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Default Resources

Cluster available resources

Node type Name(s) #Threads Memory Processor(s) GPU
standard (x38) n001 to n038 128 2 TiB 2 x AMD EPYC 7713 -
bigmem bigmem01 128 4 TiB 2 x AMD EPYC 7713 -
gpu gpu01 128 1 TiB 2 x Intel Gold 6338 4 x NVIDIA A100 80G
gpu (x2) gpu02 & gpu03 256 1.5 TiB 2 x AMD EPYC 9554 4 x NVIDIA L40S 48G
visu visu01 128 512 GiB 2 x AMD EPYC 7513 1 x NVIDIA RTX6000 24G

Disk spaces available

Path Limit Writable Description
/home/<username> 10 GB Store your configuration files
/work/user/<username> 1 TB Working directory
/save/user/<username> 250 GB Data you want to save (replication) with 30 retention days
/usr/local/bioinfo/src/ - Directory gathering all bioinformatic softwares (FAQ)
/bank - Biological banks in different format (FAQ)

If you need more space in /work or in /save you are invited to fill the resources request form.

How to get my disk quota and usage?

  • On /work:
mmlsquota -u <username> --block-size G
  • On /save and /home:
# For the global usage on savedu -csh --apparent-size /save/user/<username>/# For each folder usage on save (including hidden ones)du -csh --apparent-size /save/user/<username>/{.[^.]*,*} | sort -h# For the global usage on homedu -csh --apparent-size /home/<username>/# For each folder usage on home (including hidden ones)du -csh --apparent-size /home/<username>/{.[^.]*,*} | sort -h

Default CPU time

Academic account quota is 100 000 h/per calendar year

Beyond these 100 000 hours, you will need to submit a science project (by the resources request form) to estimate the real needs of the bioinformatics environment.

According to results from this evaluation, but also their geographical and institutional origin, users can then either continue their treatments or be invited to contribute financially to infrastructure, or be redirected to regional or national mésocentres calculation.

Non-academic account quota is 500 h/per calendar year for testing the infrastructure.

Overtime calculation will be charged (price on request).

In order to know your quota, please use the following command:

squota_cpu

Default job resource

Without any parameters all jobs are limited to:

  • 2GB (memory)
  • 1 CPU (thread)
  • 2 hours (on workq only)

CPU (threads) limitation rules

It depends on the status of your Slurm group (contributors, INRAe and/or REGION, others).

Max threads workq (group) workq (user) unlimitq (All users) unlimitq (user)
Contributors 5184 750 780 500
INRAe/Region 4409 500 780 376
Others 1296 250 780 100

In order to known the status and the limits of your account, please use:

saccount_info $(whoami)

In this command, $(whoami) will be automagically replaced by your Genotoul Bioinfo login.

If the group limit is reached, your jobs are queued with the reason “AssocGrpCpuLimit”.

Memory limitation rules

It depends on the status of your Slurm group (contributors, INRAe and/or REGION, others).

Max mem workq (group) workq (user) unlimitq (All users) unlimitq (user)
Contributors 82 TB 12 TB - 8 TB
INRAe/Region 71 TB 8 TB - 6 TB
Others 21 TB 4 TB - 2 TB

To known the status and the limits of your account:

saccount_info $(whoami)

In this command, $(whoami) will be automagically replaced by your Genotoul Bioinfo login.

If the group limit is reached, your jobs are queued with the reason “AssocGrpMemLimit”.

Job number limitation rules

Case Limit
Max job per user 2500
Max job for all users 10000
Max task array per job 2501

Time limitation rules

Slurm Partition Default Time Max Time
workq 2 hours 96 hours (4 days)
gpuq 96 hours (4 days) 96 hours (4 days)
interq 12 hours 12 hours
unlimitq, wflowq 90 days (3 months) 90 days (3 months)

Useful scripts/alias

Useful commands summary

The useful_commands command will give you a summary of some useful commands.

Useful account informations

saccount_info <username> command will gives you some useful informations of your account like:

  • account expiration date and last password change date ( every year)
  • your primary Linux group
  • your secondary Linux groups if you have some
  • status of your Linux primary group in Slurm (contributors, inraregion or others)
  • your groups' members
  • some Slurm limitations of your account

squeue long format

  • sq_long : squeue verbose with detail for: JOBID NAME USER QOS PARTITION NODES CPUS MIN_MEMORY TIME_LIMIT TIME_LEFT STATE NODELIST REASON. Can take all squeue options. See --help option for help.
  • sq_debug : squeue verbose for debug. Show COMMAND and WORKDIR for a job. Can take all squeue options. See --help option for help.
  • sq_run : sq_debug for running jobs. Can take all squeue options. See --help option for help.
  • sq_pend : sq_debug for pending jobs. Can take all squeue options. See --help option for help.

sacct long format

  • sa_debug : sacct verbose. Can take all sacct options. See --help option for help.