Hi,
You don't mention the specs. of the hardware you are trying to run on, so
there is no telling if your timings are reasonable or not. These benchmarks
(
http://ambermd.org/amber10.bench1.html) are a bit out of date but should
give you an approximate idea of what to expect.
-Dan
On Mon, Jun 23, 2014 at 5:38 AM, James Starlight <jmsstarlight.gmail.com>
wrote:
> Dear Amber users!
>
>
> Using pmemd from latest Amber together with the newest version of mpirun
> I've obtained very low performance in replica-exchange simulation using
> multi-pmemd.mpi. Below you can find my launch bash script and the output
> file from 1 replica.
>
> export AMBERHOME=/opt/amber/amber14
> pmemd="$AMBERHOME/bin/pmemd.
> MPI"
> sander="$AMBERHOME/bin/sander.MPI"
>
>
> cd /globaltmp/novikov/amber/remd
> mpirun -n 88 $pmemd -O -ng 22 -groupfile ./remd.groupfile2
>
>
>
> | Average timings for last 100 steps:
> | Elapsed(s) = 143.58 Per Step(ms) = 1435.78
> | ns/day = 0.12 seconds/ns = 717888.57
> |
> | Average timings for all steps:
> | Elapsed(s) = 143.58 Per Step(ms) = 1435.78
> | ns/day = 0.12 seconds/ns = 717888.57
>
>
> Here I performed simulation of the protein in vacuum (system of 7000 atoms)
> using implicit solvent with the applied position restrains on the part of
> my protein
>
> Production REMD input file
> &cntrl
> irest=0, ntx=1,
> nstlim=500, dt=0.002,
> irest=0, ntt=3, gamma_ln=1.0,
> temp0=300.00, ig=17461,
> ntc=2, ntf=2, nscm=1000,
> ntb=0, igb=5,
> cut=999.0, rgbmax=999.0,
> ntpr=100, ntwx=1000, ntwr=100000,
> nmropt=1, ioutfm=1,
> numexchg=1000,
> restraint_wt=1000.0, restraintmask=':1-285,325-460',
> /
> &wt TYPE='END'
> /
> DISANG=chimera_chir.dat
>
>
> Does the problem in the palatalization of this job or something wrong with
> my input file?
>
> TFH,
>
> James
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 23 2014 - 07:00:03 PDT
