HPC-Meso

High performance computing on the Aix-Marseille université mesocentre

Objectives

This repository aims at pointing to pertinent documentation pages and providing templates for main common processing steps (e.g. data importation, job submission) in the mesocentre.

Submitting jobs with Slurm

sbatch slurm command executes instructions stored in a .sh or .slurm script.

sbatch my_script.slurm

sbatch 17.02.7 documentation (current version installed in the mesocentre).

Slurm template files

The slurm_templates directory contains .slurm scripts with preset values.

# Content of the deep_learning.slurm file
#!/bin/bash
#-----------------------------------------------------#
# TEMPLATE FOR TYPICAL DEEP-LEARNING JOBS EXECUTION   #
#-----------------------------------------------------#

# Generic configuration
#SBATCH --account=<project_id>  # identifier of the related Mesocentre Project

# Mailing configuration
#SBATCH --mail-type=ALL  # Mail notification of the events concerning the job : start time, end time,…
#SBATCH --mail-user=<email_address>

# Files pattern
#SBATCH --job-name=<job_name>
#SBATCH -e %x_%j.err    #pattern is jobname_jobid
#SBATCH -o %x_%j.out    #pattern is jobname_jobid

# Computing resources
#SBATCH --partition=volta, pascal, kepler   # partition with gpu
#SBATCH --gres=gpu:1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=5
#SBATCH --time=96:00:00

To slum master and beyond

• conditionnal jobs execution

Data importation

Users are allowed to transfer data from and to the mesocentre using scp, rsync and sftp commands. Data transfer can be performed in two different ways (https://mesocentre.univ-amu.fr/sauvegarde-donnees):

1. using the [email protected] machine, if transfer does not exceed 30 min (few data). In this way, no processing time is consumed.
2. using a dedicated node either in interactive (srun) or passive (sbatch) mode for larger data import

In order to achieved secured data copy, we only provide rsync based slurm template file. Know that rsync is not optimized (very slow) for huge data through Wide Area Network (WAN).

# Content of the import_data.slurm file
#!/bin/bash
#-----------------------------------------------------#
# TEMPLATE FOR DATA IMPORTATION SBATCH JOBS EXECUTION #
#-----------------------------------------------------#

# Generic configuration
#SBATCH --account=<project_id>  # identifier of the related Mesocentre Project

# Mailing configuration
#SBATCH --mail-type=ALL  # Mail notification of the events concerning the job : start time, end time,…
#SBATCH --mail-user=<email_address>

# Files pattern
#SBATCH --job-name=<job_name>
#SBATCH -e %x_%j.err  #pattern is jobname_jobid
#SBATCH -o %x_%j.out  #pattern is jobname_jobid

# Computing resources
#SBATCH --partition=skylake  # partition with cpu only and /scratch available
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=96:00:00

# default general syntax (we already are logged in login.mesocentre.univ-amu.fr)
rsync -avzh --progress <login_host_source>@<host_source>:<path_source> <path_dest>

# default optimised syntax ((we already are logged in login.mesocentre.univ-amu.fr and
# need to copy >1G0 data)
rsync -aHAXxv --numeric-ids --delete --progress -e "ssh -T -o Compression=no -x" <login>@<host>:<path> <path_dest>

# a practical example to copy data from /envau to mesocentre
rsync -aHAXxv --numeric-ids --delete --progress -e "ssh -T -o Compression=no -x" 
<login>@<frioul.int.univ-amu.fr>:/envau/<path_source>
/scratch/<mesocentre_login>/<path_dest>