Hi Michael,
A segmentation fault is typically indicative of insufficient memory for
conducting the analysis. Indeed, I see that your lower limit for memory
usage is greater than 8 GB, which can be significant for many machines.
The quickest way to solve this problem, in my experience, is to reduce the
frame rate of your processed trajectories. That is, instead of analyzing
every 2 ps of simulation, try analyzing every 20 ps. The loss of
information will depend on the correlation time for the hydrogen bond you
are appear to be analyzing, which is difficult to know without looking at
the timeseries of the data. Best of luck!
Take care,
Samuel Bowerman
Ph.D. Candidate
Department of Physics
Illinois Institute of Technology
On Tue, Nov 8, 2016 at 7:28 AM, Michael Shokhen <michael.shokhen.biu.ac.il>
wrote:
> 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,
> Michael
>
> 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.
> # CLUSTERING OPTIONS:
> # 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.
> # DISTANCE METRIC OPTIONS:
> # rms <mask>: Use RMSD of atoms in <mask> as distance metric.
> # sieve 10 : Use <total> / 10 initial frames for clustering.
> # OUTPUT OPTIONS:
> # 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.
> # COORDINATE OUTPUT OPTIONS:
> # 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.
>
> ACTION OUTPUT:
>
> 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 - 06:30:02 PST
