[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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>>
>>
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>
--
========================================
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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