From the Amber 15 (and AmberTools 14) manual:
"Cpptraj also has a MPI version that is currently used only with
’ensemble’ trajectory input."
The MPI version of cpptraj is only for 'ensemble' runs. Use the OpenMP
version if you want some speedup for clustering (the pairwise distance
and restoration of sieved frames phases are OpenMP parallelized).
Also, I recommend updating to cpptraj from AmberTools 15.
-Dan
On Mon, Aug 17, 2015 at 8:43 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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--
-------------------------
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)
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Received on Mon Aug 17 2015 - 20:30:05 PDT
