[gmx-users] 2018: large performance variations

[Michael Brunsteiner]

Hi,I ran a few MD runs with identical input files (the SAME tpr file. mdp included below) on the same computer
with gmx 2018 and observed rather large performance variations (~50%) as in:
grep Performance */mcz1.log7/mcz1.log:Performance:       98.510        0.244
7d/mcz1.log:Performance:      140.733        0.171
7e/mcz1.log:Performance:      115.586        0.208
7f/mcz1.log:Performance:      139.197        0.172

turns out the load balancing effort that is done at the beginning gives quite different results:
grep "optimal pme grid" */mcz1.log
7/mcz1.log:              optimal pme grid 32 32 28, coulomb cutoff 1.394
7d/mcz1.log:              optimal pme grid 36 36 32, coulomb cutoff 1.239
7e/mcz1.log:              optimal pme grid 25 24 24, coulomb cutoff 1.784
7f/mcz1.log:              optimal pme grid 40 36 32, coulomb cutoff 1.200

next i tried tune_pme as in:gmx tune_pme -mdrun 'gmx mdrun' -nt 6 -ntmpi 1 -ntomp 6 -pin on -pinoffset 0 -s mcz1.tpr  -pmefft cpu -pinstride 1 -r 10
which didn't work ... in some log file it says:Fatal error:
PME tuning was still active when attempting to reset mdrun counters at step
1500. Try resetting counters later in the run, e.g. with gmx mdrun -resetstep.

i found no documentation regarding "-resetstep"  ... 

i could of course optimize the PME grid manually but since i plan to run a large numberof jobs with different systems and sizes this would be a lot of work and if possible i'd like to avoid that.
is there any way to ask gmx to perform more tests at the beginning of therun when optimizing the PME grid?or is using "-notunepme -dlb yes" an option, and does the latter require aconcurrent optimization of the domain decomposition, if so how is this done?
thanks for any help!
michael


mdp:
integrator        = md
dt                = 0.001
nsteps            = 500000
comm-grps         = System
;
nstxout           = 0
nstvout           = 0
nstfout           = 0
nstlog            = 1000
nstenergy         = 1000
;
nstlist                  = 40
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.2
cutoff-scheme            = Verlet
;
coulombtype              = PME
rcoulomb                 = 1.2
vdw_type                 = cut-off 
rvdw                     = 1.2
;
constraints              = none
;
tcoupl             = v-rescale
tau-t              = 0.1
ref-t              = 300
tc-grps            = System
;
pcoupl             = berendsen
pcoupltype         = anisotropic
tau-p              = 2.0
compressibility    = 4.5e-5 4.5e-5 4.5e-5 0 0 0
ref-p              = 1 1 1 0 0 0
;
annealing          = single
annealing-npoints  = 2
annealing-time     = 0 500
annealing-temp     = 500 480