AMBER Archive (2009)

Subject: [AMBER] ptraj clustering with sieve- unexpected Bus Error

From: Rachel Rice (rachel.l.rice_at_gmail.com)
Date: Thu Jun 25 2009 - 10:24:25 CDT

Hi all-
When I try to use ptraj's clustering tool with sieve like this:

cluster out cluster.out representative pdb average pdb all pdb means
clusters 1 rms sieve 10 random @CA,C,N

I get a Bus Error as it tries to re-read in the data for the second round of
clustering, after the initial sieve of the data. I get this Bus Error for
many different test cases on different data sets, some of these are very
small test cases so memory is not an issue.

The work-arounds that I've found are this: I can run this command above
without sieve successfully. Or, if I remove the "all pdb" command from the
line, I can leave sieve in and it runs successfully.

So in summary the above command results in Bus Error. The following two
commands (my work-arounds) work successfully:

cluster out cluster.out representative pdb average pdb all pdb means
clusters 1 rms @CA,C,N

cluster out cluster.out representative pdb average pdb means clusters 1 rms
sieve 10 random @CA,C,N

I'm running Amber10 with the latest set of BugFixes. The Bus Error occurs
when I run on OSX, I tested on Linux and instead I get a seg fault. It
occurs at the same place in the process, as ptraj attempts to re-read in the
first frame of data.

Any idea what's going on?

Thanks for your help!

Rachel Rice 

-- 
Rachel L. Rice
Ph.D. candidate, N.Baker Lab
Molecular Biophysics Graduate Program
Washington University in St. Louis
School of Medicine
http://agave.wustl.edu/
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