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File indexing completed on 2025-10-14 08:06:15
0001 #!/usr/bin/env bash 0002 # 0003 ############################################################################################################################# 0004 ##### This is an example of slurm file to submit a job to execute dsbandrepair on cluster ##### 0005 ##### In this example, each node on cluster has memory of 31 Gb. And there are 16 cpus per node. In phycal stage, the ##### 0006 ##### parallel proceeses running on each node (buy setting num_ranks_pernode) is sett based the memory required to hold ##### 0007 ##### geometry. For instance, with geometry set provided along this dsbandrepair, fbroblast and endothelium needs~4.5Gb,##### 0008 ##### while yeast need ~4.5Gb and ~1.2GB respectively. Therefore, with a node of 31Gb memory, num_ranks_pernodeP ##### 0009 ##### can be set to 6 for fiborblast and endothelium, and 16 for yeast. For chemical stage, it is better to set the ##### 0010 ##### number of chemical proceses on each node equal to the number of cpus. User should edit this file according to ##### 0011 ##### their need. ##### 0012 ############################################################################################################################# 0013 ##--------------------------------------------------------------------------------------------------------------------------## 0014 #SBATCH --job-name="dsbandrepair" 0015 #SBATCH --partition=std 0016 #SBATCH --exclusive 0017 #SBATCH --nodes=5 0018 ##SBATCH --mem=190Gb 0019 ##SBATCH --nodelist=node118 0020 num_ranks_pernodeP=6 ## Number of Physical processes on each node. 0021 num_ranks_pernodeC=16 ## Number of chemical processes on all nodes. should be 1 cpu for 1 process 0022 ## You can change above setting for your need. 0023 ##--------------------------------------------------------------------------------------------------------------------------## 0024 ## for physical stage: 0025 totalnumRankP=$(( $num_ranks_pernodeP*$SLURM_NNODES )) 0026 ## for chemicall stage: 0027 totalnumRankC=$(( $num_ranks_pernodeC*$SLURM_NNODES )) 0028 ##--------------------------------------------------------------------------------------------------------------------------## 0029 #" Check some requried files && folders 0030 physmacfile="dsbandrepair.in" #change it if you use other files for default 0031 chemmacfile="chem.in" #change it if you use other files for default 0032 flag="all" 0033 ##Read input arguments 0034 for i in "$@" 0035 do 0036 if [ $i = "-f" ] ;then shift;unset flag;flag=$1;shift;fi 0037 if [ $i = "-mP" ] ; then shift;unset physmacfile; physmacfile=$1;shift;fi 0038 if [ $i = "-mC" ] ; then shift;unset chemmacfile; chemmacfile=$1;shift;fi 0039 done 0040 ##--------------------------------------------------------------------------------------------------------------------------## 0041 0042 0043 logfolder="logs" 0044 inputfolder="chem_input" 0045 if [ ! -d $logfolder ]; then 0046 # folder to contain logfiles 0047 mkdir "$logfolder" 0048 mkdir "$logfolder/phys" 0049 mkdir "$logfolder/chem" 0050 fi 0051 ##--------------------------------------------------------------------------------------------------------------------------## 0052 #START_TIME=$SECONDS 0053 ##--------------------------------------------------------------------------------------------------------------------------## 0054 ##If $flag = "phys", then run the physStage part 0055 if [ $flag = "phys" ] || [ $flag = "all" ]; then 0056 echo "Start running physical stage................." 0057 echo "This job will run with: " 0058 echo "=====> Number of nodes: $SLURM_NNODES" 0059 echo "=====> Number of Ranks: $numRanks" 0060 mpiexec -np $totalnumRankP -npernode $num_ranks_pernodeP ./dsbandrepair $physmacfile 0061 wait 0062 echo "End running physical stage................." 0063 fi 0064 ##--------------------------------------------------------------------------------------------------------------------------## 0065 ##If $flag = "chem", then run the chemStage part 0066 wait # make sure all above processes finish before chemStage starts 0067 #sleep 1s 0068 if [ $flag = "chem" ] || [ $flag = "all" ]; then 0069 if [ -d $logfolder/chem ]; then find $logfolder/chem/ -type f -delete;fi 0070 echo "Start running chemical stage................." 0071 echo "with number of $totalnumRankC tasks.!!" 0072 echo "See $logfolder/* for running details" 0073 mpiexec -np $totalnumRankC ./dsbandrepair $chemmacfile chem $inputFolder > $logfolder/chem/log.dat 0074 wait 0075 echo "End running chemical stage on all tasks ................." 0076 fi 0077 ##--------------------------------------------------------------------------------------------------------------------------## 0078 #echo "Elasped timed for $flag stage: $(($SECONDS - $START_TIME)) sec!!!" 0079 ##--------------------------------------------------------------------------------------------------------------------------##
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