NAMD slows at startup phase 1 smp problem

From: Ryan Gordon (
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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