[gmx-users] performance issue of GROMACS

[Tomek Stępniewski]

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?
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?:
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)