[gmx-users] mdrun with append option
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Feb 1 09:03:04 CET 2011
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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