The mdinfo file output is timer-based, and it is only printed when the time
interval since the last mdinfo output exceeds the interval in secs specified
in mdinfo_flush_interval (defaults to 60 sec). The same is actually true of
mdout, but it uses mdout_flush_interval (defaults to 300 sec). With both
these files, the "flush" is achieved by a close of the file followed by an
open in append mode (only portable way to force a flush in fortran, at least
as of f90). The OS may choose to flush files itself more frequently,
typically based on some data metric. This feature exists primarily to force
the flushing of files to disk at some reasonable interval for observation;
some high performance file systems can actually run thousands of steps
before data becomes available otherwise (I seem to recollect that when I did
this, I was using bigben at psc, and you could literally complete a run
before you would see output - very efficient, but generally folks like to
know the run is doing okay by looking at mdout and/or mdinfo).
Regards - Bob Duke
----- Original Message -----
From: "Mayank Daga" <mdaga.vt.edu>
To: <amber.ambermd.org>
Sent: Tuesday, August 17, 2010 11:10 AM
Subject: [AMBER] Question about mdinfo file.
> Hi,
>
> I am a newbie using AMBER on the GPUs.
> When I run my simulations, I see two output files, mdout and mdinfo. In
> the
> mdinfo file, I see the timing details as to how many ns/day I get. The
> issue
> is some steps are always uncompleted according to this file while mdout
> lists that all the steps have been completed. Why is this discrepancy?
> For example, if I run a simulation for 10000 steps, mdinfo shows 9000
> steps
> remaining while mdout list energy values for all 10000 steps.
>
> I am using the input files as downloaded from the AMBER website and to run
> the simulation:
> ~/amber11/bin/pmemd.cuda -O -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> -x mdcrd -gpu 0
>
> Please explain this behaviour.
>
> Thanks,
> ~mayank
>
>
> --
> Mayank Daga | SyNeRGy Laboratory | Dept. of Computer Science
> Virginia Tech | http://synergy.cs.vt.edu | http://www.cs.vt.edu
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue Aug 17 2010 - 09:00:06 PDT
