64 lines
1.3 KiB
Bash
Executable File
64 lines
1.3 KiB
Bash
Executable File
#!/usr/bin/env bash
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source ./functions.sh
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source ./hosts.sh
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# ADJUSTABLE PARAMETERS
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# set directory containing jobs to be run
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jobs=( "../4-jobs/18_04_02/5w81-swiss*/" )
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step_size=1000000
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#repeats=50
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# FUNCTIONS
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# remove trailing slashes from jobs array
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jobs=(${jobs[@]%/})
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# HOSTNAME PARAMETERS
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function run_namd() {
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case "${HOSTNAME}" in
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"phy145.physiology.uab.edu") # Workstation (local)
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namd_param='/home/bryan/bin/namd/namd2 +p55 +idlepoll'
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run_workstation
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;;
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"login001") # Cheaha (Slurm)
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namd_param='charmrun ++mpiexec ++nodelist ${TMPDIR}/nodelist.${SLURM_JOBID} +p ${SLURM_NTASKS} ${namd_bin}'
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partition="short"
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ntasks=96
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nodes=4
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time="12:00:00"
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mem_per_cpu=128
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run_cheaha
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;;
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"uv.asc.edu") # ASC (Slurm script)
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namd_param="runnamd"
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queue_name_pref="large"
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num_cpus_pref=64
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cpu_time_pref="DEFAULT"
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memory_pref="16gb"
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cluster_pref='"uv|dmc"'
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run_asc
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;;
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*) # unknown
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echo "You are running on an unknown system: \"${HOSTNAME}\"..."
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echo "You must first add this machine to the resources section in run_namd.sh"
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echo "Exiting..."
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exit 1
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;;
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esac
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}
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# RUN LOOP
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for r in {1..50}; do
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for job in "${jobs[@]}"; do
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get_next_step
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copy_ffs
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create_conf
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backup
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run_namd
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done
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done
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