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.
