[gmx-developers] Slow down caused by collective parallel operation

Harry (Yicun) Ni edycni at gmail.com
Thu Mar 5 22:42:08 CET 2015

Hi All,

I am developing a new water model and implementing it in gromacs 4.5.5. The
model requires an "Allreduce" operation on a 3*natoms sized real value
array when calculating forces, and I am using "gmx_sumd" function to do
this communication.

Then, I test my model on a 500-mol water box. When I use 8 processors on 1
node, I can have the performance that I am expecting. However, if I use 24
processors on 2 nodes, usually, but not always, I got a dramatic
performance slow down where the actual time of simulation can be slower
than it on 8 processors. I am wondering if someone can give me some
suggestions on this issue. Thank you very much.

Yicun Ni
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