[gmx-users] mdrun with append option

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 2 01:01:54 CET 2011



Mark Abraham wrote:
>   On 2/02/2011 3:38 AM, Sai Pooja wrote:
>> From the website:
>>  
>> "If you change the integrator or ensemble, you should pass the 
>> checkpoint file to tpbconv only, not to mdrun, since the state might 
>> change and thus output files can not be appended."
> 
> Where was that? It could use clarification.
> 

Last sentence here:

http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.x

Looks like maybe this is some kind of obsolete statement?  Introduced May 27, 2010.

-Justin

> Mark
> 
>> So now instead of supplying the checkpoint file to mdrun I supply it 
>> to tpbconv... does this assure that the simulations start from the 
>> coordinates/velocities specified by the .cpt file?
>>  
>> Pooja
>>
>> On Tue, Feb 1, 2011 at 11:20 AM, Sai Pooja <saipooja at gmail.com 
>> <mailto:saipooja at gmail.com>> wrote:
>>
>>     Thanks Mark. So if the simulation doesn't start from the
>>     checkpoint file, from where are the initial coordinates velocities
>>     etc. taken from?... the trajectory files?
>>      
>>     Also, I could not find the environment variable... and I am not
>>     sure how to use one.
>>      
>>     Pooja
>>     On Tue, Feb 1, 2011 at 3:03 AM, Mark Abraham
>>     <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>
>>         On 1/02/2011 7:50 AM, Sai Pooja wrote:
>>>         I think I have figured out the reason. It is because I am
>>>         carrying out replica exchange (manual) after every mdrun. If
>>>         the exchange occurs, I exchange the checkpoint files, extend
>>>         the simulation by 500 steps and continue. The new simulation
>>>         starts from exchanged cptfile. It seems that whenever the
>>>         exchange occurs, the earlier log,traj files are not appended.
>>>         They are instead overwritten. the obv solution is to save and
>>>         index these files with the relevant replicas everytime an
>>>         exchange occurs.
>>
>>         This would have been good to know earlier. If replica-exchange
>>         leads to the ensemble of the .tpr not matching the ensemble of
>>         the .cpt, then IIRC 4.5.3 mdrun will refuse to start from the
>>         .cpt, which means the subsequent mdrun will start from the
>>         .tpr only. Certainly a non-appending mdrun prints a warning
>>         (or error, I forget which) message to the log file, but
>>         perhaps the use of -append (erroneously) doesn't do that.
>>         Please have a look and see if that is the issue. There is an
>>         environment variable that can be set to tell mdrun that you
>>         (think you) know what you are doing mismatching .tpr and .cpt.
>>
>>         Mark
>>
>>
>>>         However, i have a more general question. Since mdrun still
>>>         runs with the exchanged checkpoint files and starts from the
>>>         point where the previous run ended, can I be assured that an
>>>         exchange has been affected - since tpr files correspond to
>>>         the "replica-box" and cpi to the most recent exchanged replicas?
>>>          
>>>         Pooja
>>>
>>>         On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja
>>>         <saipooja at gmail.com <mailto:saipooja at gmail.com>> wrote:
>>>
>>>
>>>             I manually index checkpoint files after every mdrun. What
>>>             troubles me is the randomness with which -append fails/works.
>>>              
>>>             For eg, I have a simulation which runs from 3ns, 1ps in 1
>>>             mdrun. Now oddly enough, the logfile starts from
>>>             1184ps(in the end, I do remember the one starting from 0
>>>             but that was overwritten it seems) and the rest is
>>>             appended uptil the 3000ps step. Why would append work
>>>             from 1184ps to 3000ps but not for the previous ones?Could
>>>             it have anything to do with the network/cluster? If that
>>>             is the case is it safer to create a new file everytime
>>>             and then concatenate them after say every 100ps?
>>>              
>>>             Pooja
>>>             On Sat, Jan 29, 2011 at 6:52 PM, Mark Abraham
>>>             <Mark.Abraham at anu.edu.au
>>>             <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>>
>>>                 On 30/01/2011 10:39 AM, Sai Pooja wrote:
>>>>                 I would be happy to supply more information.. if
>>>>                 someone could please look into this.. otherwise I
>>>>                 will have to switch to storing every file and then
>>>>                 just concatenating them which seems like a rather
>>>>                 roundabout way of doing it.
>>>
>>>                 As I suggested a few emails ago, are you sure that
