Justin, The whole error was
Reading file md_rest1.tpr, VERSION 4.5.5 (single precision) NOTE: atoms involved in distance restraints should be within the longest cut-of$ ------------------------------------------------------- Program mdrun_mpi_d.openmpi, VERSION 4.5.5 Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/disre.c, line: 143 Fatal error: Time or ensemble averaged or multiple pair distance restraints do not work (yet$ For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Gabba Gabba Hey!" (The Ramones) Error on node 5, will try to stop all the nodes Halting parallel program mdrun_mpi_d.openmpi on CPU 5 out of 12 ------------------------------------------------------- and so on for each CPU :) Might it be with some PME order ? I've recieved errors about wrong PME order when tried to lauch my simulations on big ammoun of the nodes but could not find possible way to fix it :( James 14 марта 2012 г. 19:43 пользователь Justin A. Lemkul <jalem...@vt.edu>написал: > > > James Starlight wrote: > >> Mark, >> >> >> My restrains on topology consist of the next section >> >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre.itp" >> #endif >> >> [ dihedral_restraints ] >> ; ai aj ak al type label phi dphi kfac power >> ; Chi N - CA - CB - CG >> 2908 2910 2911 2912 1 1 180 0 1 2 >> >> [ distance_restraints ] >> ; ai aj type index type' low up1 up2 fac >> 1097 3201 1 1 1 0.796 0.841 0.900 1.0 >> 2948 3201 1 2 1 0.796 0.841 0.900 1.0 >> 1097 2948 1 3 1 0.796 0.841 0.900 1.0 >> 1097 2999 1 4 1 0.800 1.000 1.100 1.0 >> 1098 2034 1 5 1 0.800 1.000 1.100 1.0 >> 1098 2042 1 6 1 0.800 1.000 1.100 1.0 >> 1098 2067 1 7 1 0.800 1.000 1.100 1.0 >> 1130 3241 1 8 1 0.540 0.630 0.700 1.0 >> 546 3393 1 9 1 1.162 1.725 1.800 1.0 >> 628 3460 1 10 1 1.438 2.067 2.100 1.0 >> 637 3460 1 11 1 0.700 1.238 1.300 1.0 >> 648 2791 1 12 1 1.788 2.152 2.200 1.0 >> 648 3376 1 13 1 1.736 2.061 2.150 1.0 >> 2292 2743 1 14 1 0.200 0.300 0.350 1.0 >> 1258 2203 1 15 1 0.200 0.300 0.350 1.0 >> >> Also I've attached my md.mdp file. >> >> I have no problems with that system on my home desktop. >> >> On cluster with installed MPI I've lunch my simulation by means of below >> command >> >> grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o >> md_50ns.tpr >> >> mpiexec -np 24 mdrun_mpi_d.openmpi -v -deffnm md_50ns >> >> >> I'll be very thankful if you show me what's wrong could be with my >> initial systems because I have no any problems with my systems on my home >> desktop. On the other hand on Cluster some of my jobs ends with the errors >> ( something wrong with PME order or the error wich I've shown you with the >> ensembles of restrains) >> >> It was installed the same last version of Gromacs on cluster like on my >> desctop ( difference only in double precission with lack on my home desctop >> but present on cluster) >> >> Could you tell me in what log files I could obtain more detailed >> information of the source of such erors? I've checked only md.log as well >> as name_of_the_simulation.log. Besides there are files gromacs.err wich >> contain information about crashed simulation. >> >> >> > You didn't include the whole error in your first message, which should > read "Time or ensemble averaged or multiple pair distance restraints do not > work (yet) with domain decomposition, use particle decomposition (mdrun > option -pd)" > > Thus the error message tells you how to proceed. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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