[gmx-users] K20 test

Szilárd Páll szilard.pall at cbr.su.se
Thu Apr 11 15:58:55 CEST 2013


No, it just means that *your simulation* does not scale. The question
is very vague, hence impossible to answer without more details

However, assuming that you are not running a, say, 5000 atom system
over 6 nodes, the most probable reason is that you have 6 Sandy Bridge
nodes with 12-16 cores each and 24-32 threads supported. If you just
start mdrun with one MPI rank/node it will use 24-32 threads per
process which is way too much for parallel runs. Try running with less
threads per rank and on less nodes and see if that helps.


On Thu, Apr 11, 2013 at 3:23 PM, 陈照云 <chenzhaoyun06 at gmail.com> wrote:
> Hi!
>    When I run gromacs-4.6.1 with k20. I meet a question.
>    I have 6 nodes.And each node has one K20.And I use one process on one
> node with one gpu. But the test result shows that the runtime of one node
> is less than that of six nodes.Is the scalability of GPU not good?
> Thanks!
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