[gmx-developers] H-REMD restart

[Luca Bellucci]

Dear Mark,
I have reproduced the run with two replica.
If you want, i can send you the results with a private mail for a deepest 
check. It is about 8/9M.
Thanks
Luca

> On 01/24/11, Mark Abraham  <mark.abraham at anu.edu.au> wrote:
> > On 01/24/11, Luca Bellucci  <luca.bellucci_s3 at unimore.it> wrote:
> > > hanks Mark for quick replay.
> > > it is 4.5.3
> > > This is the log file at restart point.
> > >
> > > -----------------------------------------------------------
> > > Restarting from checkpoint, appending to previous log file.
> > >
> > > Log file opened on Sun Jan 23 23:40:07 2011
> > > Host: ionode8  pid: 2916  nodeid: 0  nnodes:  64
> > > The Gromacs distribution was built Thu Nov 18 14:35:49 CET 2010 by
> > > cin0644a at loginfn (Linux 2.6.16.60-0.42.10-ppc64 ppc64)
> > > [..]
> > > Initializing Replica Exchange
> > > Repl  There are 64 replicas:
> > > Multi-checking the number of atoms ... OK
> > > Multi-checking the integrator ... OK
> > > Multi-checking init_step+nsteps ... OK
> > > Multi-checking first exchange step: init_step/-replex ... OK
> > > Multi-checking the temperature coupling ... OK
> > > Multi-checking the number of temperature coupling groups ... OK
> > > Multi-checking the pressure coupling ... OK
> > > Multi-checking free energy ... OK
> > > [..]
> >
> > Seeing the whole logfile up to the first energy output would be more
> > helpful.
>
> Also, stderr and stdout can have useful diagnostic information here.
>
> Mark
>
> > Mark
> >
> > > Started mdrun on node 0 Sun Jan 23 23:40:07 2011
> > >
> > > > On 24/01/2011 8:57 AM, Luca Bellucci wrote:
> > > > > Dear all,
> > > > > I known that in repl_ex.c is implemented the
> > > > > H-REMD.  It seems to work, however
> > > > > H-REMD is not documented, thus I am testing it.
> > > > > I performed a test  in a BlueGene cluster:
> > > > >
> > > > > mpirun -mode VN -np 4096 mdrun_mpi_bg  -s md.tpr -np 16 -multi 128
> > > > > -replex 2000
> > > > >
> > > > > it works fine.
> > > > >
> > > > > I restarted with this command:
> > > > >
> > > > > mpirun -mode VN -np 4096 mdrun_mpi_bg   -s md.tpr -cpi state.cpt
> > > > > -append -np 16 -multi 128 -replex 2000
> > > > >
> > > > > I followed the GROMACS  "Doing Restarts" section, however it does
> > > > > not work as expected; the trajecory and energy files are
> > > > > reinitialized and I lost most of the MD informations.
> > > > > Only log files were updated as expected.
> > > >
> > > > Is this with the latest GROMACS version? If not, please try that.
> > > >
> > > > Mark
> > >
> > > --
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