From: Siva Dasetty (sdasett_at_g.clemson.edu)
Date: Tue Sep 09 2014 - 18:59:01 CDT
Dear All,
I am running a simulation of a small protein (4K atoms) in implicit solvent
using cuda enabled NAMD and I only get 2-3 ns/day computational speed when
I am using a single node with 10 (or less) processors and 2 gpus (k20's).
However if I try to increase the number of nodes, I get the following error
"CUDA-enabled NAMD requires at least one patch per process."
and if I increase the number of processors >10 in a single node, I also get
the following note "MPI_ABORT was invoked on rank 4 in communicator
MPI_COMM_WORLD
with errorcode 1." along with the above fatal error.
I tried to follow previous threads in the archive list but couldn't
understand anything much about this (
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/11376.html).
Is this because my system size is too small ? or am I doing something
absurd while executing the job?
I have seen better benchmarks reported by NVDIA (
http://www.nvidia.com/docs/IO/122634/NAMD-benchmark-report.pdf) and others (
http://www.ks.uiuc.edu/Research/gpu/files/ICMS-Edinburgh/GB.pdf).
Thanks,
-- Siva
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