From: Antonio Frances Monerris (antonio.frances_at_uv.es)
Date: Mon Sep 19 2022 - 09:40:37 CDT
Dear NAMD users,
I am trying to run NAMD 2.14 in a scientific cluster operating with the Slurm job manager. My goal is to distribute the simulation into several nodes to accelerate the simulation timings. Each node has 36 physical CPUs (2 sockets of 18 processors each).
Some info on the software versions:
Converse/Charm++ Commit ID: v6.10.2-0-g7bf00fa-namd-charm-6.10.2-build-2020-Aug-05-556
Info: NAMD 2.14 for Linux-x86_64-verbs-smp
This is the command I run:
srun -N 10 charmrun ++n 10 ++ppn 35 namd2 +setcpuaffinity +idlepoll $NAMD_INPUT > $NAMD_OUTPUT
It runs. However, I do not obtain what I want. The output prints these sentences, 10 times each:
Charm++> Running in SMP mode: 10 processes, 35 worker threads (PEs) + 1 comm threads per process, 350 PEs total
Charm++> Running on 1 hosts (2 sockets x 18 cores x 1 PUs = 36-way SMP)
Charm++> Warning: the number of SMP threads (360) is greater than the number of physical cores (36), so threads will sleep while idling. Use +CmiSpinOnIdle or +CmiSleepOnIdle to control this directly.
Info: Running on 350 processors, 10 nodes, 1 physical nodes.
The two first sentences are coherent with my purpose, but not the last two. Later, NAMD prints the statistics for the same steps also ten times each. It seems that instead of running one simulation in 10 nodes, it is repeating the same simulation 10 times, one per node. This seems to be confirmed by the .dcd file, which contains only the number of frames covered by the output (they are not multiplied by 10). The time per step does not significantly change when varying the number of nodes, coherently with my diagnostic.
What am I missing? Can someone help me with the submission, please?
Many thanks for reading.
With sincere regards,
Antonio
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