Commit 0934c527 authored by Ryan Randles Jones's avatar Ryan Randles Jones
Browse files

update readme

parent cf3a83da
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
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 --partition=express
#SBATCH --mem-per-cpu=4000
module load cuda10.0/toolkit
module load Anaconda3
......@@ -22,34 +18,25 @@ else
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
Configuring the environment
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
```
module load Anaconda3/2019.10
Under Extra jupyter arguments, specify
```
--notebook-dir=/data/user/$USER/slurm-ds
```
For partition, specify
```
pascalnodes
```
\ No newline at end of file
For partition, set partition to
express
for time up to 2 hours. Also make sure to specify the number of hours field to match. For up to 12 hours, the
short
partition can be used.
After the Jupyter notebook is started, click on the blue "Connect to Jupyter" button.
Once the Jupyter session is active, select the slurm-2sql notebook. Then change the kernel, via Kernel->Change kernel->Python [conda env:.conda-slurm-ds]
Verify the environment loaded correctly by running the first cell of the slurm-2sql notebook (with the library imports)
Creating a text version of sacct output
If we have to create a database from sacct
directoryToUse="/data/user/$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.txt
\ No newline at end of file
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