| Geant4 Cross Reference |
1 #!/usr/bin/env bash
2 #
3 ##############################################
4 ##### This is an example of slur
5 ##### In this example, each node on cluster ha
6 ##### parallel proceeses running on each node
7 ##### geometry. For instance, with geometry se
8 ##### while yeast need ~4.5Gb and ~1.2GB resp
9 ##### can be set to 6 for fiborblast and endot
10 ##### number of chemical proceses on each node
11 ##### their need.
12 ##############################################
13 ##--------------------------------------------
14 #SBATCH --job-name="dsbandrepair"
15 #SBATCH --partition=std
16 #SBATCH --exclusive
17 #SBATCH --nodes=5
18 ##SBATCH --mem=190Gb
19 ##SBATCH --nodelist=node118
20 num_ranks_pernodeP=6 ## Number of Physical pro
21 num_ranks_pernodeC=16 ## Number of chemical p
22 ## You can change above setting for your need.
23 ##--------------------------------------------
24 ## for physical stage:
25 totalnumRankP=$(( $num_ranks_pernodeP*$SLURM_N
26 ## for chemicall stage:
27 totalnumRankC=$(( $num_ranks_pernodeC*$SLURM_N
28 ##--------------------------------------------
29 #" Check some requried files && folders
30 physmacfile="dsbandrepair.in" #change it if y
31 chemmacfile="chem.in" #change it if you use ot
32 flag="all"
33 ##Read input arguments
34 for i in "$@"
35 do
36 if [ $i = "-f" ] ;then shift;unset flag;fl
37 if [ $i = "-mP" ] ; then shift;unset physm
38 if [ $i = "-mC" ] ; then shift;unset chemm
39 done
40 ##--------------------------------------------
41
42
43 logfolder="logs"
44 inputfolder="chem_input"
45 if [ ! -d $logfolder ]; then
46 # folder to contain logfiles
47 mkdir "$logfolder"
48 mkdir "$logfolder/phys"
49 mkdir "$logfolder/chem"
50 fi
51 ##--------------------------------------------
52 #START_TIME=$SECONDS
53 ##--------------------------------------------
54 ##If $flag = "phys", then run the physStage pa
55 if [ $flag = "phys" ] || [ $flag = "all" ]; th
56 echo "Start running physical stage........
57 echo "This job will run with: "
58 echo "=====> Number of nodes: $SLURM_NNODE
59 echo "=====> Number of Ranks: $numRanks"
60 mpiexec -np $totalnumRankP -npernode $num_
61 wait
62 echo "End running physical stage..........
63 fi
64 ##--------------------------------------------
65 ##If $flag = "chem", then run the chemStage pa
66 wait # make sure all above processes finish be
67 #sleep 1s
68 if [ $flag = "chem" ] || [ $flag = "all" ]; th
69 if [ -d $logfolder/chem ]; then find $logf
70 echo "Start running chemical stage........
71 echo "with number of $totalnumRankC tasks.
72 echo "See $logfolder/* for running details
73 mpiexec -np $totalnumRankC ./dsbandrepair
74 wait
75 echo "End running chemical stage on all ta
76 fi
77 ##--------------------------------------------
78 #echo "Elasped timed for $flag stage: $(($SECO
79 ##--------------------------------------------