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KOMAL BADI
createAndParseSACCT
Commits
f44de1a4
Commit
f44de1a4
authored
Mar 24, 2020
by
William Stonewall Monroe
Browse files
Merge branch 'Branch' into 'master'
Branch See merge request
rc-data-science/createandparsesacct!5
parents
11da58b5
4642d869
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README.md
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f44de1a4
A yml and a set of instructions to build a functioning environment for the Research Computing
# 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
```
#!/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/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
After the environment is created, you can start up an interactive Jupyter notebook session through rc.uab.edu to check if the environment works.
Under environment setup, specify
```
# Load required modules
module load cuda10.0/toolkit
module load Anaconda3
```
Under Extra jupyter arguments, specify
```
--notebook-dir=/data/user/$USER/slurm-ds
```
For partition, specify
```
pascalnodes
```
\ No newline at end of file
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