User’s Guide¶

Directory layout and basic workflow¶

generatemc will create following directory structure for each run:

run_20170219_122904               # main directory, new one is created for each generatemc call
    collect.sh                    # call to copy output files to output directory
    input                         # reference directory with copy of input files
        sample_fluka.inp          # non-modified copy of original Fluka input files
    submit.sh                     # call to submit jobs to the cluster
    workspace                     # workspace used to store modified input files and temporary storage for output
        main_run.sh               # this script will be called by batch system and redirect the execution to specific worker
        job_0001                  # working directory of worker no 1
            sample_fluka.inp      # copy of input file, with adapted RNG seed and output file path
            run.sh                # run script executed by worker no 1
        job_0002
            sample_fluka.inp
            run.sh
        job_0003
            sample_fluka.inp
            run.sh

After executing submit.sh script, output files will be created in the workspace directory. Each parallel job will store its output in separate directory:

run_20170219_122904
   collect.sh
   input
       sample_fluka.inp
   submit.sh
   workspace
       main_run.sh
       job_0001
           sample_fluka.inp
           run.sh
           TODO                  # TODO
       job_0002
           sample_fluka.inp
           run.sh
           TODO                  # TODO
       job_0003
           sample_fluka.inp
           run.sh
           TODO                  # TODO

In order to collect all files in a single place, run collect.sh script. This will result in following new files:

run_20170219_122904
    collect.sh
    input
        sample_fluka.inp
    submit.sh
    output                        # TODO
        TODO                      # TODO
    workspace
        main_run.sh
        job_0001
            sample_fluka.inp
            run.sh
        job_0002
            sample_fluka.inp
            run.sh
        job_0003
            sample_fluka.inp
            run.sh

Advanced options¶

There are several advanced options in the generator, customising the workflow.

After executing generatemc command a directory will be created (i.e. run_20170219_122904), by default in the same location as the input configuration files. In order to change the location of generated directory, use the –workspace option. For example after typing:

generatemc.py -p 10000 -j 20 tests/res/sample_fluka.inp

A directory tests/res/run_20170717_195410 will be created. Now providing a workspace option:

generatemc.py -p 10000 -j 20 tests/res/sample_fluka.inp --workspace mydir

will result in new directory mydir/run_20170717_195557

Another useful option is the ability to provide additional options for scheduler and for Monte-Carlo binary. The first one can be used i.e. to specify directly the walltime for job execution:

generatemc.py -p 10000 -j 20 tests/res/sample_fluka.inp --scheduler_options "[--walltime=2:00:00]"

Not additional square brackets added to distringuish between generatemc and scheduler options.

One could also specify additional options to Monte-Carlo binary files. For example to add an user-defined particle source in Fluka one can use its “-e” option:

generatemc.py -p 10000 -j 20 tests/res/sample_fluka.inp --mc_engine_options "[-e flukadpm3_sobp]"

If the Monte-Carlo input file contains links to external file (i.e. sobp.dat file required by flukadpm3_sobp then the simulation will run only if links to these external files are created in the workspace. To do so, please specify in such case list of these external files using -x switch:

generatemc.py -p 10000 -j 20 tests/res/sample_fluka.inp --mc_engine_options "[-e flukadpm3_sobp]" -x ./sobp.dat