[gmx-users] gromacs 3.3.3 vs 4.0.3 performance

[Dimitris Dellis]

David van der Spoel wrote:
> Dimitris Dellis wrote:
>>
>> 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.
>
> try turning off optimize_fft
>
Though better with optimize_fft = no,
performce of 3.3.3 is still better.
v4.0.3    1.389 hr/ns (from 1.665)



>>>
>>> -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.
>>
>>>>
>>>> ------------------------------------------------------------------------ 
>>>>
>>>>
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before 
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www 
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090130/0f04c019/attachment.html>