Following is the entire cpptraj output:
CPPTRAJ: Trajectory Analysis. V4.15.0 (AmberTools V20.00)
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 01/13/20 17:36:28
| Available memory: 7.793 GB
INPUT: Reading input from 'sys-clustering-dpeaks.cpptraj'
[parm APN.prmtop]
Reading 'APN.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
[trajin gamd-no-reimaged-ts10ps-lenns-APN.nc]
Reading 'gamd-no-reimaged-ts10ps-lenns-APN.nc' as Amber NetCDF
[cluster C0 dpeaks epsilon 4 dvdfile dvdfile choosepoints auto runavg
runavg.dat deltafile delta.dat sieve 200]
CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (all
atoms) best-fit
---------------------------------------------------------------------------
Warning: The dpeaks algorithm is still under development. USE WITH CAUTION!
---------------------------------------------------------------------------
DPeaks: Cutoff (epsilon) for determining local density is 4
Discrete density calculation.
Density vs min distance to point with next highest density
written to dvdfile
Attempting to choose density peaks automatically.
Running avg of delta vs distance written to runavg.dat
Delta of distance minus running avg written to delta.dat
Initial clustering sieve value is 200 frames.
Only non-sieved frames will be used to calc within-cluster average.
Pairwise distance data set is 'C0[PWD]'
Representative frames will be chosen by closest distance to cluster
centroid.
[go]
Warning: One or more analyses requested creation of default COORDS DataSet.
CREATECRD: Saving coordinates from Top APN.prmtop to "_DEFAULTCRD_"
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: APN.prmtop, 15 atoms, 1 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (1 total):
0: 'gamd-no-reimaged-ts10ps-lenns-APN.nc' is a NetCDF AMBER trajectory
with coordinates, time, box, Parm APN.prmtop (Orthogonal box) (reading
250000 of 250000)
Coordinate processing will occur on 250000 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'APN.prmtop' (1 actions):
0: [createcrd _DEFAULTCRD_]
Warning: COORDS data sets do not store times.
Estimated memory usage (250000 frames): 51.000 MB
----- gamd-no-reimaged-ts10ps-lenns-APN.nc (1-250000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 250000 frames and processed 250000 frames.
TIME: Avg. throughput= 616579.0713 frames / second.
ACTION OUTPUT:
ANALYSIS: Performing 1 analyses:
0: [cluster C0 dpeaks epsilon 4 dvdfile dvdfile choosepoints auto runavg
runavg.dat deltafile delta.dat sieve 200]
Starting clustering.
Mask [*] corresponds to 15 atoms.
Estimated pair-wise matrix memory usage: > 3.123 MB
Pair-wise matrix set up with sieve, 250000 frames, 1250 sieved
frames.
Calculating pair-wise distances.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete.
Memory used by pair-wise matrix and other cluster data: 4.128 MB
Starting DPeaks clustering, discrete density calculation.
Determining local density of each point.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Finding closest neighbor point with higher density for each point.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90%
Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.
Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.
Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.
Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.
Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.
Segmentation fault (core dumped)
--
You can find a copy of the dvdfile as attached.
I will try the gauss option to see how it works ...
Thank you,
Yinglong
On Tue, Jan 14, 2020 at 9:47 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Can you provide me (either in reply to this or off list) your entire
> cpptraj output and the contents of dvdfile?
>
> This could happen with very sparse density I think, although its
> difficult to say without exactly replicating. You could potentially
> try the 'gauss' keyword for Gaussian density instead of discrete
> density.
>
> -Dan
>
> On Mon, Jan 13, 2020 at 8:10 PM Yinglong Miao <yinglong.miao.gmail.com>
> wrote:
> >
> > Hi Dan,
> >
> > It’s the latest version as in AMBER git repository.
> >
> > Thanks,
> > Yinglong
> >
> >
> > > On Jan 13, 2020, at 6:20 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > >
> > > What version of cpptraj are you using?
> > >
> > > -Dan
> > >
> > > On Mon, Jan 13, 2020 at 6:51 PM <yinglong.miao.gmail.com> wrote:
> > >>
> > >> Hello,
> > >>
> > >> I tried to use the dpeaks algorithm for clustering with the following
> > >> command:
> > >> cluster C0 dpeaks epsilon 4 dvdfile dvdfile choosepoints auto runavg
> > >> runavg.dat deltafile delta.dat sieve 200
> > >>
> > >> But keep getting the following output with error:
> > >> ...
> > >> Finding closest neighbor point with higher density for each point.
> > >> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90%
> > >> Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor
> is -1.
> > >> Segmentation fault (core dumped)
> > >>
> > >> I will appreciate any suggestions that would fix this ...
> > >>
> > >> Thanks,
> > >> Yinglong
> > >>
> > >> Yinglong Miao, Ph.D.
> > >> Assistant Professor
> > >> Center for Computational Biology and
> > >> Department of Molecular Biosciences
> > >> University of Kansas
> > >> http://miao.compbio.ku.edu
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
> >
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- application/octet-stream attachment: dvdfile
Received on Tue Jan 14 2020 - 08:30:02 PST
