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