Gromacs on Intel CoreI7

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created: 1270232965|%e %B %Y, %H:%M
TAGS: gromacs troubleshooting


Recently, I had a new computer in the lab, with Intel Core I7 CPU. I wanted to test the performances with a heavy Gromacs simulation on 4 cores, leaving hyper-threading (HT) enabled. I have noticed that at a certain point, randomly, Gromacs stopped to write the output files (.xtc, .edr, .log), even though all the four cores were running at 100%.

I have googled a bit and ended up on a discussion on the Gromacs mailing list, where I found two different suggestions: disable the HT and update openmpi.

I didn't want to disable the HT, so I have checked the version of openmpi installed via synaptic under ubuntu 9.1 and it was the 1.3.something. The discussion suggested there was a bug in that version, so I have updated to the last version of openmpi (1.4.1) and everything now is running smoothly. Better to uninstall with synaptic the old version. Of course, you also need to recompile mdrun.

I have also noticed the during the execution, mdrun jumps from core to core, but this should be a "feature" of HT: I don't know how bad this can affect the efficiency (speed) of the calculation. I haven't had time to disable the HT and try again.

Hope this can help.

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