[gmx-users] problem in extending a simulation run

[manindersingh rajawat]

Thanks Mark

> I want extend a 100ns run to 150 ns. For this I use following commands:

I have these files from previous run before running following commands:
ener.edr, md.log, traj.trr, traj_comp.xtc, state.cpt, state_prev.cpt
>
> gmx convert-tpr -s md_100ns.tpr -extend 50000 -o md_150ns.tpr
>
> gmx mdrun -v -deffnm md_150ns -c md_150ns.pdb

these commands generate new files: md_150ns.edr, md_150ns.log,
md_150ns.trr, md_150ns.xtc

> But mdrun taken it as a new run


Sure. You implied that the checkpoint file was called md_150ns, but no such
file existed ;-)
yes you are right, here is the error

> and began a full 150ns run:
> starting mdrun 'Protein in water'
> 75000000 steps, 150000.0 ps
>
> so i stopped it, and run with checkpoint input as following:
>
> gmx mdrun -v -s md_150ns.tpr -cpi state.cpt -c md_150ns.pdb
>
> Reading checkpoint file state.cpt generated: Fri Mar 24 05:39:47 2017
>
>
>   Version mismatch,
>     current program: VERSION 5.0.6
>     checkpoint file: VERSION 5.0.2
>

Generally you should continue simulations with the same version of GROMACS
you started, but there is unlikely to be a problem in this case.


>   Build time mismatch,
>     current program: Mon Jul 27 05:11:28 UTC 2015
>     checkpoint file: Fri Oct 24 17:49:05 UTC 2014
>
>   Build user mismatch,
>     current program: buildd at lgw01-56 [CMAKE]
>     checkpoint file: buildd at roseapple [CMAKE]
>
>   Build host mismatch,
>     current program: Linux 3.19.0-23-generic x86_64
>     checkpoint file: Linux 3.2.0-61-generic x86_64
>
> Gromacs patchlevel, binary or parallel settings differ from previous run.
> Continuation is exact, but not guaranteed to be binary identical.
>
> Using 1 MPI thread
> Using 4 OpenMP threads
> Compiled SIMD instructions: SSE2 (Gromacs could use AVX2_256 on this
> machine, which is better)
>

I would get GROMACS compiled properly for my expensive hardware so that it
runs more than twice as fast...

How can I make my system fast..?

Don't have multiple simulations writing to md.log at the same time.

ok, you point out that the gmx mdrun -v -deffnm md_150ns -c md_150ns.pdb
overwritten the md.log and state.cpt files of the previous run. therefore
its showing the error. But it also generated new files as i stated above.
Please clear my doubt

