Re: [gmx-users] trjconv gets stuck on frame
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) - frame320 time 128.000- frame300 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? 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.
Re: [gmx-users] trjconv gets stuck on frame
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) - frame320 time 128.000- frame300 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? 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
Re: [gmx-users] trjconv gets stuck on frame
Hi, Parallel file systems do give uneven service (e.g. one file has a chunk that lives somewhere that was under high load right when you asked for it...), so given that you can read the files normally on a normal filesystem, then you should double-check Stampede's user guides for how to make best use of their file systems, and/or take up the issue further with the admins there. Cheers, Mark On Mon, Oct 27, 2014 at 11:40 AM, Eric Smoll ericsm...@gmail.com wrote: 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) - frame320 time 128.000- frame300 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?
Re: [gmx-users] trjconv gets stuck on frame
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) - frame320 time 128.000- frame300 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.
Re: [gmx-users] trjconv gets stuck on frame
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. 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. 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) - frame320 time 128.000- frame300 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? 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.
