[gmx-users] trjconv gets stuck on frame

[Eric Smoll]

Hi Mark,

i understand. It wasn't getting stuck in one place, if I skip over the
problem time when executed from the beginning the slowdown still occurs.

I am working on the Stampede Supercomputer using their install of gromacs
and for reasons I do not understand, this extremely slow processing only
occurs for some trajectories on Stampede. Thinking there was some problem
with the login nodes, I tried this on a compute node with the same results
- slow processing.

I transferred my trajectory to my laptop, installed the same version of
gromacs, and processed it with trjconv at a reasonable speed.

Best,
Eric


On Mon, Oct 27, 2014 at 5:33 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On Sun, Oct 26, 2014 at 11:44 PM, Eric Smoll <ericsmoll at gmail.com> wrote:
>
> > Hi Mark,
> >
> > Thank you for responding so rapidly. I should note that identical
> > processing (I use a script) on the trajectories produced by slightly
> > different chemical systems had no problem and trajconv produced a
> complete
> > processed trajectory.
> >
> > However, when processing the problematic few with trajconv, the
> trajectory
> > that is output is incomplete (the trjconv output has fewer frames than
> the
> > input trajectory).
> >
> > This is definitely not problem with the change in output frequency of
> > progress reports to the terminal.
> >
> > I am not sure if the -b flag is telling me anything. I move it around and
> > it still seems to get stuck. I have ~30,000 atoms in my system. The first
> > 120 ps are processed in ~ 5 seconds. The next 4 ps take ~ 30 sec. My
> > trajectory is many nanoseconds long.
> >
>
> The point is to try to see whether the issue happens x steps into the
> trajectory, or only at around t=120ps. Does it happen if you are using -pbc
> somethingelse? Does it happen if you copy the file to some other filesystem
> before using -pbc whole? One needs to find a pattern before one can guess
> where the problem might lie.
>
>
> > Again, my other chemically similar systems do no hang like this and the
> > simulation procedure is scripted so it is consistent across my different
> > chemical systems.
> >
>
> OK. It's possible your simulation system is doing something pathological in
> that trajectory, which somehow does not agree with the implementation of
> -pbc whole (I'm guessing wildly here), but one would need to try the above
> kinds of experiments to probe that, and or visualize the trajectory in some
> viewing program.
>
> Mark
>
> I am using gromacs/4.6.5.
> >
> > Best,
> > Eric
> >
> > On Sun, Oct 26, 2014 at 5:21 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > The output does drop in frequency at some point, so that might be all
> you
> > > are seeing. Experiment with -b and values around the putative problem
> > area.
> > >
> > > Mark
> > > On Oct 26, 2014 6:59 PM, "Eric Smoll" <ericsmoll at gmail.com> wrote:
> > >
> > > > Hello Gromacs users,
> > > >
> > > > I have a trajectory file script18_o.trr that I am trying to process.
> > > Using
> > > > gmxcheck, this file appears to be complete. When I execute the
> command
> > > > below
> > > >
> > > > trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr
> -o
> > > > tmp1.trr -pbc whole << EOF
> > > > 0
> > > > EOF
> > > >
> > > > the code moves quickly through the first few hundred frames only to
> > > > consistently get stuck on frame 300...
> > > >
> > > > trn version: GMX_trn_file (single precision)
> > > >  ->  frame    320 time  128.000        ->  frame    300 time  120.000
> > > >
> > > > How do I troubleshoot the problem?
> > > >
> > > > -Eric
> > > > --
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