On Fri, Aug 18, 2017 at 6:13 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Fri, Aug 18, 2017 at 8:41 AM manindersingh rajawat <
> rajawat.manindersingh at gmail.com> wrote:
>
> > Dear all,
> >
> > I want extend a 100ns run to 150 ns. For this I use following commands:
> >
> > gmx convert-tpr -s md_100ns.tpr -extend 50000 -o md_150ns.tpr
> >
> > gmx mdrun -v -deffnm md_150ns -c md_150ns.pdb
> >
> > But mdrun taken it as a new run
>
>
> Sure. You implied that the checkpoint file was called md_150ns, but no such
> file existed ;-)
>
>
> > and began a full 150ns run:
> > starting mdrun 'Protein in water'
> > 75000000 steps, 150000.0 ps
> >
> > so i stopped it, and run with checkpoint input as following:
> >
> > gmx mdrun -v -s md_150ns.tpr -cpi state.cpt -c md_150ns.pdb
> >
> > Reading checkpoint file state.cpt generated: Fri Mar 24 05:39:47 2017
> >
> >
> >   Version mismatch,
> >     current program: VERSION 5.0.6
> >     checkpoint file: VERSION 5.0.2
> >
>
> Generally you should continue simulations with the same version of GROMACS
> you started, but there is unlikely to be a problem in this case.
>
>
> >   Build time mismatch,
> >     current program: Mon Jul 27 05:11:28 UTC 2015
> >     checkpoint file: Fri Oct 24 17:49:05 UTC 2014
> >
> >   Build user mismatch,
> >     current program: buildd at lgw01-56 [CMAKE]
> >     checkpoint file: buildd at roseapple [CMAKE]
> >
> >   Build host mismatch,
> >     current program: Linux 3.19.0-23-generic x86_64
> >     checkpoint file: Linux 3.2.0-61-generic x86_64
> >
> > Gromacs patchlevel, binary or parallel settings differ from previous run.
> > Continuation is exact, but not guaranteed to be binary identical.
> >
> > Using 1 MPI thread
> > Using 4 OpenMP threads
> > Compiled SIMD instructions: SSE2 (Gromacs could use AVX2_256 on this
> > machine, which is better)
> >
>
> I would get GROMACS compiled properly for my expensive hardware so that it
> runs more than twice as fast...
>
>
> > WARNING: This run will generate roughly 19040 Mb of data
> >
> > starting mdrun 'Protein in water'
> > 75000000 steps, 150000.0 ps (continuing from step 50000000, 100000.0 ps).
> > step 50000600
> >
> > It starts well from the checkpoint, but due to little confusion i stopped
> > it. and ran the following command:
> >
> > gmx mdrun -v -s md_150ns.tpr -cpi state_prev.cpt -c md_150ns.pdb
> >
> > It gives the following error
> >
> > Reading file md_150ns.tpr, VERSION 5.0.6 (single precision)
> > Changing nstlist from 5 to 40, rlist from 1.2 to 1.223
> >
> >
> > Reading checkpoint file state_prev.cpt generated: Fri Mar 24 05:36:56
> 2017
> >
> >
> >   Version mismatch,
> >     current program: VERSION 5.0.6
> >     checkpoint file: VERSION 5.0.2
> >
> >   Build time mismatch,
> >     current program: Mon Jul 27 05:11:28 UTC 2015
> >     checkpoint file: Fri Oct 24 17:49:05 UTC 2014
> >
> >   Build user mismatch,
> >     current program: buildd at lgw01-56 [CMAKE]
> >     checkpoint file: buildd at roseapple [CMAKE]
> >
> >   Build host mismatch,
> >     current program: Linux 3.19.0-23-generic x86_64
> >     checkpoint file: Linux 3.2.0-61-generic x86_64
> >
> > Gromacs patchlevel, binary or parallel settings differ from previous run.
> > Continuation is exact, but not guaranteed to be binary identical.
> >
> >
> > -------------------------------------------------------
> > Program gmx, VERSION 5.0.6
> > Source code file:
> > /build/gromacs-EDw7D5/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c,
> line:
> > 2204
> >
> > Fatal error:
> > Failed to lock: md.log. Already running simulation?
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > When i run the previous command, that is
> >
> > gmx mdrun -v -s md_150ns.tpr -cpi state.cpt -c md_150ns.pdb
> >
> > It starts giving the same error to this also.
> >
> > Reading checkpoint file state.cpt generated: Fri Mar 24 05:39:47 2017
> >
> >
> >   Version mismatch,
> >     current program: VERSION 5.0.6
> >     checkpoint file: VERSION 5.0.2
> >
> >   Build time mismatch,
> >     current program: Mon Jul 27 05:11:28 UTC 2015
> >     checkpoint file: Fri Oct 24 17:49:05 UTC 2014
> >
> >   Build user mismatch,
> >     current program: buildd at lgw01-56 [CMAKE]
> >     checkpoint file: buildd at roseapple [CMAKE]
> >
> >   Build host mismatch,
> >     current program: Linux 3.19.0-23-generic x86_64
> >     checkpoint file: Linux 3.2.0-61-generic x86_64
> >
> > Gromacs patchlevel, binary or parallel settings differ from previous run.
> > Continuation is exact, but not guaranteed to be binary identical.
> >
> >
> > -------------------------------------------------------
> > Program gmx, VERSION 5.0.6
> > Source code file:
> > /build/gromacs-EDw7D5/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c,
> line:
> > 2204
> >
> > Fatal error:
> > Failed to lock: md.log. Already running simulation?
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > Please help me to resolve it.
> >
>
> Don't have multiple simulations writing to md.log at the same time.
>
> You'll also have fewer problems if you stop trying to manage your own file
> names. If you want multiple parts that you have to manually recombine
> later, use mdrun -noappend -s your.tpr -cpi. Otherwise mdrun -s your.tpr
> -cpi and let the defaults do their job.
>
> Mark
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-- 
Maninder Singh
Research Fellow,
LSN-104, Computational Biology and Bioinformatics Unit,
Molecular and Structural Biology Division,
CSIR-Central Drug Research Institute,
Sector-10, Janakipuram Extension,
Sitapur road,
Lucknow
India-226031
M: +919129206276
Email: rajawat.manindersingh at gmail.com