auto_namd initial commit

auto_namd/run.sh

@@ -0,0 +1,63 @@
+#!/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