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.
