[gmx-users] GROMACS 5.1.2 performance

[Mark Abraham]

Hi,

Something about your job start-up is a) strange and b) not what you asked
for. Get one node working in a way that you understand. Then two.

Mark

On Wed, 14 Dec 2016 23:57 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/14/16 6:44 AM, Neha Gandhi wrote:
> > Dear list,
> >
> > I think the question on gromacs performance on cpu cluster has been
> raised
> > many times in the mailing list. My apologies for reiterating the
> question.
> > I am using a system ~80000 atoms with virtual sites (hence timestep of 4
> > fs). The job hasn't completed yet but it seems that the jobs are running
> > slower than my experience running with older versions of GROMACS.
> >
> > Here is the job script
> > #!/bin/bash -l
> > #PBS -N sgk
> > #PBS -l walltime=24:00:00
> > #PBS -l select=6:ncpus=16:mpiprocs=16:mem=20gb
> > #PBS -j oe
> >
> > export OMP_NUM_THREADS=1
> >
> > module purge
> > module load gromacs/5.1.2-foss-2016a-hybrid
> > mpirun -np 96 gmx_mpi mdrun -v -deffnm npt
> >
> >
> > and the output log indicates load imbalance :
> >
> > Number of logical cores detected (48) does not match the number reported
> by
> > OpenMP (10).
> > Consider setting the launch configuration manually!
> >
> > Running on 6 nodes with total 248 logical cores
>
> This says 248 cores but it sounds like you're only trying to use 96.
> Perhaps
> your job is fighting with others on those nodes and choking everything.
> mdrun
> will try to use all available resources unless properly instructed to do
> otherwise.
>
> Talk to your sysadmin if you're having performance or usage issues.
> That's what
> they're paid to do!
>
> >   Logical cores per node:   40 - 48
> > Hardware detected on host cl3n073 (the node of MPI rank 0):
> >   CPU info:
> >     Vendor: GenuineIntel
> >     Brand:  Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
> >     Family:  6  model: 63  stepping:  2
> >     CPU features: apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm
> > mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
> sse2
> > sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> >     SIMD instructions most likely to fit this hardware: AVX_256 -
> AVX2_256
> >     SIMD instructions selected at GROMACS compile time: AVX_256
> >
> >
> > DD  step 34999  vol min/aver 0.553  load imb.: force 46.2%  pme
> mesh/force
> > 0.506
> >
> >            Step           Time         Lambda
> >           35000       70.00000        0.00000
> >
>
> 35000 steps -> 70 ps means your time step is only 2 fs, not 4.  Check your
> inputs if you expected otherwise.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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