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64 lines
2.1 KiB
Bash
64 lines
2.1 KiB
Bash
#!/bin/bash
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# This script was generated to run on {{ simulation.hpc_system }}.
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#PBS -N {{ simulation.segment_id }}
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#PBS -A {{ pbs.account_name }}
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#PBS -q {{ pbs.queue }}
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#PBS -l walltime={{ pbs.walltime }}
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#PBS -l select={{ pbs.select }}:ncpus={{ pbs.ncpus }}:mpiprocs={{ pbs.mpiprocs }}:ompthreads={{ pbs.ompthreads }}{{ pbs.other }}+{{ pbs.select2 }}:ncpus={{ pbs.ncpus }}:mpiprocs={{ pbs.helper_mpiprocs }}:ompthreads={{ pbs.helper_ompthreads }}{{ pbs.other }}
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#PBS -m abe
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#PBS -j oe
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echo "Job $PBS_JOBID started at `date` on `hostname`."
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# Specify the ID string for the run.
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export RUNID=$PBS_JOBNAME
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# Some HPC systems do not start the job in the correct directory.
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# Move to the intended directory. This will move the job to the correct
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# directory on problem systems, such as pleiades (for some users), and have no
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# effect on other systems.
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cd $PBS_O_WORKDIR
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# Load the required modules for kaiju.
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module purge
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{%- for module in pbs.modules %}
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module load {{ module }}
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{%- endfor %}
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module list
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# Define the kaiju installation location.
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export KAIJU_INSTALL_DIR={{ pbs.kaiju_install_directory }}
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# Set kaiju-related environment variables.
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# This script sets KAIJUHOME and other environment variables.
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source $KAIJU_INSTALL_DIR/scripts/setupEnvironment.sh
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# Add the kaiju build bin directory to PATH.
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export PATH={{ pbs.kaiju_build_directory }}/bin:$PATH
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# Set other environment variables.
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{{ pbs.additional_environment_variables -}}
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export MPI_TYPE_DEPTH=32
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export OMP_STACKSIZE=100M
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export OMP_NUM_THREADS={{ pbs.helper_ompthreads }}
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echo "The active environment variables are:"
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printenv
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# Copy the node file for use by the placer command.
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nodefile=nodefile.$PBS_JOBID
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cp $PBS_NODEFILE $nodefile
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# Copy the main executable.
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cp {{ pbs.kaiju_build_directory }}/bin/voltron_mpi.x ./voltron_mpi.x
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# Run the model. Direct output from the program is saved in a text file.
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EXE=./voltron_mpi.x
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OUTPUT_FILE="$EXE-{{ simulation.segment_id }}.out"
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echo "Running $EXE on model $RUNID."
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{{ pbs.mpiexec_command }} $EXE $RUNID.xml &>> $OUTPUT_FILE
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echo "Job $PBS_JOBID ended at `date` on `hostname`."
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