From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Sep 10 2014 - 16:32:32 CDT
Does the simulation slow down during the run? Unless your protein is
somehow restrained (e.g., by MDFF grid forces) it will likely drift off of
the initial patch grid.
On Tue, 9 Sep 2014, Siva Dasetty wrote:
> 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 (
> http://www.nvidia.com/docs/IO/122634/NAMD-benchmark-report.pdf) and others (
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