[gmx-users] performance issue of GROMACS

[Szilárd Páll]

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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