[Beowulf] Any Gaussian users out there?

Mikhail Kuzminsky 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 
works OK.

Yours
Mikhail


>
>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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