[gmx-users] gromacs 3.3.3 vs 4.0.3 performance

[Dimitris Dellis]

Justin A. Lemkul wrote:
>
>
> Dimitris Dellis wrote:
>> Hi.
>> I run the same  (exactly) simulations with v3.3.3 and v4.0.3, on the 
>> same 64bit Q6600/DDR2-1066 machine, gcc-4.3.2 ,fftw-3.2.
>> I found that the performance of 4.0.3 is roughly 30% lower than 3.3.3 
>> (30% higher hours/ns), for few systems (512 molecules of 5-15 sites, 
>> nstlist=10) I tried.
>> This happens with single precision serial and parallel, np=2,4 
>> (openmpi  1.3) versions and only when electrostatics (PME) are present.
>> With Simple LJ potentials the performance is exactly the same.
>> Is there any speed comparison 3.3.3 vs 4.0.3 available ?
>> D.D.
>>
>
> Can you show us your .mdp file?  What did grompp report about the 
> relative PME load?  These topics have been discussed a few times; 
> you'll find lots of pointers on optimizing performance in the list 
> archive.
>
> -Justin
>
Hi Justin,
These are from the small system, no I/O only 1k steps.
grompp.mdp
===========
integrator               = md
dt                       = 0.0010
nsteps                   = 1000
nstxout                  = 0
nstvout                  = 0
nstlog                   = 1000
nstcomm                  = 10
nstenergy                = 0
nstxtcout                = 0
nstlist                  = 10
ns_type                  = grid
dispcorr                 = AllEnerPres
tcoupl                   = berendsen
tc-grps                  = System
ref_t                    = 293.15
gen_temp                 = 293.15
tau_t                    = 0.2
gen_vel                  = no
gen_seed                 = 123456
constraints              = none
constraint_algorithm     = shake
dispcorr                 = AllEnerPres
energygrps               = System 
rlist                    = 1.6
vdw-type                 = Cut-off
rvdw                     = 1.6
coulombtype              = PME
fourierspacing           = 0.12
pme_order                = 4
ewald_rtol               = 1.0e-5
optimize_fft             = yes
rcoulomb                 = 1.6

related 4.0.3 grompp output
Estimate for the relative computational load of the PME mesh part: 0.19

4.0.3 mdrun serial timings (near zero omitted)

 Coul(T) + LJ                     576.513824       31708.260    71.5
 Outer nonbonded loop               8.489390          84.894     0.2
 Calc Weights                       6.006000         216.216     0.5
 Spread Q Bspline                 128.128000         256.256     0.6
 Gather F Bspline                 128.128000        1537.536     3.5
 3D-FFT                          1088.769682        8710.157    19.6
 Solve PME                         18.531513        1186.017     2.7

parallel 4.0.3 np=4
 Average load imbalance: 5.2 %
 Part of the total run time spent waiting due to load imbalance: 2.3 %
 Performance:     96.086      7.380     14.414      1.665

3.3.3 mdrun serial timings
 Coul(T) + LJ                    576.529632    31709.129760    72.0
 Outer nonbonded loop              8.487860       84.878600     0.2
 Spread Q Bspline                128.128000      256.256000     0.6
 Gather F Bspline                128.128000     1537.536000     3.5
 3D-FFT                         1088.769682     8710.157456    19.8
 Solve PME                        17.986469     1151.133984     2.6

parallel 3.3.3 np=4
Performance:    144.132     12.556     21.600      1.111

D.D.

>>
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