cc_staff
153
edits
NAMD: Difference between revisions
Jump to navigation
Jump to search
Add UCX version
(Marked this version for translation) |
(Add UCX version) |
||
| Line 39: | Line 39: | ||
<!--T:12--> | <!--T:12--> | ||
Note: Using a verbs library is more efficient than using OpenMPI, hence only verbs versions are provided on systems where those are supported. Currently | Note: Using a verbs or UCX library is more efficient than using OpenMPI, hence only verbs or UCX versions are provided on systems where those are supported. Currently those versions do not work on cedar as they are incompatible with the communications fabric, so use MPI versions instead. | ||
<!--T:29--> | <!--T:29--> | ||
| Line 78: | Line 78: | ||
<!--T:17--> | <!--T:17--> | ||
'''NOTE''': Verbs versions will not run on Cedar because of its different interconnect. Use the MPI version instead. | '''NOTE''': Verbs versions will not run on Cedar because of its different interconnect. Use the MPI version instead. | ||
'''NOTE''': Verbs versions will also not run on Béluga because of its incompatible infiniband kernel drivers. Use the UCX version instead. | |||
</translate> | </translate> | ||
{{File | {{File | ||
| Line 101: | Line 102: | ||
NAMD2=`which namd2` | NAMD2=`which namd2` | ||
$CHARMRUN ++p $P ++nodelist $NODEFILE $NAMD2 +idlepoll apoa1.namd | $CHARMRUN ++p $P ++nodelist $NODEFILE $NAMD2 +idlepoll apoa1.namd | ||
}} | |||
<translate> | |||
== UCX jobs == <!--T:16--> | |||
This example uses 80 processes in total on 2 nodes, each node running 40 processes, thus fully utilizing its 80 cores. This script assumes full nodes are used, thus ntasks/nodes should be 40 (on Béluga). For best performance, NAMD jobs should use full nodes. | |||
<!--T:17--> | |||
'''NOTE''': UCX versions will not run on Cedar because of its different interconnect. Use the MPI version instead. | |||
</translate> | |||
{{File | |||
|name=ucx_namd_job.sh | |||
|lang="sh" | |||
|contents= | |||
#!/bin/bash | |||
# | |||
#SBATCH --ntasks 80 # number of tasks | |||
#SBATCH --nodes=2 | |||
#SBATCH --ntasks-per-node=40 | |||
#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 namd-ucx/2.13 | |||
srun --mpi=pmi2 namd2 apoa1.namd | |||
}} | }} | ||
<translate> | <translate> | ||
== MPI jobs == <!--T:18--> | == MPI jobs == <!--T:18--> | ||
'''NOTE''': Use this only on Cedar, where verbs versions will not work. | '''NOTE''': Use this only on Cedar, where verbs and UCX versions will not work. | ||
</translate> | </translate> | ||
{{File | {{File | ||