Biophysics LEO
- Name of the cluster:
LEO
- Institution:
Max Planck Institute of Biophysics
Login nodes:
|
|
Hardware Configuration:
- 2 login node leo[01-02]
- 2 x AMD EPYC 9454 48-Core Processor @ 2.75 GHz96 cores per nodehyper-threading enabled - 2 threads per core755 GB RAM
- 11 execution nodes leo[001-001]
- 2 x AMD EPYC 9454 48-Core Processor @ 2.75 GHz96 cores per nodehyper-threading enabled - 2 threads per core755 GB RAM
- 8 execution nodes leog[101-108]
- 2 x AMD EPYC 9554 64-Core Processor @ 3.10 GHz128 cores per nodehyper-threading enabled - 2 threads per core755 GB RAM8 x NVIDIA L40S GPUs per node
- 3 execution nodes leog[201-203]
- 2 x AMD EPYC 9554 64-Core Processor @ 3.10 GHz64 cores per nodehyper-threading disabled - 1 threads per core1.5 TB RAM4 x NVIDIA H100 GPUs per node
- node interconnect
based on Mellanox Technologies InfiniBand fabric (Speed: 200Gb)
Filesystems:
GPFS-based with total size of 7.5 PB and independent inode space for the following filesets:
- /u
shared home filesystem; GPFS-based; user quotas (250 GB data, 512k files/) enforced; quota can be checked with ‘/usr/lpp/mmfs/bin/mmlsquota’. NO BACKUPS YET
- /leo/work
shared scratch filesystem; GPFS-based; no quotas enforced. NO BACKUPS !
- /leo/data
shared scratch filesystem; GPFS-based; no quotas enforced. NO BACKUPS !
- /cryo/*
- only on leo[01-02]read-only
Compilers and Libraries:
Hierarchical environment modules are used at MPCDF to provide software packages and enable switching between different software versions. User have to specify the needed modules with explicit versions at login and during the startup of a batch job. Not all software modules are displayed immediately by the module avail command, for some user first needs to load a compiler and/or MPI module. You can search the full hierarchy of the installed software modules with the find-module command.
Batch system based on Slurm
The batch system on LEO is the Slurm Workload Manager. A brief introduction into the basic commands (srun, sbatch, squeue, scancel, …) can be found on the Raven home page. For more detailed information, see the Slurm handbook. See also the sample batch scripts which must be modified for LEO cluster.
Current Slurm configuration on LEO:
default turnaround time: 2 hours
current max. turnaround time (wallclock): 24 hours
p.leo partition include all batch nodes in exclusive usage and is default
s.leo partition can be used for serial jobs and can be shared
Useful tips:
By default run time limit used for jobs that don’t specify a value is 2 hours. Use --time option for sbatch/srun to set a limit on the total run time of the job allocation but not longer than 24 hours
Default memory per node in the shared partition is 47000 MB. To grant the job access to all of the memory on each node use --mem=0 option for sbatch/srun
The OpenMP codes require a variable OMP_NUM_THREADS to be set. This can be obtained from the Slurm environment variable $SLURM_CPUS_PER_TASK which is set when --cpus-per-task is specified in a sbatch script (an example is on help information page)
To use GPUs add in your slurm scripts --gres option and choose how many GPUs and/or which model of them to have: #SBATCH --gres=gpu:type:X, where type is either l40s or h100 and X is a number of resources (1-8 for l40s and 1-4 for h100)
GPU cards are in default compute mode.
Support:
For support please create a trouble ticket at the MPCDF helpdesk