From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Thu Dec 06 2018 - 14:51:38 CST
Namd has no reource scheduler for clusters. Please share your submit script so that we can see what is being attempted.
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On December 6, 2018 at 12:41:55 PM PST, McGuire, Kelly <mcg05004_at_byui.edu> wrote:
I just tried, for the first time, submitting 10 minimization jobs from the same bash submit script. Usually, using the CUDA NAMD version with 4 GPUs, an individual minimization job finishes in 15-20 seconds. If I try submitting 10 minimization jobs on 10 nodes, with 24 cpus per node, 64 GB per node, and 4 GPUs per node, it takes about 2 minutes to finish the minimization jobs. It seems that each job is not getting their own node and set of GPUs. How does NAMD handle parallel jobs like this?
Kelly L. McGuire
Department of Physiology and Developmental Biology
Brigham Young University
Provo, UT 84602
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