auto_namd initial commit

auto_namd/hosts.sh

@@ -0,0 +1,128 @@
+##########################################
+## HOSTNAMES                                                                               ##
+##########################################
+
+function run_cheaha() {
+  echo "#!/usr/bin/env bash" > temp_sbatch
+  echo "#SBATCH --ntasks=${ntasks}" >> temp_sbatch
+  echo "#SBATCH --partition=${partition}" >> temp_sbatch
+  echo "#SBATCH --time=${time}" >> temp_sbatch
+  echo "#SBATCH --mem-per-cpu=${mem_per_cpu}" >> temp_sbatch
+  echo "#SBATCH --nodes=${nodes}" >> temp_sbatch
+  echo "#SBATCH --job-name=${job}_${this_step}_${final_step_num}" >> temp_sbatch
+  echo '# Load module(s)' >> temp_sbatch
+  echo 'module load rc/NAMD/2.12' >> temp_sbatch
+
+  # generate temp NAMD nodelist
+  echo 'for n in `echo ${SLURM_NODELIST} | scontrol show hostnames`; do' >> temp_sbatch
+  echo '  echo "host $n ++cpus 24" >> ${TMPDIR}/nodelist.${SLURM_JOBID}' >> temp_sbatch
+  echo 'done' >> temp_sbatch
+
+  # calculate ppn
+  echo 'PPN=$(expr $SLURM_NTASKS / $SLURM_NNODES - 1)' >> temp_sbatch
+  echo 'P="$(($PPN * $SLURM_NNODES))"' >> temp_sbatch
+  
+  # find namd location
+  echo 'namd_bin="$(which namd2)"' >> temp_sbatch
+  
+  echo "$(echo "${namd_param}") ${conf} > ${out}" >> temp_sbatch
+  
+  # cleanup temp NAMD nodelist
+  echo 'rm ${TMPDIR}/nodelist.${SLURM_JOBID}' >> temp_sbatch
+  
+  # submit using sbatch
+  sbatch temp_sbatch
+  rm temp_sbatch
+}
+
+function run_workstation() {
+  $(echo "${namd_param}") ${conf} > ${out}
+ }
+ 
+function run_asc() {
+  job_name_pref=${job##*.}_${this_step}_${final_step_num}
+  
+  /apps/scripts/check_ssh
+  /apps/scripts/qquery program=namd input=$conf
+  
+  # create ~/.asc_queue
+  
+  echo 'start_time_pref=SOONEST' > ${HOME}/.asc_queue
+  echo "job_name_pref=${job_name_pref}" >> ${HOME}/.asc_queue
+  echo "queue_name_pref=${queue_name_pref}" >> ${HOME}/.asc_queue
+  echo "num_cpus_pref=${num_cpus_pref}" >> ${HOME}/.asc_queue
+  echo "cpu_time_pref=${cpu_time_pref}" >> ${HOME}/.asc_queue
+  echo "memory_pref=${memory_pref}" >> ${HOME}/.asc_queue
+  echo "cluster_pref=${cluster_pref}" >> ${HOME}/.asc_queue
+  
+  if [ -f qfile ]
+  then
+    read queue time memory sttime num_cpus < qfile
+    rm qfile
+  else
+    echo "ERROR: qfile not found"
+    echo "       Make sure you have write permissions in this directory"
+    exit
+  fi
+   
+  # get limits
+  limits=`/apps/scripts/set_limits $time $num_cpus NA $memory NA NA`
+  
+  # get qos
+  qos=`/apps/scripts/set_qos $queue`
+  
+  # get constraints
+  constraints="--constraint=dmc|uv"  # both clusters, not KNL
+  
+  echo '#!/usr/bin/env bash' > temp_sbatch
+  echo 'pwd="$(pwd)"' >> temp_sbatch
+  echo 'echo "pwd: $pwd"' >> temp_sbatch
+  echo '#  set the workdir variable' >> temp_sbatch
+  echo "export workdir=/scratch/${LOGNAME}/${job##*./}" >> temp_sbatch
+  echo 'echo "workdir: $workdir"' >> temp_sbatch
+  echo '# load modules' >> temp_sbatch
+  echo 'source /opt/asn/etc/asn-bash-profiles-special/modules.sh' >> temp_sbatch
+  echo 'module purge' >> temp_sbatch
+  echo 'if [ ! -d $workdir ]' >> temp_sbatch
+  echo 'then' >> temp_sbatch
+  echo '  mkdir -p $workdir' >> temp_sbatch
+  echo 'fi' >> temp_sbatch
+  echo 'export TEMPDIR=$workdir' >> temp_sbatch
+  echo 'export TMPDIR=$workdir' >> temp_sbatch
+  echo 'export CONV_RSH=ssh' >> temp_sbatch
+  echo '# run from the current directory' >> temp_sbatch
+  echo "./cp_wild_r $job \$workdir" >> temp_sbatch
+  echo 'sleep 15' >> temp_sbatch
+  echo 'cd $workdir' >> temp_sbatch
+  echo 'export uv_test=`hostname | grep uv | wc -l`' >> temp_sbatch
+  echo 'export dmc_test=`hostname | grep dmc | wc -l`' >> temp_sbatch
+  echo '# code for the DMC' >> temp_sbatch
+  echo 'if [ $dmc_test == "1" ]' >> temp_sbatch
+  echo 'then' >> temp_sbatch
+  echo '  module purge' >> temp_sbatch
+  echo '  module load namd/2.12_ibverbs' >> temp_sbatch
+  echo '  namd_bin="$(which namd2)"' >> temp_sbatch
+  echo '  # run NAMD' >> temp_sbatch
+  echo '  alias mpiexec="srun"' >> temp_sbatch
+  echo "  charmrun +p $num_cpus_pref ++mpiexec \${namd_bin} ${conf##*/} > ${out##*/}" >> temp_sbatch
+  echo 'fi' >> temp_sbatch
+  echo '# code for the UV' >> temp_sbatch
+  echo 'if [ "$uv_test" == "1" ]' >> temp_sbatch
+  echo 'then' >> temp_sbatch
+  echo '  module purge' >> temp_sbatch
+  echo '  module load namd/2.12' >> temp_sbatch
+  echo '  namd_bin="$(which namd2)"' >> temp_sbatch
+  echo '  # run NAMD' >> temp_sbatch
+  echo "  charmrun +p $num_cpus_pref \${namd_bin} ${conf##*/} > ${out##*/}" >> temp_sbatch
+  echo 'fi' >> temp_sbatch
+  echo 'sleep 10' >> temp_sbatch
+  echo 'cd ${pwd}' >> temp_sbatch
+  echo "./cp_wild_r \$workdir $job" >> temp_sbatch
+  echo 'sleep 15' >> temp_sbatch
+  echo 'rm -r $workdir' >> temp_sbatch
+  echo 'exit 0' >> temp_sbatch
+
+  sbatch $qos  -J $job_name_pref --begin=$sttime --requeue $limits $constraints temp_sbatch
+  rm temp_sbatch
+
+}