[Beowulf] Any Gaussian users out there?
kus at free.net
Mon Jan 8 11:30:31 EST 2007
In message from Joe Landman <landman at scalableinformatics.com> (Sun, 07
Jan 2007 22:49:55 -0500):
>I found a neat ... feature ... of Linux while getting g03 running in
>SMP on cluster nodes. Long story, but the folks I am doing this for
>don't have/want to use Linda. They asked us to help them get g03
>operational in SMP parallel. This wasn't painful. Have it
>integrated into SGE and our SICE interface now as well.
>Basic idea is that we are getting a kernel exception in the VFS layer
>only when running with 2 or more CPUs on an SMP node. Shows up only
>on SuSE 9.3 nodes. The other nodes are RHEL 3 based (2.4 kernel, but
>hey, its really stable).
We have working g03 C02 w/SMP parallelization under SuSE 9.0 for
x86-64 (2.6 kernel, but more old than f0r 9.3 ). In particular, xfs
>I don't want to post a nasty-looking trap here.
>The problem occurs with both xfs and jfs. Haven't had the chance to
>try ext3 yet, though if the issue is in the vfs layer, I can't see
>how changing the underlying block device is going to alter the layers
>(VFS) above it.
>The net effect of this is that it runs great on the 2.4 based
>machines, but gets SIGKILLs when running on the 2.6 based SuSE 9.3
>machines. Looks like the app is tickling the OS bug. I can
>repeatably cause this trap, though it seems to occur at "random"
>places, well, not really. The way Gaussian runs, it has "links" which
>are binary modules which execute a particular portion of the
>calculation (its pretty neat really). Each link is read in from the
>disk. This VFS bug gets triggered regardless of local or remote FS.
>Any Gaussian users out there see that? Does a kernel upgrade fix it?
>Inquiring minds want to know ...
>Joseph Landman, Ph.D
>Founder and CEO
>Scalable Informatics LLC,
>email: landman at scalableinformatics.com
>web : http://www.scalableinformatics.com
>phone: +1 734 786 8423
>fax : +1 734 786 8452 or +1 866 888 3112
>cell : +1 734 612 4615
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