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Update job submission instructions from PBS to Slurm #197

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Update job submission instructions from PBS to Slurm #197

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27 changes: 14 additions & 13 deletions running_matlab_jobs.md
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Original file line number Diff line number Diff line change
Expand Up @@ -18,25 +18,26 @@ fname='randnums.csv';
csvwrite(fname,rmatrix);
quit
```
This program can be submitted using batch mode with the command `matlab -r my_program`. In this command the `-r` flag is telling MATLAB to run your script `my_program.m` in batch mode. Notice that when calling a script with batch mode you leave off the extension `.m`. This command works if you are running on a local machine, however, when running jobs at CARC you need to submit your job to the job scheduler using a PBS script. For those unfamiliar with PBS scripts explanations and example scripts can be found [here](http://carc.unm.edu/user-support/using-carc-systems/running-jobs/sample-pbs-scripts.html). To submit our MATLAB program to the Wheeler job scheduler we would put our batch command in a PBS script similar to the one below:
This program can be submitted using batch mode with the command `matlab -r my_program`. In this command the `-r` flag is telling MATLAB to run your script `my_program.m` in batch mode. Notice that when calling a script with batch mode you leave off the extension `.m`. This command works if you are running on a local machine, however, when running jobs at CARC you need to submit your job to the job scheduler using a Slurm script. For those unfamiliar with Slurm scripts explanations and example scripts can be found [here][(https://github.com/UNM-CARC/QuickBytes/blob/master/Intro_to_slurm.md)]. To submit our MATLAB program to the Easley or Hopper job scheduler we would put our batch command in a Slurm script similar to the one below:

```bash
#!/bin/bash

# Commands specific to the job scheduler requesting resources, naming your job, and setting up email alerts regarding job status.
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=8
#PBS -N my_matlab_job
#PBS -m abe
#PBS -M [email protected]
# Commands specific to the job scheduler requesting resources, naming your job, and setting up email alerts regarding job status #SBATCH --job-name=my_matlab_job
#SBATCH --time=1:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --mail-type=ALL
#SBATCH [email protected]
#SBATCH --output=slurm-%j.out

# Change to the directory that you submitted your PBS script from.
cd $PBS_O_WORKDIR
# Change to the directory that you submitted your Slurm script from.
cd "$SLURM_SUBMIT_DIR"

# Loading the MATLAB software module. The specific module name is system dependent.
module load matlab/R2017a
module load matlab/R2023a

# Calling MATLAB in batch mode to run your program.
# Calling MATLAB in batch mode to run your program.
matlab -nojvm -nodisplay -r my_program > /dev/null
```

Expand All @@ -45,8 +46,8 @@ There are a couple of additions to our batch mode command when calling MATLAB on
```bash
matlab -nojvm -nodisplay -r my_program > my_program.output
```
Now that you have your program and your PBS script you can submit your job to the job scheduler using the `qsub` command:
Now that you have your program and your Slurm script you can submit your job to the job scheduler using the `sbatch` command:

```bash
qsub my_matlab_job.pbs
sbatch my_matlab_job.sbatch
```