AMBER Archive (2009)

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

From: Rachel Rice (
Date: Thu Jun 25 2009 - 21:36:06 CDT

I set ulimit -n unlimited. There are 2 files in my working directory, the
two test data sets had 200 and 941 snapshots in them, respectively.
A ulimit problem doesn't explain
why it works with my "workaround" command (changing "all pdb" to the
default setting).
 At least to my understanding.

I cannot give up on sieve, I have a total dataset of microseconds of MD.

Hopefully we can figure it out.


On Thu, Jun 25, 2009 at 9:28 PM, David Watson <> wrote:

> Did you >try< ulimit -n ?
> How many files are in your working directory when it bombs?
> Try typing
> ls | wc -l #That's a pipe after ls, not another l
> and then
> ulimit -n
> If you see that the number of files is close to or greater than the what is
> reported by the "ulimit -n" command, then you actually are running into the
> problem I mentioned.
> The response returned with the "ulimit" command without arguments says
> "unlimited" on macosx and doesn't have anything to do with reality.
> You must set the number of open files per process to something greater
> using something like "ulimit -n 1024".
> I went through this exact problem with the sieve command, and apart from
> using "ulimit" command the only other option was to give up on using sieve.
> Well, that's my take on it anyway, and I could be totally off base.
> Perhaps there is a bug where files descriptors aren't being properly
> disposed of during the sieve routine, but that's a question for the powers
> that be.
> On Jun 25, 2009, at 7:54 PM, Rachel Rice wrote:
> I get the bus error even with ulimit set to "unlimited". The error does
>> not
>> happen when the program is trying to write output files- it appears to
>> occur
>> when it attempts to read in data for the second set of clustering.
>> On Thu, Jun 25, 2009 at 1:53 PM, David Watson <>
>> wrote:
>> Rachel,
>>> Check the following message from the archive:
>>> I hope that helps.
>>> _______________________________________________
>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

Rachel L. Rice
Ph.D. candidate, N.Baker Lab
Molecular Biophysics Graduate Program
Washington University in St. Louis
School of Medicine
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