Slurm Usage

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**Quick IntroductionIntroduction**

A queue in Slurm is called a partition. User commands are prefixed with '''s'''`s`.

**Useful CommandsCommands**

*- sacct,`sacct`, sbatch,`sbatch`, sinfo,`sinfo`, sprio,`sprio`, squeue,`squeue`, srun,`srun`, sshare,`sshare`, sstate`sstate`, etc...
sbatch- #`sbatch`: sends jobs to the slurmSlurm queue
sinfo- #`sinfo`: general info about slurmSlurm
squeue- #`squeue`: inspect queue
- `sinfo -lNe #lNe`: more detailed info reporting with long format and nodes listed individually
- `scancel 22 #22`: cancel job 22
- `scontrol show job 2 #2`: show control info on job 2

**Examples:
<pre>**

```bash
# find the quequeue names:
[user@computer ~]$ sinfo
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
basic* up infinite 1 idle

# test a job submission (don't run)
sbatch --test-only slurm_test.sh

# run a job
sbatch slurm_test.sh
```

</pre>

=== **Example Slurm job filefile:**

===
<pre>

```bash
#!/bin/bash
## SLURM REQUIRED SETTINGS
#SBATCH --partition=basic
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1

## SLURM reads %x as the job name and %j as the job ID
#SBATCH --output=%x-%j.out
#SBATCH --error=%x-%j.err

# Output some basic info with job
pwd; hostname; date;

# requires ED2_HOME env var to be set
cd $ED2_HOME/run

# Job to run
./ed2
</pre>```

**Another Example:
<pre>**

```bash
#!/bin/bash
#
#SBATCH -p basic # partition name (aka queue)
#SBATCH -c 1 # number of cores
#SBATCH --mem 100 # memory pool for all cores
#SBATCH -t 0-2:00 # time (D-HH:MM)
#SBATCH -o slurm.%N.%j.out # STDOUT
#SBATCH -e slurm.%N.%j.err # STDERR

# code or script to run
for i in {1..100000}; do
echo $RANDOM >> SomeRandomNumbers.txt
donesort SomeRandomNumbers.txt
```

</pre>**Python Example:**

====Python Example====
The output goes to a file in your home directory called `hello-python-*.out,out`, which should contain a message from python.
<pre>Python.

```bash
#!/bin/bash

## SLURM REQUIRED SETTINGS1G
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1

## SLURM reads %x as the job name and %j as the job ID
#SBATCH --output=%x-%j.out
#SBATCH --error=%x-%j.err

#SBATCH --job-name=hello-python # create a short name for your job
#SBATCH --time=00:01:00 # total run time limit (HH:MM:SS)

## Example use of Conda:

# first source bashrc (with conda.sh), then conda can be used
source ~/.bashrc

# make sure conda base is activated
conda activate

# Other conda commands go here

## run python
python hello.py
```

</pre>

`hello.pypy` should be something like this:
<pre>

```python
print('Hello from python!Python!')
</pre>```

=== **Computer FactsFacts:**

===

Find out facts about the computer for the job file

<pre>```bash
# number of cores?
grep 'cpu cores' /proc/cpuinfo | uniq

# memory
[emery@bellows ~]$ free -h
total used free shared buff/cache available
Mem: 1.5Ti 780Gi 721Gi 1.5Gi 8.6Gi 721Gi
Swap: 31Gi 0B 31Gi

</pre>

=== nodes vs tasks vs cpus vs cores ===
Here's a very good writeup: https://researchcomputing.princeton.edu/support/knowledge-base/scaling-analysis. For most of our use cases, one node and one task is all that is needed (More than this requires special code such as mpi4py (MPI = Message Passing Interface).
<pre>
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=N
</pre>
is the correct way to request N cores for a job. Just replace N in that config with the number of cores you need

To get the max value for N for a computer:
<pre>
scontrol show node | grep CPU
</pre>
produces 'CPUTot'

Quoting directly from: https://login.scg.stanford.edu/faqs/cores/
Also useful: https://stackoverflow.com/questions/65603381/slurm-nodes-tasks-cores-and-cpus

=== See Also ===
https://www.carc.usc.edu/user-information/user-guides/hpc-basics/slurm-templates

https://docs.rc.fas.harvard.edu/kb/convenient-slurm-commands/

https://csc.cnsi.ucsb.edu/docs/slurm-job-scheduler

Genomics related:
https://wiki.itap.purdue.edu/display/CGSB/How-to+Genomics

Python:
https://rcpedia.stanford.edu/topicGuides/jobArrayPythonExample.html