[gmx-users] gmx4.0.3: simulations do not run on 16 processors but do run on 10

Ángel Piñeiro angel.pineiro at usc.es
Tue May 5 11:36:01 CEST 2009

Dear all,
I am trying to run some simulations on our institutional cluster using
gmx4.0.3. My systems are membrane proteins in lipid bilayers although
for the error I am getting I do not think this is important (this is
just my impression because a couple of months ago I got something
similar with a completely different system). My simulation setups seem
to be OK since I ran them locally (on one processor) with no problems
(exactly the same tpr created in the cluster and copied to my PC) but
when I submit the jobs to the queue of our cluster some simulations stop
just after starting. This incidence seems to be a bit random although I
noticed that some simulations that do not run on 16 processors do run on
10. For some cases a core file is generated together with traj.* and
energy.edr files with 0 bytes but in other cases the simulation just
stop without producing any information. Our administrator is
investigating if it is a problem with MPI or the gmx installation but I
would like to know if there is some known bug in gmx4.0.3 that could be
responsible for this.

I found this message in the gmx users mailing list that perhaps could be
related... although it seems a bit old:

Thanks for any help,


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