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.abra...@gmail.com> wrote: > On Sun, Oct 26, 2014 at 11:44 PM, Eric Smoll <ericsm...@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.abra...@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" <ericsm...@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 > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? 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