[gmx-users] About the binary identical continuation by restarting from the checkpoint file

[Mark Abraham]

GuoGuangjun wrote:
> Hi,
>  
> I change to Gromacs 4.0.4 now, and perform NPT with four CPU cores. 
> The results of continuation runs are still different from the undivided 
> run. Neither phenomenon described previously disappears.

The first phenomenon is a non-problem. The files are identical modulo
PBC, which means they are equivalent from the point of view of
continuing a simulation.

The second may be a minor issue. MD is chaotic, and small differences in
inputs will propagate to become large differences in output. Differences
of that order of magnitude don't take you out of the ensemble you're
modelling. However it ought to be possible to do as you are trying to do
- unless some domain decomposition partitioning artefact is to blame.
Please file a bugzilla with at least your input .tpr and output .trr
files, with your complete procedure described, as below.

Mark

> ------------------------------------------------------------------------
> From: gmx3 at hotmail.com
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] About the binary identical continuation by 
> restarting from the checkpoint file
> Date: Tue, 24 Feb 2009 14:44:07 +0100
> 
> Hi,
> 
> Are you running NPT, single processor with 4.0.3?
> Then you are experiencing the bug that the box is not updated in the 
> checkpoint file.
> Please change to 4.0.4.
> 
> Berk
> 
> ------------------------------------------------------------------------
> From: guogj at hotmail.com
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] About the binary identical continuation by 
> restarting from the checkpoint file
> Date: Tue, 24 Feb 2009 08:37:38 +0000
> 
> Hi, Mark,
>  
> 
> I reduce the length of test runs to only 6 steps now. The binary 
> identical continuation still cannot be obtained. I use gmxcheck to 
> compare the results according to your suggestions and I find two reasons 
> to cause different trajectories.
> 
>  
> 
> One is a water molecule happening to span the Y-boundary of the 
> simulation box. In the undivided run, the molecule locates at the +Y 
> direction while it occurs at the ¨CY direction in the continuous run. The 
> differences of Y-coordinates are exactly the box length. Certainly, X 
> and Z coordinates in the two runs are indeed identical.
> 
>  
> 
> The other one is the velocities of many atoms being different in the 
> fifth or sixth digits. The case becomes more and more serious with time.
> 
>  
> 
> After I change the different initial gro files, the first phenomenon 
> disappears because no spanning-boundary water occurs. However, the 
> second one is always there no matter which Gromacs is used, the 
> single-precision or the double-precision. So, my question is how to 
> obtain the binary identical continuation.
> 
>  
> 
> regards,
> 
> Guang-Jun
> 
>  
>  
> 
>  > Date: Mon, 23 Feb 2009 14:37:06 +1100
>  > From: Mark.Abraham at anu.edu.au
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] About the binary identical continuation by 
> restarting from the checkpoint file
>  >
>  > GuoGuangjun wrote:
>  > > Hi, All
>  > >
>  > >
>  > >
>  > > Before to perform long simulations, I think it is necessary to do
>  > > continuous runs. I make several tests
>  > >
>  > > to check the reliability of restart by using the checkpoint file. 
> First,
>  > > I do a 6ps-long run, and then do it
>  > >
>  > > again by two parts, that is, the first half (3 ps) starts from the 
> same
>  > > initial gro file, followed by its
>  > >
>  > > second half. Here are my operations:
>  > >
>  > >
>  > >
>  > > grompp -f 6ps1.mdp -c water.gro -p water.top -o 6ps1.tpr
>  > >
>  > > mpirun -np 4 mdrun -s 6ps1.tpr -o 6ps1.trr -x 6ps1.xtc -e 6ps1.edr 
> -dlb no
>  > >
>  > >
>  > >
>  > > grompp -f 3ps.mdp -c water.gro -p water.top -o 3ps.tpr
>  > >
>  > > mpirun -np 4 mdrun -s 3ps.tpr -o 6ps2.trr -x 6ps2.xtc -e 6ps2.edr -dlb
>  > > no -cpo 3ps.cpt
>  > >
>  > >
>  > >
>  > > tpbconv -s 3ps.tpr -extend 3.0 -o 6ps2.tpr -cont
>  > >
>  > > mpirun -np 4 mdrun -s 6ps2.tpr -o 6ps2.trr -x 6ps2.xtc -e 6ps2.edr 
> -dlb
>  > > no -cpi 3ps.cpt -append
>  > >
>  > >
>  > >
>  > > The log file tells me----¡°Restarting from checkpoint, appending to
>  > > previous log file.¡± However, when I
>  > >
>  > > check the binary files, such as 6ps1.trr and 6ps2.trr, the cmp command
>  > > tells me they are not identical.
>  >
>  > Use gmxcheck for this test. This will give you either confirmation that
>  > you're achieving your objective, or enough information to find out 
> why not.
>  >
>  > > During these tests, I have turned off the gen_vel, optimize_fft, and
>  > > dynamic load balancing (dlb) according
>  > >
>  > > to Gromacs manual and previous posters. How to obtain the binary
>  > > identical continuation? My computational
>  > >
>  > > environments are Gromacs 4.0.3, lammpi 7.1.4, Redhat Linux, two AMD
>  > > Opteron CPUs with dual cores
>  > >
>  > > in each, 500 SPC water molecules, and the NPT ensemble.
>  >
>  > Your approach looks right to me.
>  >
>  > Mark
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