Hi
What is the memory trace for it with gdb?
http://stackoverflow.com/questions/2876357/determine-the-line-of-c-code-that-causes-a-segmentation-fault
Hai
> On May 31, 2016, at 7:14 PM, Yinglong Miao <yimiao.ucsd.edu> wrote:
>
> 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
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
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Received on Tue May 31 2016 - 17:00:02 PDT
