hello,
I am having 13010 atoms in my system.
the cpu that i am using has the following details:
Intel E5-2670 series CPUs with 16 cores/node and has 64 GB RAM.
the command line i am using is :
#mpirun -machinefile $PBS_NODEFILE -np $NPROCS $AMBERHOME/bin/sander.MPI -O
-i min.in -p fib.prmtop -c fib.inpcrd -r min.rst -o min.out
mpirun -machinefile $PBS_NODEFILE -np $NPROCS $AMBERHOME/bin/pmemd.MPI -O
-i heat1.in -p fib.prmtop -c min.rst -r heat1.rst -o heat1.out -x heat1.nc
-inf heat1.mdinfo
my min.in file has the following parameters:
Stage 1 - minimisation of fibril
&cntrl
imin=1, maxcyc=1000, ncyc=500,
cut=999., rgbmax=999.,igb=8, ntb=0,
ntpr=100
/
using 1 node I am getting a speed of :
Average timings for last 50 steps:
| Elapsed(s) = 33.80 Per Step(ms) = 675.91
| ns/day = 0.06 seconds/ns = 1351821.64
|
| Average timings for all steps:
| Elapsed(s) = 26982.45 Per Step(ms) = 674.56
| ns/day = 0.06 seconds/ns = 1349122.30
using 2 nodes I am getting a speed of :
Average timings for last 150 steps:
| Elapsed(s) = 51.65 Per Step(ms) = 344.37
| ns/day = 0.13 seconds/ns = 688733.19
|
| Average timings for all steps:
| Elapsed(s) = 13726.02 Per Step(ms) = 343.15
| ns/day = 0.13 seconds/ns = 686300.95
using 8 nodes:
Average timings for last 250 steps:
| Elapsed(s) = 23.90 Per Step(ms) = 95.62
| ns/day = 0.45 seconds/ns = 191236.85
|
| Average timings for all steps:
| Elapsed(s) = 955.23 Per Step(ms) = 95.52
| ns/day = 0.45 seconds/ns = 191045.67
using 10 nodes i am getting a speed of:
Average timings for last 200 steps:
| Elapsed(s) = 16.28 Per Step(ms) = 81.42
| ns/day = 0.53 seconds/ns = 162838.32
|
| Average timings for all steps:
| Elapsed(s) = 3224.53 Per Step(ms) = 80.61
| ns/day = 0.54 seconds/ns = 161226.62
On 25 June 2018 at 00:19, David A Case <david.case.rutgers.edu> wrote:
> On Sun, Jun 24, 2018, Chhaya Singh wrote:
>
> > I am trying to perform a simulation having a protein using implicit
> solvent
> > model using force field ff14sbonlysc with igb = 8.
> > I am getting a very low speed using 2 nodes. the speed i get now is less
> a
> > ns/ day.
>
> It would help a lot to know how many atoms are in your protein. Less
> crucial, but still important, would be to know what cpu you are using.
> (Or is this actually a GPU simulation?) When you say "2 nodes", exactly
> what is meant? Can you provide the command line that you used to run
> the simulation?
>
> Some general hints (beyond the good advice that Carlos has already
> given.):
>
> a. be sure you are using pmemd.MPI, not sander.MPI (if pmemd is
> available)
> b. if possible, see if increasing the number of MPI threads helps
> c. you can run tests with a cutoff (cut and rgbmax) of 20 or 25: you
> will still have some artifacts from the cutoff, but they may be
> small enough to live with.
> d. if you system is indeed quite large, you may benefit from the
> hierarchical charge partitioning (GB-HCP) model. See the manual
> for details.
>
> ....dac
>
>
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>
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Received on Mon Jun 25 2018 - 00:00:02 PDT
