Thanks. I used the exactly same program (same installation and same environment variable).
How come this error depends on the *.mdp file? I don't get it with typical simulations such as md with PME etc, but I get it with this Dry_Martini mdp file (using sd, reaction field etc.). Myunggi Yi 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.
