Berk Hess wrote:
Hi,
If your comm group is a single molecule, it will work in serial.
In parallel it will only work when no part of the molecule crosses
the edge of the box at any time.
Hi,
Yes, this is definitely the reason of my problem because at later times
the surface groups crosses the box..
Now, I guess using constraints might be a cure..
Thanks a lot for your help
Bests
Aykut
Berk
> Date: Wed, 31 Mar 2010 12:53:16 +0200
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] Parallel pulling with Gromacs 4.0.7: COMM
mode problem
>
> Berk Hess wrote:
> > 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
> Hi
> Should I not use comm mode angular for parallel running or never no
> matter it is parallel or not?
> But that is what I have been using (for single machine) for many
> simulations without any problem.
> I saw the warning but it looks like there is no crossing between the
> init_grp0 and the periodic box
> and this warning appears only for parallel runs not for single machine
> cases.
>
> thanks
>
> Aykut
> >
> > > Date: Wed, 31 Mar 2010 12:32:43 +0200
> > > From: [email protected]
> > > To: [email protected]
> > > 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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