[gmx-users] Hard lock up

David spoel at xray.bmc.uu.se
Fri Oct 8 21:17:26 CEST 2004

On Fri, 2004-10-08 at 21:06, Bill (William) Triest wrote:
> I'm an undergrad student worker, and running gromacs under linux is
> locking up one of our systems.  Version 3.1 used to run fine, until 3.2
> was installed.  3.2 started locking up the system (and I mean LOCKING it
> up, you can ssh into the box, you can't ctrl-c to kill it) etc.  They
> tried reverting to 3.1, but its still causing problems.  It only happens
> on large jobs, but we have a nearly identical box (running 3.1) that can
> run the jobs fine.  Since the lockups only happen while running gromacs,
> and the machine does see some other loads (vmware and custom written
> software), I think its related to gromacs.  The box is currently running
> red hat 9, and is an smp machine (and yes I did try the mapi version,
> and I did ensure that the installed version of lam was as the same major
> version).  I tried googling for the problem, so I'm just hoping for
> pointers as to where to start RTFMing.
Does this happen to be an Athlon box?
In that case you may want to upgrade to 3.2.1 in which a workaround for
a bug in the Athlon was introduced. On the other hand, the bug was in
3.1 also.

Otherwise gromacs stresses the CPU really hard. Could it be heating
problems? Do you have temperature sensors on the chips? Could be a
broken fan or a rotten memory chip too...

If you are "sure" the hardware is not too blame, give us some more info
on the kind of jobs that crash the machine.
> Thanks,
> William Triest
> Student Worker - Linux
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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