AMBER Archive (2009)

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

From: David Watson (dewatson_at_olemiss.edu)
Date: Thu Jun 25 2009 - 13:53:16 CDT

Rachel,

Check the following message from the archive:
http://archive.ambermd.org/200901/0303.html

I hope that helps.

On Jun 25, 2009, at 10:24 AM, Rachel Rice wrote:

> 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

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