[gmx-users] difference of calculation time between the numbers of fep-lambdas values
nao.morishita at takeda.com
nao.morishita at takeda.com
Tue Apr 28 02:34:55 CEST 2015
Hi Justin and Hannes,
Thank you for the replay.
I apologize for the insufficient information.
Actually, I calculated them with couple-moltype = solute and init-lambda-state = 1.
The other parameters except for fep-lambdas, the number of core(8) and hardware were same.
When I look at "REAL CCLE AND TIME ACCOUNTING" in log file, there is large difference in "PME redist. X/F".
What makes it much longer?
I would appreciate any comments or concerns.
Input1(fep-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0)
****************************************************************************************
Computing: Nodes Th. Count Wall t (s) G-Cycles %
-----------------------------------------------------------------------------
Domain decomp. 8 1 250000 100.985 2100.559 0.2
DD comm. load 8 1 501 0.004 0.082 0.0
Neighbor search 8 1 250001 351.227 7305.783 0.8
Comm. coord. 8 1 2500001 74.248 1544.405 0.2
Force 8 1 2500001 8671.720 180378.288 20.8
Wait + Comm. F 8 1 2500001 49.926 1038.492 0.1
PME mesh 8 1 2500001 31496.259 655145.855 75.6
Write traj. 8 1 547 0.275 5.710 0.0
Update 8 1 2500001 284.487 5917.540 0.7
Constraints 8 1 5000002 396.070 8238.552 1.0
Comm. energies 8 1 250001 7.876 163.837 0.0
Rest 8 250.084 5201.928 0.6
-----------------------------------------------------------------------------
Total 8 41683.159 867041.031 100.0
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
PME redist. X/F 8 1 7500003 26513.015 551490.632 63.6
PME spread/gather 8 1 10000004 3879.936 80705.579 9.3
PME 3D-FFT 8 1 10000004 702.656 14615.765 1.7
PME 3D-FFT Comm. 8 1 20000008 264.536 5502.543 0.6
PME solve 8 1 5000002 127.236 2646.610 0.3
-----------------------------------------------------------------------------
Core t (s) Wall t (s) (%)
Time: 332678.400 41683.159 798.1
11h34:43
(ns/day) (hour/ns)
Performance: 10.364 2.316
Finished mdrun on node 0 Thu Apr 2 06:31:45 2015
*********************************************************************************
Input2(fep-lambdas = 0.0 0.1 0.2)
*********************************************************************************
Computing: Nodes Th. Count Wall t (s) G-Cycles %
-----------------------------------------------------------------------------
Domain decomp. 8 1 250000 85.779 1784.259 0.5
DD comm. load 8 1 501 0.003 0.072 0.0
Neighbor search 8 1 250001 312.515 6500.517 1.7
Comm. coord. 8 1 2500001 69.584 1447.387 0.4
Force 8 1 2500001 4219.963 87778.089 23.5
Wait + Comm. F 8 1 2500001 46.401 965.178 0.3
PME mesh 8 1 2500001 12342.326 256728.717 68.8
Write traj. 8 1 520 0.150 3.117 0.0
Update 8 1 2500001 262.237 5454.706 1.5
Constraints 8 1 5000002 368.111 7656.961 2.1
Comm. energies 8 1 250001 6.524 135.712 0.0
Rest 8 227.039 4722.575 1.3
-----------------------------------------------------------------------------
Total 8 17940.633 373177.290 100.0
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
PME redist. X/F 8 1 7500003 7982.056 166032.158 44.5
PME spread/gather 8 1 10000004 3327.975 69224.129 18.5
PME 3D-FFT 8 1 10000004 645.036 13417.186 3.6
PME 3D-FFT Comm. 8 1 20000008 259.876 5405.587 1.4
PME solve 8 1 5000002 118.906 2473.318 0.7
-----------------------------------------------------------------------------
Core t (s) Wall t (s) (%)
Time: 143196.260 17940.633 798.2
4h59:00
(ns/day) (hour/ns)
Performance: 24.079 0.997
Finished mdrun on node 0 Fri Apr 3 19:11:15 2015
*********************************************************************************
Best regards,
Nao
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Hannes Loeffler
Sent: Monday, April 27, 2015 10:48 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Cc: gmx-users at gromacs.org
Subject: Re: [gmx-users] difference of calculation time between the numbers of fep-lambdas values
On Mon, 27 Apr 2015 09:05:05 -0400
Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
>
>
> On 4/27/15 9:02 AM, Hannes Loeffler wrote:
> > On Mon, 27 Apr 2015 07:43:51 -0400
> > Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
> >
> >> Note that without couple-moltype, you're going to be decoupling the
> >> whole system, which is (1) not what you want for calculating
> >> solvation free energy and (2) extremely slow. There is an inherent
> >> slowdown when running the free energy code, but it should not be so
> >> large.
> >
> > Really? I just looked into the code yesterday and I think that if
> > you do not set couple-moltype, none of the coupling code is ever
> > triggered. I have only played a bit with relative free energies
> > (Gromacs 4.6) where I think you don't need any of the couple-
> > parameters at all.
> >
>
> Maybe I got that backwards. For relative free energies, this is true
> (we're doing these now); topological differences are all that are
> needed. For an absolute solvation free energy, one needs
> couple-moltype unless the B-state (dummy) is explicitly defined in
> the topology, AFAIK. If there is no couple-moltype, and no B-state
> defined in the topology, I'm not sure what the code would even be
> doing, actually.
I think it runs a normal MD simulation for each lambda. A quick test
with a A-state only topology and no couple- parameters gives only
gradients with zero value. In fact, the output file says
There are 0 atoms and 0 charges for free energy perturbation
Cheers,
Hannes.
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