GBIS using CUDA enabled NAMD

From: Siva Dasetty (
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
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 (

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 ( and others (



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