[AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped)

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Tue, 8 Nov 2016 13:28:06 +0000

Dear Amber experts,

I faced the error running clustering analysis in frames of CPPTRAJ

(I am using currently AMBER 14 and AMBER TOOLS 15).

See below for details the cluster.analysis.in file

and the end of the text with system reporting error

What changes in the command lines must be done?

Thank you for your help,

cluster.analysis.in file

# Cluster analysis with cpptraj.

# Load topology trajectory
parm ../*.prmtop
trajin ../19_/prod3.mdcrd
trajin ../20_/prod4.mdcrd
trajin ../21_/prod5.mdcrd
trajin ../22_/prod6.mdcrd
trajin ../23_/prod7.mdcrd
trajin ../24_/prod8.mdcrd
trajin ../25_/prod9.mdcrd
trajin ../26_/prod10.mdcrd
trajin ../27_/prod11.mdcrd
trajin ../28_/prod12.mdcrd
trajin ../29_/prod13.mdcrd
trajin ../30_/prod14.mdcrd
trajin ../31_/prod15.mdcrd
trajin ../32_/prod16.mdcrd
trajin ../33_/prod17.mdcrd
center :1-11340 mass origin
autoimage origin
# Remove ions so they do not appear in output structures.
strip :WAT,Cl-,Na+,OL,PA,PE
# Cluster analysis command:
# C0: Cluster output data set(s) name.
# dbscan: Use the DBSCAN (density based) clustering algorithm.
# minpoints: Minimum # of points to form a cluster.
# epsilon: Distance cutoff for forming cluster.
# sievetoframe: Restore sieved frames by comparing to all cluster frames,
# not just centroid.
# rms <mask>: Use RMSD of atoms in <mask> as distance metric.
# sieve 10 : Use <total> / 10 initial frames for clustering.
# out <file>: Write cluster number versus time to file.
# summary <file>: Write overall clustering summary to file.
# info <file>: Write detailed cluster results (including DBI, pSF etc) to file.
# cpopvtime <file> normframe: Write cluster population vs time to <file>,
# normalized by # frames.
# repout <file prefix> repfmt pdb: Write cluster representatives to files with
# PDB format.
# singlerepout <file> singlerepfmt netcdf: Write cluster representatives to
# single file with NetCDF format.
# avgout <file> avgfmt restart: Write average over all frames in each cluster
# to separate files with Amber restart file
# format.
distance C0 :111.OG :164.NE2
cluster data C0 clusters 10 epsilon 3.0 summary summary.dat info info.dat

The system error report final fragment:

----- prod17.mdcrd (1-5000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 65465 frames and processed 65465 frames.
TIME: Trajectory processing: 156.4525 s
TIME: Avg. throughput= 418.4336 frames / second.


ANALYSIS: Performing 1 analyses:
  0: [cluster data C0 clusters 10 epsilon 3.0 summary summary.dat info info.dat]
        Starting clustering.
        Calculating pair-wise distances.
        Estimated pair-wise matrix memory usage: > 8174.1348 MB
        Pair-wise matrix set up, 65465 frames
Segmentation fault (core dumped)

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Received on Tue Nov 08 2016 - 05:30:02 PST
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