[gmx-users] performance issue of GROMACS

[Tomek Stępniewski]

Hi Szilad,
thank You for your response,
I attach the log file

2017-09-19 15:19 GMT+02:00 Szilárd Páll <pall.szilard at gmail.com>:

> PS: A bit of extrapolation from my standard historical benchmark data
> shows that regular cut-off kernels should run at ~3.0 ms/step, so
> force shift will be ~3.5-4 ms/step (with nstlist=20 and 2 fs step);
> assuming 70% CPU-GPU overlap that's 5-5.5 ms/step which corresponds to
> ~35 ns/day (with 2 fs).
>
> That's just a rough estimate, though, and it assumes that you have
> enough CPU cores for a balanced run.
>
> --
> Szilárd
>
>
> On Tue, Sep 19, 2017 at 3:16 PM, Szilárd Páll <pall.szilard at gmail.com>
> wrote:
> > On Tue, Sep 19, 2017 at 2:20 PM, Tomek Stępniewski
> > <tm.stepniewski at gmail.com> wrote:
> >> Hi everybody,
> >> I am running gromacs 5.1.4 on a system that uses NVIDIA Tesla K40m,
> >> surprisingly I get a speed of only 15 ns a day when carrying out nvt
> >> simulations, my colleagues say that on a new GPU like this with my
> system
> >> size it should be around 60 ns a day,
> >> are there any apparent errors in my input files that might hhinder the
> >> simulation?
> >
> > 15 ns/day seems a bit low, but I can't say for sure if it's far too
> > low. Can you share logs?
> >
> >> input file:
> >> integrator              = md
> >> dt                      = 0.002
> >> nsteps                  = 100000000
> >> nstlog                  = 10000
> >> nstxout                 = 50000
> >> nstvout                 = 50000
> >> nstfout                 = 50000
> >> nstcalcenergy           = 100
> >> nstenergy               = 1000
> >> ;
> >> cutoff-scheme           = Verlet
> >> nstlist                 = 20
> >> rlist                   = 1.2
> >> coulombtype             = pme
> >> rcoulomb                = 1.2
> >> vdwtype                 = Cut-off
> >> vdw-modifier            = Force-switch
> >> rvdw_switch             = 1.0
> >> rvdw                    = 1.2
> >> ;
> >> tcoupl                  = Nose-Hoover
> >> tc_grps                 = PROT   MEMB   SOL_ION
> >> tau_t                   = 1.0    1.0    1.0
> >> ref_t                   = 310 310 310
> >> ;
> >> constraints             = h-bonds
> >> constraint_algorithm    = LINCS
> >> continuation            = yes
> >> ;
> >> nstcomm                 = 100
> >> comm_mode               = linear
> >> comm_grps               = PROT   MEMB   SOL_ION
> >> ;
> >> refcoord_scaling        = com
> >>
> >> the system has around 70,000 atoms,
> >>
> >> can this issue depend on the CUDA drivers?:
> >
> > A bit, but not to a factor of 4.
> >
> >> CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda
> compiler
> >> driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on
> >> Tue_Jan_10_13:22:03_CST_2017;Cuda compilation tools, release 8.0,
> V8.0.61
> >> CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=
> >> compute_30,code=sm_30;-gencode;arch=compute_35,code=
> >> sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=
> >> compute_50,code=sm_50;-gencode;arch=compute_52,code=
> >> sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=
> >> compute_61,code=sm_61;-gencode;arch=compute_60,code=
> >> compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;;
> >> ;-march=core-avx2;-Wextra;-Wno-missing-field-
> initializers;-Wpointer-arith;-
> >> Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;-
> >> fexcess-precision=fast;-Wno-array-bounds;
> >> CUDA driver:        8.0
> >> CUDA runtime:       8.0
> >> GPU info:
> >>     Number of GPUs detected: 1
> >>     #0: NVIDIA Tesla K40m, compute cap.: 3.5, ECC: yes, stat: compatible
> >>
> >> NOTE: GROMACS was configured without NVML support hence it can not
> exploit
> >>       application clocks of the detected Tesla K40m GPU to improve
> >> performance.
> >>       Recompile with the NVML library (compatible with the driver used)
> or
> >> set application clocks manually.
> >>
> >>
> >> Using GPU 8x8 non-bonded kernels
> >>
> >> I will be extremely grateful for any help,
> >> best
> >>
> >> --
> >> Tomasz M Stepniewski
> >> Research Group on Biomedical Informatics (GRIB)
> >> Hospital del Mar Medical Research Institute (IMIM)
> >> --
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-- 
Tomasz M Stepniewski
Research Group on Biomedical Informatics (GRIB)
Hospital del Mar Medical Research Institute (IMIM)