mirror of
https://github.com/JHUAPL/kaiju.git
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70 lines
2.0 KiB
Bash
70 lines
2.0 KiB
Bash
#!/bin/bash
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#PBS -N {{ job_name }}
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#PBS -A {{ account }}
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#PBS -q {{ queue }}
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#PBS -l job_priority={{ job_priority }}
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#PBS -l select=1:ncpus=128
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#PBS -l walltime={{ walltime }}
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#PBS -j oe
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#PBS -m abe
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echo "Job $PBS_JOBID started at `date` on `hostname` in directory `pwd`."
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echo 'Loading modules.'
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module --force purge
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{%- for module in modules %}
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module load {{ module }}
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{%- endfor %}
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echo 'The currently loaded modules are:'
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module list
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echo 'Loading python environment.'
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mage_test_root=$HOME
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if [ -d "${mage_test_root}/miniconda3" ]; then
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echo 'Loading local miniconda3'
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mage_miniconda3="${mage_test_root}/miniconda3"
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mage_conda="${mage_miniconda3}/bin/conda"
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__conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"
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if [ $? -eq 0 ]; then
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eval "$__conda_setup"
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else
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if [ -f "$mage_miniconda3/etc/profile.d/conda.sh" ]; then
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. "$mage_miniconda3/etc/profile.d/conda.sh"
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else
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export PATH="$mage_miniconda3/bin:$PATH"
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fi
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fi
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unset __conda_setup
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else
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echo 'Loading conda module'
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module load conda
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fi
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conda activate {{ conda_environment }}
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echo "The current conda environment is ${CONDA_PREFIX}."
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echo 'Setting up MAGE environment.'
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source {{ kaijuhome }}/scripts/setupEnvironment.sh
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echo "The kaiju software is located at ${KAIJUHOME}."
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echo 'Setting environment variables.'
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export TMPDIR={{ tmpdir }}
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export SLACK_BOT_TOKEN={{ slack_bot_token }}
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export OMP_NUM_THREADS=128
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export MPI_TYPE_DEPTH=32
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export KMP_STACKSIZE=128M
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export MAGE_TEST_ROOT="{{ mage_test_root }}"
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export MAGE_TEST_SET_ROOT={{ mage_test_set_root }}
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export BRANCH_OR_COMMIT={{ branch_or_commit }}
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echo 'The active environment variables are:'
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printenv
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# Run the comparison.
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cmd="python $KAIJUHOME/testingScripts/compare_mage_runs_numerical.py -sv --run_description='MAGE reproducibility check' {{ xml1 }} {{ xml2 }} >& compare_mage_runs_numerical.out"
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echo "Run comparison command is:"
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echo $cmd
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eval $cmd
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echo "Job $PBS_JOBID ended at `date` on `hostname` in directory `pwd`."
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