Commit ab6ec853 authored by Ryan Randles Jones's avatar Ryan Randles Jones
Browse files

Update README.md

parent cf3a83da
......@@ -6,8 +6,7 @@ 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
......@@ -23,12 +22,8 @@ else
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.
......@@ -37,9 +32,7 @@ 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
......@@ -48,8 +41,26 @@ Under Extra jupyter arguments, specify
--notebook-dir=/data/user/$USER/slurm-ds
```
For partition, specify
For partition, set partition to
```
express
```
for time up to 2 hours. Also make sure to specify the number of hours field to match. For up to 12 hours, the
```
short
```
partition can be used.
After the Jupyter notebook is started, click on the blue "Connect to Jupyter" button.
Once the Jupyter session is active, select the `slurm-2sql` notebook. Then change the kernel, via `Kernel->Change kernel->Python [conda env:.conda-slurm-ds]`
Verify the environment loaded correctly by running the first cell of the `slurm-2sql` notebook (with the library imports)
# Creating a text version of sacct output
If we have to create a database from sacct
```
directoryToUse="/data/user/$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
```
pascalnodes
```
\ No newline at end of file
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