String Method with Swarms of Trajectories (SMwST) Performance

From: Alexander Adams (xadams_at_umich.edu)
Date: Thu Jul 11 2019 - 10:43:25 CDT

Dear NAMD users,

I am attempting to perform SMwST on a membrane embedded transport protein,
as done in the Exploring Complex Transition Pathways tutorial
<http://www.ks.uiuc.edu/Training/Tutorials/namd/confsamp-tutorial/confsamp.pdf>.I
achieve expected performance (several hours/iteration) for ~20 iterations,
then experience a dramatic slowdown where it is common for runs of a single
iteration to time out after 24-48 hours. I've experienced this on 2
separate clusters and see only minor (<10%) changes in NAMD's reported
performance speed. I have noticed that most of the failed runs have the
memory usage swell from 700 Mb to 93 Gb, though some still complete despite
this behavior.

I apologize for the slim information, but I'm not sure what will best help
in the debugging process. Thanks in advance for your assistance!

Alex Adams

-- 
University of Michigan, Ann Arbor
Ph.D. Candidate - Mayes Lab
College of Engineering - Chemical Engineering

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