[gmx-users] problem in extending a simulation run
manindersingh rajawat
rajawat.manindersingh at gmail.com
Fri Aug 18 13:08:12 CEST 2017
Thanks Tasneem,
But later when I run the following commands on files from my backup data.
It works well
gmx convert-tpr -s md_100ns.tpr -extend 50000 -o md_150ns.tpr
Reading toplogy and stuff from md_100ns.tpr
Reading file md_100ns.tpr, VERSION 5.0.2 (single precision)
Extending remaining runtime of by 50000 ps (now 75000000 steps)
Writing statusfile with starting step 0 and length 75000000
steps...
time 0.000 and length 150000.000 ps
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.
starting mdrun 'Protein in water'
75000000 steps, 150000.0 ps (continuing from step 50000000, 100000.0 ps).
step 50244000
Inspite of version mismatch, it running. But i dont know how the version
mismatch is going to affect the results. And what happened with my files of
the previous run which i mentioned in previous mail. And why its showing
the fatal error : Failed to lock: md.log. Already running simulation?
Please help me to understand them
Thanks
On Fri, Aug 18, 2017 at 3:20 PM, Tasneem Kausar <tasneemkausar12 at gmail.com>
wrote:
> 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
> > --
> > Gromacs Users mailing list
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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
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