broken down in pieces with comments between |
| Provide the possibility to have a "dry runs" where all scripts are prepared and can be checked, without actually starting the jobs. That is very useful to avoid having to chase running jobs with wrong settings. | Provide the possibility to have a "dry runs" where all scripts are prepared and can be checked, without actually starting the jobs. That is very useful to avoid having to chase running jobs with wrong settings. | ||
| + | |||
| + | The following code can be executed with: | ||
| + | < | ||
| + | $ ./ | ||
| + | </ | ||
| < | < | ||
| Line 94: | Line 112: | ||
| - | + | Base macro and config files have to be copied previously to the output directory and will be used as starting point for the job specific ones. | |
| + | The directory structure for all input and output files is constructed. | ||
| < | < | ||
| # base scripts to be completed for single jobs | # base scripts to be completed for single jobs | ||
| Line 112: | Line 130: | ||
| mkdir -p $outpath/ | mkdir -p $outpath/ | ||
| </ | </ | ||
| + | |||
| + | |||
| + | The main loop on the jobs to be started (200 in this example) starts here. For each job config and macro files are completed, the job script is constructed and the job submitted if it is not a dry run. | ||
| < | < | ||
| for i in `seq 0 199`; do | for i in `seq 0 199`; do | ||
software/himster2.1568195213.txt.gz · Last modified: 2022/01/14 18:44 (external edit)