Just a little more information: I previously ran cpptraj within a batch
script, now as I run it alone, it output the following error:
0% 10% 20% 30% Segmentation fault (core dumped)
Thanks,
Yinglong
On Tue, May 31, 2016 at 12:44 PM, Yinglong Miao <yimiao.ucsd.edu> wrote:
> Hi Dan,
>
> Thanks for your reply. I also tried DBSCAN and seems dpeaks works better -
> really hope dpeaks with full functionality will be available soon.
>
> And here is my input file:
>
> ----
> parm protein.prmtop
> trajin md-reimaged.nc
> ## RMSD
> reference pro.pdb
> rms reference out rmsd-clustering.dat
> :5-27,42-62,80-101,122-144,167-189,210-230,245-264.CA
> rmsd :278.*&!.H= reference nofit out rmsd-lig-clustering.dat
> strip :1-277
> cluster C0 \
> dpeaks epsilon 1 dvdfile density_vs_dist.dat choosepoints auto
> distancecut 1.0 runavg runavg.dat deltafile delta.dat \
> rms :1.*&!.H= nofit \
> sieve 1 \
> out cnumvtime.dat \
> summary summary.dat \
> info info.dat \
> cpopvtime cpopvtime.agr normframe \
> repout rep repfmt pdb \
> singlerepout singlerep.nc singlerepfmt netcdf \
> avgout Avg avgfmt restart
> go
> ----
>
> Yinglong
>
>
> On Tue, May 31, 2016 at 12:03 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
>> 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
>> > _______________________________________________
>> > AMBER-Developers mailing list
>> > AMBER-Developers.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>>
>>
>> --
>> -------------------------
>> 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)
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
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>>
>
>
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Received on Tue May 31 2016 - 16:30:02 PDT
