[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing
Jiaqi Lin
jqlin at mit.edu
Tue Jan 20 21:18:45 CET 2015
Hi Mark,
Thanks for reply. I put the md.log files in the following link
https://www.dropbox.com/sh/d1d2fbwreizr974/AABYhSRU03nmijbTIXKKr-rra?dl=0
There are four log files
1.GMX 4.6.5 -tunepme (the coulombic cutoff is tuned to 3.253)
2.GMX 4.6.5 -notunepme rcoulomb= 3.3 , fourierspace = 0.33
3.GMX 4.6.5 -notunepme rcoulomb= 3.3 , fourierspace = 0.14
4.GMX 4.6.5 -notunepme rcoulomb= 1.4 , fourierspace = 0.14
Note that the LR Coulombic energy in the first one is almost twice the
value of that in the second one, whereas the grid spacing in both cases
are nealy the same.
Only the first one gives a strong electrostatic interaction of a
nanoparticle with a lipid bilayer under ionic imbalance. In other cases
I do not observe such a strong interaction.
GMX 5.0.1 give the same results as GMX 4.6.5 using Group cutoff. Thanks
Regards
Jiaqi
On 1/19/2015 3:22 PM, Mark Abraham wrote:
> On Thu, Jan 15, 2015 at 3:21 AM, Jiaqi Lin <jqlin at mit.edu> wrote:
>
>> Dear GMX developers,
>>
>> I've encounter a problem in GROMACS concerning the auto-tuning feature of
>> PME that bugged me for months. As stated in the title, the auto-tuning
>> feature of mdrun changed my coulomb cutoff from 1.4 nm to ~3.3 nm (stated
>> in md.log) when I set -npme to be 28 (128 total CPU cores), and this giving
>> me interesting simulation results. When I use -notunepme, I found Coulomb
>> (SR) and recip. giving me same energy but the actual simulation result is
>> different. This i can understand: scaling between coulombic cut-off/grid
>> size theoretically give same accuracy to electrostatics (according to GMX
>> manual and PME papers), but there actually some numerical error due to grid
>> mapping and even if the energy is the same that does not mean system
>> configuration has to be the same (NVE ensemble: constant energy, different
>> configuration).
>>
> Total electrostatic energy should be approximately the same with different
> PME partitions.
>
>
>> However the thing i don't understand is the following. I am interested in
>> the result under large coulomb cut-off, so I try to manually set cut-off
>> and grid space with -notunepme, using the value tuned by mdrun previously.
>> This give me complete different simulation result, and the energy is also
>> different. I've tried to set rlist, rlistlong, or both to equal rcoulomb
>> (~3.3) still does not give me the result produced by auto-tuning PME.
>
> In what sense is the result different?
>
>
>> In addition, simulation speed dramatically reduces when I set rcoulomb to
>> be ~3.3 (using -tunepme the speed remains nearly the same no matter how
>> large the cutoff is tuned to). I've tested this in both GMX 4.6.5 and
>> 5.0.1, same thing happens, so clearly it's not because of versions. Thus
>> the question is: what exactly happened to PME calcualtion using the
>> auto-tuning feature in mdrun, why it does give different results when I
>> manually set the coulomb cutoff and grid space to the value tuned by mdrun
>> without the auto-tuning feature (using -notunepme)? Thank you for help.
>>
> For the group scheme, these should all lead to essentially the same result
> and (if tuned) performance. If you can share your various log files on a
> file-sharing service (rc 1.4, rc 3.3, various -tunepme settings, 4.6.5 and
> 5.0.1) then we can be in a position to comment further.
>
> Mark
>
>
>> additional info: I use Group cutoff-scheme , rvdw is 1.2.
>>
>>
>> md.log file:
>> DD step 9 load imb.: force 29.4% pme mesh/force 3.627
>>
>> step 30: timed with pme grid 280 280 384, coulomb cutoff 1.400: 1026.4
>> M-cycles
>> step 50: timed with pme grid 256 256 324, coulomb cutoff 1.464: 850.3
>> M-cycles
>> step 70: timed with pme grid 224 224 300, coulomb cutoff 1.626: 603.6
>> M-cycles
>> step 90: timed with pme grid 200 200 280, coulomb cutoff 1.822: 555.2
>> M-cycles
>> step 110: timed with pme grid 160 160 208, coulomb cutoff 2.280: 397.0
>> M-cycles
>> step 130: timed with pme grid 144 144 192, coulomb cutoff 2.530: 376.0
>> M-cycles
>> step 150: timed with pme grid 128 128 160, coulomb cutoff 2.964: 343.7
>> M-cycles
>> step 170: timed with pme grid 112 112 144, coulomb cutoff 3.294: 334.8
>> M-cycles
>> Grid: 12 x 14 x 14 cells
>> step 190: timed with pme grid 84 84 108, coulomb cutoff 4.392: 346.2
>> M-cycles
>> step 190: the PME grid restriction limits the PME load balancing to a
>> coulomb cut-off of 4.392
>> step 210: timed with pme grid 128 128 192, coulomb cutoff 2.846: 360.6
>> M-cycles
>> step 230: timed with pme grid 128 128 160, coulomb cutoff 2.964: 343.6
>> M-cycles
>> step 250: timed with pme grid 120 120 160, coulomb cutoff 3.036: 340.4
>> M-cycles
>> step 270: timed with pme grid 112 112 160, coulomb cutoff 3.253: 334.3
>> M-cycles
>> step 290: timed with pme grid 112 112 144, coulomb cutoff 3.294: 334.7
>> M-cycles
>> step 310: timed with pme grid 84 84 108, coulomb cutoff 4.392: 348.0
>> M-cycles
>> optimal pme grid 112 112 160, coulomb cutoff 3.253
>> DD step 999 load imb.: force 18.4% pme mesh/force 0.918
>>
>> At step 1000 the performance loss due to force load imbalance is 6.3 %
>>
>> NOTE: Turning on dynamic load balancing
>>
>> Step Time Lambda
>> 1000 20.00000 0.00000
>>
>> Energies (kJ/mol)
>> Bond G96Angle LJ (SR) Coulomb (SR) Coul. recip.
>> 1.98359e+05 1.79181e+06 -1.08927e+07 -7.04736e+06 -2.32682e+05
>> Position Rest. Potential Kinetic En. Total Energy Temperature
>> 6.20627e+04 -1.61205e+07 4.34624e+06 -1.17743e+07 3.00659e+02
>> Pressure (bar) Constr. rmsd
>> 2.13582e+00 1.74243e-04
>>
>>
>> Best
>> Jiaqi
>>
>>
>>
>> --
>> Jiaqi Lin
>> postdoc fellow
>> The Langer Lab
>>
>> --
>> Gromacs Users mailing list
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--
Jiaqi Lin
postdoc fellow
The Langer Lab
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