NAMD slows at startup phase 1 smp problem

From: Ryan Gordon (rg563_at_drexel.edu)
Date: Mon Jan 12 2015 - 12:24:31 CST

I am having some trouble running NAMD 2.10 for Linux-x86_64-MPI-smp-CUDA. I am running on 128 processors, 128 nodes, and 8 physical nodes. The warning I am getting at the beginning is as follows:

Charm++> Warning: the number of SMP threads (32) is greater than the number of physical cores (16), so threads will sleep while idling. Use +CmiSpinOnIdle or +CmiSleepOnIdle to control this directly.

I am not sure how to address this issue, and it seems to take a long time for "startup phase 1" to run compared to the other startup phases. Has anyone else had similar problems?

--
Ryan GordonPh.D. Candidate
Chemical and Biological Engineering
Drexel University
CBEGSA Vice President

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