On 4/27/15 8:34 PM, nao.morish...@takeda.com wrote:
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?
Please upload full .log files to a file-sharing service.
The first run is systematically slower than the second. Nothing else was
running on this hardware? The machine was the same, or identical hardware?
Same GROMACS binaries?
-Justin
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-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Hannes
Loeffler
Sent: Monday, April 27, 2015 10:48 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Cc: gmx-us...@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 <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote:
On 4/27/15 9:02 AM, Hannes Loeffler wrote:
On Mon, 27 Apr 2015 07:43:51 -0400
Justin Lemkul <jalem...@vt.edu<mailto:jalem...@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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