[gmx-users] problem in extending a simulation run

[Tasneem Kausar]

As error says you have run previous simulation on gromacs-5.0.2 and now you
are running with gromacs 5.0.6

On 18 Aug 2017 12:11, "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 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
>
>   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)
>
> 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.
>
> Thanks
> --
> 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
> --
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