Ángel Piñeiro wrote:
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.
You should start by updating to 4.0.4 and investigating with that.
I found this message in the gmx users mailing list that perhaps could be related... although it seems a bit old: http://www.gromacs.org/pipermail/gmx-users/2003-August/006793.html
Too old to be relevant. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
