cc_staff
229
edits
NAMD: Difference between revisions
UCX GPU jobs
m (add category BiomolecularSimulation) |
(UCX GPU jobs) |
||
| Line 131: | Line 131: | ||
}} | }} | ||
<translate> | <translate> | ||
== UCX GPU jobs == | |||
This example is for Béluga and it assumes that full nodes are used, which gives best performance for NAMD jobs. It uses 8 processes in total on 2 nodes, each process(task) using 10 threads and 1 GPU. This fully utilizes Béluga GPU nodes which have 40 cores and 4 GPUs per node. Note that 1 core per task has to be reserved for a communications thread, so NAMD will report that only 72 cores are being used but this is normal. | |||
To use this script on other clusters, please look up the specifications of their available nodes and adjust --cpus-per-task and --gres=gpu: options accordingly. | |||
'''NOTE''': UCX versions will not run on Cedar because of its different interconnect. | |||
{{File | |||
|name=ucx_namd_job.sh | |||
|lang="sh" | |||
|contents= | |||
#!/bin/bash | |||
#SBATCH --ntasks 8 # number of tasks | |||
#SBATCH --nodes 2 | |||
#SBATCH --cpus-per-task=10 # number of threads per task (process) | |||
#SBATCH --gres=gpu:4 | |||
#SBATCH --mem=0 # memory per node, 0 means all memory | |||
#SBATCH -o slurm.%N.%j.out # STDOUT | |||
#SBATCH -t 0:05:00 # time (D-HH:MM) | |||
#SBATCH --account=def-specifyaccount | |||
module load StdEnv/2020 intel/2020.1.217 cuda/11.0 namd-ucx-smp/2.14 | |||
NUM_PES=$(expr $SLURM_CPUS_PER_TASK - 1 ) | |||
srun --mpi=pmi2 namd2 ++ppn $NUM_PES apoa1.namd | |||
}} | |||
== MPI jobs == <!--T:18--> | == MPI jobs == <!--T:18--> | ||