Dear amber
the error I am getting is as below
CPPTRAJ: Trajectory Analysis. V14.09 MPI
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
Running on 8 threads
Reading 'plain.prmtop' as Amber Topology
INPUT: Reading Input from STDIN
[trajin no_water_no_ion.mdcrd ]
Reading 'no_water_no_ion.mdcrd' as Amber Trajectory
[cluster :1-6 clusters epsilon 2.0 out cnumvtime.dat summary
avg.summary.dat nofit savepairdist cpopvtime cpop.agr ]
Warning: No clustering algorithm specified; defaulting to 'hieragglo'
CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask
[:1-6]), no fitting
Hierarchical Agglomerative: epsilon 2.000, average-linkage.
Cluster # vs time will be written to cnumvtime.dat
Cluster pop vs time will be written to cpop.agr
Summary of cluster results will be written to avg.summary.dat
Warning: One or more analyses requested creation of default COORDS DataSet.
CREATECRD: Saving coordinates from Top plain.prmtop to "_DEFAULTCRD_"
---------- RUN BEGIN -------------------------------------------------
DATASETS:
2 data sets:
_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 0 (<1 MB) 0 atoms
clusters "clusters" (integer), size is 0
DATAFILES:
cnumvtime.dat (Standard Data File): clusters
cpop.agr (Grace File):
Warning: Set 'clusters' contains no data.
Warning: File 'cnumvtime.dat' has no sets containing data.
Warning: File 'cpop.agr' has no sets containing data.
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.0029 seconds.
what is the mistake I am doing !
On Mon, Aug 17, 2015 at 10:55 PM, Kenneth Huang <kennethneltharion.gmail.com
> wrote:
> Hi,
>
> Is cpptraj itself not running, or is it crashing with an error message?
> That's a fine distinction to be made, since it looks like you're running it
> on a cluster. If it is the former, it possible that the cluster environment
> itself might have some issues.
>
> Best,
>
> Kenneth
>
> On Mon, Aug 17, 2015 at 10:43 PM, Lara rajam <lara.4884.gmail.com> wrote:
>
> > Dear amber !
> >
> > I would like to do Cpptraj for clustering in MPI
> > I am using qsub to submit the script
> >
> > I used the input file as below
> >
> > trajin no_water_no_ion.mdcrd
> >
> > cluster :1-6 clusters epsilon 2.0 outcnumvtime.dat summary
> avg.summary.dat
> > nofit savepairdist cpopvtime cpop.agr
> >
> >
> > I tried giving it as
> >
> > cpptraj.MPI -p *.prmtop < input.ptraj > output
> >
> >
> > It is not doing the clustering
> >
> >
> > but if i give the same in serial it is giving the cluster results
> >
> >
> >
> > how to do this in .MPI ? thank you
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
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> here could not dream of heaven?
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Received on Mon Aug 17 2015 - 20:30:04 PDT
