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KOMAL BADI
createAndParseSACCT
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8c217b75
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8c217b75
authored
Mar 20, 2020
by
Saisri Vegesna
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A yml and a set of instructions to build a functioning environment for the Research Computing
# clone this repo:
```
$git clone https://gitlab.rc.uab.edu/rc-data-science/createandparsesacct.git /data/user/saisri/slurm-ds
```
Now load the Anaconda module and create environment on Cheaha cluster:
# clone this repo and update with the job composer
Copy and paste the following job script into a job composer job on rc.uab.edu
```
$module load Anaconda3
$conda env create -f environment-slurm-ds.yml
#!/bin/bash
#SBATCH --partition=pascalnodes
#SBATCH --gres=gpu:1
#SBATCH --mem-per-cpu=4000
module load cuda10.0/toolkit
module load Anaconda3
FOLDER
=
/data/user/
$USER
/slurm-ds
URL
=
https://gitlab.rc.uab.edu/rc-data-science/createandparsesacct.git
if
[
!
-d
"
$FOLDER
"
]
;
then
git clone
"
$URL
"
"
$FOLDER
"
conda
env
create
-f
/data/user/
$USER
/slurm-ds/environment-slurm-ds.yml
else
cd
$FOLDER
git pull
"
$URL
"
conda
env
update
-f
/data/user/
$USER
/slurm-ds/environment-slurm-ds.yml
fi
```
If we have to create a database from sacct
```
directoryToUse="/data/user/$USER/
VariousNeurology/user/
"
sacct -P -u $USER --starttime=2019-01-01 --format user,start,jobid,jobname,state,partition,maxrss,reqmem,reqcpus,node,nnodes,elapsed >> "$directoryToUse"
userusage
.db
directoryToUse="/data/user/$USER/
group
"
sacct -P -u $USER --starttime=2019-01-01 --format user,start,jobid,jobname,state,partition,maxrss,reqmem,reqcpus,node,nnodes,elapsed >> "$directoryToUse"
group
.db
```
# Check to see if the environment works
...
...
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