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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Received on Mon Jul 06 2009 - 11:15:28 PDT
