Hi,
On Tue, May 31, 2016 at 11:36 AM, Yinglong Miao <yinglong.miao.gmail.com> wrote:
> This may be also a question on the Users mailing list, but as I try the
> cpptraj density peaks (dpeaks) clustering (which is great!), I notice the
> following warning regarding seiving frames:
> ...
> Restoring sieved frames.
> FIXME: Adding sieved frames not yet supported.
>
> I'm wondering whether this will be coded in the near future.
Eventually, 'dpeaks' clustering is still under development and I don't
have a time frame for when it will be complete. As is stated in the
output, 'dpeaks' as currently implemented should be used with caution.
You may want to try the DBSCAN method which also density based and is
a little better tested.
> Also is there
> a limit on the data size for the clustering other than memory usage? The
> workstation I'm running has ~64G memory, but the program exited in the
> middle of matrix calculation (crashed?) even with apparently enough memory:
>
> Estimated pair-wise matrix memory usage: > 16.587 GB
> Pair-wise matrix set up, 91068 frames
> 0% 10% 20% 30% mkdir: cannot create directory
> `cluster-dpeaks-e1-ncstep1-sieve1': File exists
That doesn't look like a memory error to me. Can you provide your
exact cpptraj input?
-Dan
>
> Any suggestions will be appreciated,
>
> Yinglong
>
> Yinglong Miao, Ph.D.
> Research Specialist I, Howard Hughes Medical Institute
> Assistant Project Scientist, Department of Pharmacology
> University of California, San Diego
> Tel: 858-822-0255; Email: yimiao.ucsd.edu
> http://mccammon.ucsd.edu/~ymiao/
> http://gamd.ucsd.edu
> _______________________________________________
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue May 31 2016 - 12:30:03 PDT
