[gmx-developers] Restarting with different parallel configuration

[Anton Feenstra]

Oliver Beckstein wrote:
> Hi Josh,
> 
> 
>>I am not sure if this is the correct list for this question, but it
>>seems to be a good match for this list.  
> 
> 
> In the future, I'd send messages like this to gmx-users.
> 
> 
>>Is there a method to take the output or checkpoint files (I use .trr)
>>from a parallel run of gromacs and use it as input for another parallel
>>run that has a different number of nodes?  The goal is to create a
> 
> 
> You have to rerun grompp with the new number of nodes but you can have
> grompp read the starting configuration from a trr with velocities and the
> edr (for the coupling stuff). In this case you might also set "gen_vel =
> no" and "unconstrained_start = yes" (see man grompp) in the mdp file 
> (using sed comes to mind...).

Best way to do it, keeping the runs as contiguous as possible, is to make
a new .tpr file for the starting conformation (exactly the same as the first
one you made to start the run in the first place). Then you can use tpbconv
with the new .tpr file (which differs only in 'np') and the .trr file from
your ongoing run. You could even generate several .tpr file before you start,
which gives you the choice between several numbers of CPU's, doing something
like (csh style):

#> foreach i ( 1 2 4 6 8 )
#>   grompp -np $i -o topol_np$i.tpr
#> end

Then, with mdrun and/or tpbconv, you can pick the 'topol_np?.tpr' of your
choice (and it could even be dynamic automatically, switching np in mid-run!).

(Note that if you used grompp -shuffle, this procedure will be a bit more
complex!)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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