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Saisri Vegesna
SacctDataAnalysis
Commits
82483573
Commit
82483573
authored
5 years ago
by
Saisri Vegesna
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82483573
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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