-
Notifications
You must be signed in to change notification settings - Fork 0
/
submit.sh
51 lines (43 loc) · 1.36 KB
/
submit.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
#!/bin/bash
#SBATCH --mail-type=END,FAIL
#SBATCH --output=log_%x.log
#SBATCH --signal=B:USR1@240
#SBATCH --job-name=test
#SBATCH --time=2-2:00:00
# for node fixing
#SBATCH --exclusive # for exclusively one node
#SBATCH --partition=xeon40
#SBATCH -N 1 # minimum of 1 nodes
#SBATCH -n 40 # 40 mpi processor total for one node
ulimit -s unlimited
# setting up of anaconda environment. Optional
source /home/energy/surna/anaconda3/etc/profile.d/conda.sh
conda activate sure_svol
pyscript=$1
verbose="info" # change the verbose to other level for parallel python
#The following parameters are set to default.
# The values will only change if number of input arguments are > 2.
reactions_csv="./csvs/reactions.csv"
mol_csv="./csvs/qm9_bonds_energies.csv"
g4mp2_csv="./csvs/qm9_g4mp2_Nq.csv"
output_dir="./outputs/"
nprocs=1
indices="Node_0.json"
if [[ $# -gt 2 ]]; then
reactions_csv=$2
mol_csv=$3
g4mp2_csv=$4
output_dir=$5
nprocs=$6
indices=$7
verbose=$8
fi # To understand this, refer to the automated running bash script.
echo "submit script, parallel python reaction: $pyscript"
echo "submit script, reactions_csv: $reactions_csv"
echo "submit script, molecules_csv: $_mol_csv"
python3 $pyscript --rid_csv $reactions_csv \
--mol_data $mol_csv \
--g4mp2_en $g4mp2_csv \
--out_dir $output_dir --log $verbose \
--nprocs $nprocs --indices $indices
echo "finished"