[gmx-users] parallel run crashes only when shuffled

Mikko Huhtala mhuhtala at abo.fi
Tue Oct 1 15:43:50 CEST 2002

I tried to use grompp with '-shuffle' to setup up a simulation for 4
processors. The system is a protein dimer, one small-molecule ligand
in each monomer, water and some ions. The suffled simulation crashes
after 15 steps and some LINCS warnings with a fatal pressure scaling
error (= system explodes). The exact same starting conformation runs
on 4 processors just fine when it is set up without the suffle.

I know that shuffle probably does not improve things much for a system
like this, so I am happily running the unshuffled configuration. I was
simply wondering if I missed something obvious or is this a bug in
Gromacs? I am running version gromacs-3.1.4-1 (rpm) with
lam-6.5.4-usysv.1 (rpm) on Pentium 4 Xeons.


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