[gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem
Berk Hess
gmx3 at hotmail.com
Wed Mar 31 12:41:27 CEST 2010
Hi,
I am not aware of any issues with parallel pulling in 4.0.7.
Did you see this note in your log file:
comm-mode angular will give incorrect results when the comm group
partially crosses a periodic boundary
If your system is periodic, you should not use comm mode angular.
Berk
> Date: Wed, 31 Mar 2010 12:32:43 +0200
> From: aerbas at ph.tum.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem
>
> Hi everybody
>
> There is still a problem about pulling code running in parallel. For
> COMM_GRP active, you have the positions (pullx.xvg) and forces
> (pullf.xvg) relative to the absolute coordinates instead of your
> reference group.
>
> comm_mode=angular
> comm_grps= surface
>
> and for pulling part
> init_grps=surface
>
> should give you the coordinates and the forces with respect to the
> surface as expected. However, in parallel running that is not the case
> as can be seen from the pull output files given below.
>
> On single machine, everything works well.
> At the moment, it seems the best thing to do is to calculate forces
> from positions by counting the motion of the reference group.
>
> thanks and
> bests
>
> > Dear Aykut:
> >
> > 1. Did you see the log file message:
> >
> > "comm-mode angular will give incorrect results when the comm group
> > partially crosses a periodic boundary"
> indeed, I saw this. But the surface which is roughly 5nm, is approx.
> 0.5 nm away from the box. There is no way of any crossing.
> And for G3 and G4 on single machine, you do not have such a warning
> >
> > 2. You say "Actually you might be right about the domain
> > decomposition", but it seems like you didn't run it on gmx 4 in serial
> > or with particle decomposition.
> >
> very very sorry about this, I forgot to append that log for single
> machine with G4
>
>
> log file for G4 on single machine
> *******************************************
> Enabling SPC water optimization for 3021 molecules.
>
> Configuring nonbonded kernels...
> Testing x86_64 SSE2 support... present.
>
>
> Removing pbc first time
>
> Will apply umbrella COM pulling in geometry 'position'
> between a reference group and 1 group
> Pull group 0: 5181 atoms, mass 56947.551
> Pull group 1: 13 atoms, mass 116.120
>
> Initializing LINear Constraint Solver
>
>
> -------- -------- --- Thank You --- -------- --------
>
> Center of mass motion removal mode is Angular
> We have the following groups for center of mass motion removal:
> 0: DIAM
>
> There are: 14359 Atoms
> Max number of connections per atom is 94
> Total number of connections is 403131
> Max number of graph edges per atom is 4
> Total number of graph edges is 30690
>
> Constraining the starting coordinates (step 0)
>
> Constraining the coordinates at t0-dt (step 0)
> RMS relative constraint deviation after constraining: 2.35e-07
> Initial temperature: 300.447 K
>
>
> > I wish you the best of luck, I'm out of ideas here.
> >
> thanks anyways
> > Chris.
> >
> > -- original message --
> >
> > Hi
> >
> > Actually you might be right about the domain decomposition
> >
> >
> > G3 pull.pdo output file on single machine
> >
> > focus on the 2nd and 3rd columns which are x and y positions of the
> > surface: almost *unchanged* as expected for COMM_grps=surface option
> > *************
> > 20000.000000 3.149521 1.576811 5.770928
> > 7.149521 1.874820 1.676811
> > 20000.201172 3.149521 1.576812 5.761463
> > 7.149541 1.880746 1.676812
> > 20000.400391 3.149520 1.576813 5.771702
> > 7.149560 1.867692 1.676813
> > 20000.601562 3.149519 1.576813 5.797871
> > 7.149579 1.879650 1.676813
> > 20000.800781 3.149518 1.576812 5.794115
> > 7.149598 1.887728 1.676812
> > 20001.000000 3.149517 1.576813 5.778761
> > 7.149617 1.870823 1.676813
> > 20001.201172 3.149518 1.576815 5.783334
> > 7.149638 1.849283 1.676815
> > 20001.400391 3.149517 1.576815 5.780031
> > 7.149658 1.877158 1.676815
> > .....
> > .....
> > 39999.402344 3.149799 1.576911 2.249830
> > 9.149739 1.604563 1.676911
> > 39999.601562 3.149797 1.576911 2.209385
> > 9.149757 1.622380 1.676911
> > 39999.800781 3.149792 1.576911 2.215503
> > 9.149773 1.653246 1.676911
> > 40000.000000 3.149791 1.576912 2.221903
> > 9.149791 1.659781 1.676912
> >
> >
> >
> > G4 pull.xvg output (in parellel), 2nd and 3rd columns which are x and y
> > positions of the surface: *changing*, contradiction to COMM_grps=surface
> > option
> >
> > *********
> > 0.4000 3.1498 2.997 -0.391131 -0.331925
> > 0.8000 3.14903 2.99499 -0.391976 -0.346309
> > 1.2000 3.14753 2.99846 -0.372158 -0.407621
> > 1.6000 3.14635 3.00695 -0.337084 -0.422437
> > 2.0000 3.14465 3.00585 -0.306999 -0.474991
> > 2.4000 3.14365 3.00408 -0.30164 -0.48047
> > 2.8000 3.14338 3.00447 -0.285076 -0.483861
> > 3.2000 3.14361 3.00119 -0.226717 -0.460955
> > ........
