[gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

Daniel Adriano Silva M dadriano at gmail.com
Fri Oct 30 02:28:12 CET 2009

Dear Gromacs users,

I am experimenting the next problem on an infiniband-cluster (8
intel-cores per node, GROMACS compiled with icc 11.1, all run through

I have a molecule (protein 498aa, solvated or in vacuum I get the same
problem at any box shape), when I try to SD minimize it with
mvapich2-mdrun, it minimizes well with 1, 2 or 3 cores and reaches
convergence in around 1000steps, however any further combination (4,5,
...n cores) makes it to immediately stop (less than 20 steps) with:

"Steepest Descents converged to machine precision...".

Further if I take "the 1 core minimized structure" and try to make a
solvated-pr dynamics(2fs, MD, NTP, etc.) it also works with 1
processor, but with more cores it begins immediately to bring LINCS
warnings: and dies:

"Too many LINCS warnings" or "Water molecule starting at atom 16221
can not be settled"

For a "long time" I had made another md simulations on this cluster
with the same mdps and other proteic systems, and I only see this
behavior with this particular protein, of course  before send this
mail I re-tested previuos-working tprs.
Finally, the most suspicious is that I have another very similar
8-core box (with the same processors) but with gromacs gcc compiled,
and it actually runs very well the same problematic molecule (even the
same tpr) with mpi and 8-cores.
What do you think??? Please, if you have some tpr to test something send it.

Daniel Silva

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