Quick start guide 🇬🇧

Account

To access the IGBMC cluster, you must use your IGBMC IT account.

More information about how to manage your IGBMC IT account on Compte numérique IGBMC

Log in

On Linux/Mac, simply use ssh client like OpenSSH :

Copy

ssh <IGBMC login>@hpc.igbmc.fr

IGBMC HPC login

ifb> # We can follow the execution of my job JobID JobName Partition Account AllocCPUS State ExitCode 2901891 python training taskforce 1 COMPLETED 0:0 2902160 python training taskforce 4 COMPLETED 0:0 2902316 python training taskforce 1 COMPLETED 0:0 2902472 myscript.+ training taskforce 1 COMPLETED 0:0 2902472.bat+ batch taskforce 1 COMPLETED 0:0 2902472.0 sleep taskforce 1 COMPLETED 0:0 2902472.1 echo taskforce 1 COMPLETED 0:0 2902472.2 sleep taskforce 1 COMPLETED 0:0 2902472.3 python taskforce 1 COMPLETED 0:0

asciinema.org

On Windows, you can use clients like PuTTY

Please see the Logging in page for further details.

Data

Storage

Several volumes of data storage are available on the IGBMC cluster.

Please see the Space2 service page for further details about scientific projects data storage

Transfer

SSH protocol (or SFTP - SSH File Transfer Protocol) is the only protocol available. But, you can use many clients to download your data from the cluster (scp, rsync, wget, ftp, etc.).

Software

To use softwares like blast, python, gcc, etc. we have to "load" them using module commands (Environment Modules):

• List available software : module avail
• Load blast in your environment : module load blast
• Load a specific version : module load blast/2.2.25

You can also use singularity or conda directly.

Please see the Conda or Singularity pages for further details

Submit a job

The computing works are done by submitting "jobs" to the workload manager Slurm.

You must use Slurm to execute your jobs.

1. Write a bash script

This script must contain your commands to execute. Many editors are available (see editors page). Here, inside myscript.sh, we launch a bowtie command and just print some truth.

#!/bin/bash
bowtie2 -x hg19 -1 sample_R1.fq.gz -2 sample_R2.fq.gz -S sample_hg19.sam
echo "Enjoy slurm ! It's highly addictive."

2. Add options and requirements

You can specify several options to your jobs (name, number of CPU, amount of memory, time limit, etc.). All this parameter take place in the beginning of the script with the #SBATCH directive (just after the shebang #!/bin/bash). Here we specify the job name and the amount of memory required.

#!/bin/bash

#SBATCH --job-name=bowtie
#SBATCH --mem=40GB

bowtie2 -x hg19 -1 sample_R1.fq.gz -2 sample_R2.fq.gz -S sample_hg19.sam

echo "Enjoy slurm ! It's highly addictive."

3. Launch your job with sbatch

sbatch myscript.sh

The command return a jobid to identify your job. See more usefull information below (Slurm commands).

4. Follow your job

The status goes successively from PENDING (PD) to RUNNING (R) and finally COMPLETED (C) (and job disappear from the queue). So if your job is not displayed, your jobs is finished (with success or with error).

squeue

5. See output

The output of the script (standard output and standard error) is live written. Default output file is slurm-[jobid].out in your working directory. And of course, if you have some result files like sample_hg19.sam, these files will be available.

Notes

• All nodes have access to the data (/shared/home, /shared/space2 or /shared/genome).
• All softwares are available on the nodes, but we have to load them inside the script with command module load [module].
• All jobs are contained and can not use more resources than defined (CPU, memory).
• Jobs which exceed limits (memory or time, values by default or set) are killed.
• It’s possible to be connected on a compute node when a job is running (ssh cpu-node-XX).

Slurm commands

If you are used to PBS/Torque/SGE/LSF/LoadLeveler, refer to the Rosetta Stone of Workload Managers

• Submit a job: sbatch myscript.sh
• Information on jobs: squeue
• Information on my jobs: squeue -u $USER
• Information on running job: scontrol show job <jobid>
• Delete a job: scancel <jobid>

Please see the SLURM user guide page for further details.

Don’t hesitate to have also a look at the sbatch official documentation

Script template

Just an example. Customize it to meet your needs.

#!/bin/bash################################ Slurm options #################################
### Job name
#SBATCH --job-name=demo_job
### Limit run time "days-hours:minutes:seconds"
#SBATCH --time=01:00:00
### Requirements
#SBATCH --partition=igbmc
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem-per-cpu=8GB
### Email
#SBATCH --mail-user=email@address
#SBATCH --mail-type=ALL
### Output
#SBATCH --output=/shared/home/<user>/demojob-%j.out
################################################################################

echo '########################################'
echo 'Date:' $(date --iso-8601=seconds)
echo 'User:' $USER
echo 'Host:' $HOSTNAME
echo 'Job Name:' $SLURM_JOB_NAME
echo 'Job Id:' $SLURM_JOB_ID
echo 'Directory:' $(pwd)
echo '########################################'
# modules loading
module load ...
# What you actually want to launch
echo 'Waooouhh. Awesome.'
echo '########################################'
echo 'Job finished' $(date --iso-8601=seconds)