NAMD hangs in parallel on OSX

From: Michael Grabe (
Date: Fri Jan 27 2006 - 12:37:38 CST

Hello NAMD Users,

I have a small cluster of 4 dual processor Xserves running Mac Server
OSX 10.3,
and I use NAMD 2.5b1 with charmrun. I did not compile NAMD on the
cluster, I
use the precompiled binaries.

I can always run parallel jobs on all the machines, but recently I have
been finding
that the system hangs at a random point during the MD simulation. If I
run 'top'
I see that two NAMD programs are spawned on each node, and that they are
at 0% CPU usage. At this point, the output file just stops being
printed to.
I have to kill the program and restart things. Then it will go fine.

Does anyone have any idea why this is happening to me? Actually it is
getting worse, I could complete maybe 9 out of 10 simulations (long
ones too), but now it seems like I hang all the time.

Any ideas?

Thanks for everyones help.

Michael Grabe, Ph.D.
Rock Hall RH482
1550 4th Street
San Francisco, CA 94143-0725
tel: ++ 415.476.0421

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