Hi, Your system is exploding, some atoms end up with coordinates of around 10^9 which then throw off the PBC code that tries to put atoms back in the box. This will normally not happen as constraining will already fail with such huge coordinates, I think, so technically it is a bug, we could handle this corner-case better.
However, if you need to verify your system setup as it is unstable (not well equilibrated or the time-step too long). -- Szilárd On Thu, Mar 29, 2018 at 3:50 PM, Myunggi Yi <myun...@pukyong.ac.kr> wrote: > Dear Szilard, > > Can you run this simulation? > > Simulation doesn't crush and doesn't generate error message. > It take forever without updating report in log file or other output files. > > Is this a bug? > > > > On Thu, Mar 29, 2018 at 7:58 AM, Szilárd Páll <pall.szil...@gmail.com> > wrote: > >> Thanks. Looks like the messages and error handling is somewhat >> confusing; you must have the OMP_NUM_THREADS environment variable set >> which (just as setting -ntomp), without setting -ntmpi too is not >> supported. >> >> Either let mdrun decide about the thread count or set -ntmpi manually. >> >> -- >> Szilárd >> >> >> On Wed, Mar 28, 2018 at 7:10 PM, Myunggi Yi <myun...@pukyong.ac.kr> wrote: >> > Does it work? >> > >> > https://drive.google.com/open?id=1n5m1tNGbnV7oZnuAEgZ7gSP6qA6HluNl >> > >> > How about this? >> > >> > >> > Myunggi Yi >> > >> > On Wed, Mar 28, 2018 at 12:20 PM, Mark Abraham <mark.j.abra...@gmail.com >> > >> > wrote: >> > >> >> Hi, >> >> >> >> Attachments can't be accepted on the list - please upload to a file >> sharing >> >> service and share links to those. >> >> >> >> Mark >> >> >> >> On Wed, Mar 28, 2018 at 6:16 PM Myunggi Yi <myun...@pukyong.ac.kr> >> wrote: >> >> >> >> > I am attaching the file. >> >> > >> >> > Thank you. >> >> > >> >> > Myunggi Yi >> >> > >> >> > On Wed, Mar 28, 2018 at 11:40 AM, Szilárd Páll < >> pall.szil...@gmail.com> >> >> > wrote: >> >> > >> >> > > Again, please share the exact log files / description of inputs. >> What >> >> > > does "bad performance" mean? >> >> > > -- >> >> > > Szilárd >> >> > > >> >> > > >> >> > > On Wed, Mar 28, 2018 at 5:31 PM, Myunggi Yi <myun...@pukyong.ac.kr> >> >> > wrote: >> >> > > > Dear users, >> >> > > > >> >> > > > I have two questions. >> >> > > > >> >> > > > >> >> > > > 1. I used to run typical simulations with the following command. >> >> > > > >> >> > > > gmx mdrun -deffnm md >> >> > > > >> >> > > > I had no problem. >> >> > > > >> >> > > > >> >> > > > Now I am running a simulation with "Dry_Martini" FF with the >> >> following >> >> > > > input. >> >> > > > >> >> > > > >> >> > > > integrator = sd >> >> > > > tinit = 0.0 >> >> > > > dt = 0.040 >> >> > > > nsteps = 1000000 >> >> > > > >> >> > > > nstlog = 5000 >> >> > > > nstenergy = 5000 >> >> > > > nstxout-compressed = 5000 >> >> > > > compressed-x-precision = 100 >> >> > > > >> >> > > > cutoff-scheme = Verlet >> >> > > > nstlist = 10 >> >> > > > ns_type = grid >> >> > > > pbc = xyz >> >> > > > verlet-buffer-tolerance = 0.005 >> >> > > > >> >> > > > epsilon_r = 15 >> >> > > > coulombtype = reaction-field >> >> > > > rcoulomb = 1.1 >> >> > > > vdw_type = cutoff >> >> > > > vdw-modifier = Potential-shift-verlet >> >> > > > rvdw = 1.1 >> >> > > > >> >> > > > tc-grps = system >> >> > > > tau_t = 4.0 >> >> > > > ref_t = 310 >> >> > > > >> >> > > > ; Pressure coupling: >> >> > > > Pcoupl = no >> >> > > > >> >> > > > ; GENERATE VELOCITIES FOR STARTUP RUN: >> >> > > > gen_vel = yes >> >> > > > gen_temp = 310 >> >> > > > gen_seed = 1521731368 >> >> > > > >> >> > > > >> >> > > > >> >> > > > If I use the same command to submit the job. >> >> > > > I got the following error. I don't know why. >> >> > > > >> >> > > > ------------------------------------------------------- >> >> > > > Program: gmx mdrun, version 2018.1 >> >> > > > Source file: src/gromacs/taskassignment/resourcedivision.cpp >> (line >> >> 224) >> >> > > > >> >> > > > Fatal error: >> >> > > > When using GPUs, setting the number of OpenMP threads without >> >> > specifying >> >> > > the >> >> > > > number of ranks can lead to conflicting demands. Please specify >> the >> >> > > number >> >> > > > of >> >> > > > thread-MPI ranks as well (option -ntmpi). >> >> > > > >> >> > > > For more information and tips for troubleshooting, please check >> the >> >> > > GROMACS >> >> > > > website at http://www.gromacs.org/Documentation/Errors >> >> > > > ------------------------------------------------------- >> >> > > > >> >> > > > >> >> > > > So I did run simulation with the following command. >> >> > > > >> >> > > > >> >> > > > gmx mdrun -deffnm md -ntmpi 1 >> >> > > > >> >> > > > >> >> > > > Now the performance is extremely bad. >> >> > > > Since yesterday, the log file still reporting the first step's >> >> energy. >> >> > > > >> >> > > > 2. This is the second question. Why? >> >> > > > >> >> > > > Can anyone help? >> >> > > > >> >> > > > >> >> > > > Myunggi Yi >> >> > > > -- >> >> > > > 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 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.