> > ..........
> > 2838.0000 3.20024 0.662325 1.7185 0.986139
> > 2838.4000 3.19435 0.661913 1.74023 1.0404
> > 2838.8000 3.18835 0.666171 1.8073 1.02766
> > 2839.2000 3.18264 0.658261 1.81687 0.999429
> > 2839.6000 3.17766 0.668439 1.82782 1.05693
> >
> >
> > here is the log file for G4 (pulling) run in parallel
> >
> > ********************************
> > Initializing Domain Decomposition on 32 nodes
> > Dynamic load balancing: auto
> > Will sort the charge groups at every domain (re)decomposition
> > Initial maximum inter charge-group distances:
> > two-body bonded interactions: 0.507 nm, LJ-14, atoms 5186 5197
> > multi-body bonded interactions: 0.507 nm, Proper Dih., atoms 5186 5197
> > Minimum cell size due to bonded interactions: 0.557 nm
> > Maximum distance for 5 constraints, at 120 deg. angles, all-trans:
> > 0.200 nm
> > Estimated maximum distance required for P-LINCS: 0.200 nm
> > Guess for relative PME load: 0.20
> > Will use 24 particle-particle and 8 PME only nodes
> > This is a guess, check the performance at the end of the log file
> > Using 8 separate PME nodes
> > Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> > Optimizing the DD grid for 24 cells with a minimum initial size of
> > 0.697 nm
> > The maximum allowed number of cells is: X 9 Y 4 Z 9
> > Domain decomposition grid 4 x 2 x 3, separate PME nodes 8
> >
> > comm-mode angular will give incorrect results when the comm group
> > partially crosses a periodic boundary
> > Interleaving PP and PME nodes
> > This is a particle-particle only node
> >
> > Domain decomposition nodeid 0, coordinates 0 0 0
> >
> > Table routines are used for coulomb: TRUE
> > Table routines are used for vdw: FALSE
> > Will do PME sum in reciprocal space.
> >
> > -------- -------- --- Thank You --- -------- --------
> > Using a Gaussian width (1/beta) of 0.25613 nm for Ewald
> > Cut-off's: NS: 0.8 Coulomb: 0.8 LJ: 0.8
> > System total charge: -0.000
> > Generated table with 3600 data points for Ewald.
> > Tabscale = 2000 points/nm
> > Generated table with 3600 data points for LJ6.
> > Tabscale = 2000 points/nm
> > Generated table with 3600 data points for LJ12.
> > Tabscale = 2000 points/nm
> > Generated table with 3600 data points for 1-4 COUL.
> > Tabscale = 2000 points/nm
> > Generated table with 3600 data points for 1-4 LJ6.
> > Tabscale = 2000 points/nm
> > Generated table with 3600 data points for 1-4 LJ12.
> > Tabscale = 2000 points/nm
> >
> > Enabling SPC water optimization for 3021 molecules.
> >
> > Configuring nonbonded kernels...
> >
> >
> > Removing pbc first time
> >
> > Will apply umbrella COM pulling in geometry 'position'
> > between a reference group and 1 group
> > Pull group 0: 5181 atoms, mass 56947.551
> > Pull group 1: 13 atoms, mass 116.120
> >
> > Initializing Parallel LINear Constraint Solver
> >
> >
> >
> > Linking all bonded interactions to atoms
> > There are 85833 inter charge-group exclusions,
> > will use an extra communication step for exclusion forces for PME
> >
> > The initial number of communication pulses is: X 1 Y 1 Z 1
> > The initial domain decomposition cell size is: X 1.58 nm Y 1.58 nm Z
> > 2.23 nm
> >
> > The maximum allowed distance for charge groups involved in
> > interactions is:
> > non-bonded interactions 0.800 nm
> > (the following are initial values, they could change due to box
> > deformation)
> > two-body bonded interactions (-rdd) 0.800 nm
> > multi-body bonded interactions (-rdd) 0.800 nm
> > atoms separated by up to 5 constraints (-rcon) 1.575 nm
> >
> > When dynamic load balancing gets turned on, these settings will change
> > to:
> > The maximum number of communication pulses is: X 1 Y 1 Z 1
> > The minimum size for domain decomposition cells is 0.800 nm
> > The requested allowed shrink of DD cells (option -dds) is: 0.80
> > The allowed shrink of domain decomposition cells is: X 0.51 Y 0.51 Z 0.36
> > The maximum allowed distance for charge groups involved in
> > interactions is:
> > non-bonded interactions 0.800 nm
> > two-body bonded interactions (-rdd) 0.800 nm
> > multi-body bonded interactions (-rdd) 0.800 nm
> > atoms separated by up to 5 constraints (-rcon) 0.800 nm
> >
> >
> > Making 3D domain decomposition grid 4 x 2 x 3, home cell index 0 0 0
> >
> > Center of mass motion removal mode is Angular
> > We have the following groups for center of mass motion removal:
> > 0: DIAM
> >
>
> --
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