>>>                 -cpi file exists? If your numerical suffixes are
>>>                 indexing restarts, then unless you've done some
>>>                 manual copying that you haven't told us about, it
>>>                 won't. Your filename scheme seems a bit contorted -
>>>                 like you're trying to do the work that GROMACS 4.5.x
>>>                 will just do for you if you let it.
>>>
>>>                 Otherwise, you'll have to do some detective work with
>>>                 gmxcheck on the -cpi to see what might be the issue.
>>>
>>>                 In your case, an initial
>>>
>>>                 mdrun -deffnm rex_3
>>>
>>>                 (perhaps save some copies while you're experimenting)
>>>                 and subsequently
>>>
>>>                 tpbconv -extend <blah> -f rex_3 -o rex_3
>>>                 mdrun -deffnm rex_3 -append
>>>
>>>                 will work and be much simpler than whatever you're
>>>                 trying to do with filenames :-)
>>>
>>>                 Mark
>>>
>>>
>>>>
>>>>                 On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja
>>>>                 <saipooja at gmail.com <mailto:saipooja at gmail.com>> wrote:
>>>>
>>>>                     This is the command:
>>>>                      
>>>>                     nbs submit -command
>>>>                     "(/usr/local/gromacs/4.5.1/bin/mdrun_mpi -s
>>>>                     rex_3.tpr -e rex_3 -c after_rex_3 -cpi restart3
>>>>                     -cpo restart3 -ap
>>>>                     pend -g rexlog3 -x rextraj3);" -nproc 1 -name
>>>>                     "GENHAM-DIHEDRAL-3" -mail start end
>>>>                      
>>>>                     Pooja
>>>>
>>>>                     On Fri, Jan 28, 2011 at 4:20 PM, Mark Abraham
>>>>                     <Mark.Abraham at anu.edu.au
>>>>                     <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>>>
>>>>                         On 29/01/2011 3:56 AM, Sai Pooja wrote:
>>>>
>>>>                             Hi,
>>>>                             I am using tpbconv and mdrun to extend a
>>>>                             simulation. I use it with the append
>>>>                             option but the files still get
>>>>                             overwritten or erased. Can someone help
>>>>                             me in this regard?
>>>>                             Pooja
>>>>                             Commands (in python)
>>>>                             cmd = '(%s/tpbconv -extend %f -s
>>>>                             rex_%d.tpr -o rex_%d.tpr)'
>>>>                             %(GROMPATH,dtstep,i,i)
>>>>                                  os.system(cmd)
>>>>                                  time.sleep(1)
>>>>                                  cmd  = 'nbs submit -command "'
>>>>                                  cmd += '(%s/mdrun_mpi -noh
>>>>                             -noversion -s rex_%d.tpr -e rex_%d -c
>>>>                             after_rex_%d -cpi restart%d -cpo
>>>>                             restart%d -append -g rexlog%d -x
>>>>                             rextraj%d >/dev/null); '
>>>>                             %(GROMPATH,i,i,i,i,i,i,i)
>>>>                                  cmd += '" '
>>>>                                  cmd += '-nproc 1 '
>>>>                                  cmd += '-name "GENHAM-DIHEDRAL-%d"
>>>>                             '%(i)
>>>>                                  cmd += '-mail start end '
>>>>                                  cmd += '-elapsed_limit 16h >> rexid'
>>>>                                  os.system(cmd)
>>>>
>>>>
>>>>                         More useful for diagnostic and
>>>>                         record-preservation purposes is to construct
>>>>                         the cmd string and print it to stdout (or
>>>>                         something).
>>>>
>>>>                         At the moment it is far from clear that your
>>>>                         -cpi file exists for the new run.
>>>>
>>>>                         Mark
>>>>                         -- 
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>>>>
>>>>
>>>>
>>>>                     -- 
>>>>                     Quaerendo Invenietis-Seek and you shall discover.
>>>>
>>>>
>>>>
>>>>
>>>>                 -- 
>>>>                 Quaerendo Invenietis-Seek and you shall discover.
>>>
>>>
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>>
>>
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>>     -- 
>>     Quaerendo Invenietis-Seek and you shall discover.
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>>
>>
>>
>> -- 
>> Quaerendo Invenietis-Seek and you shall discover.
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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