Parallel Jobs

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Dec 06 2018 - 14:36:45 CST

  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

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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