Re: [gmx-users] Error using double precision
[EMAIL PROTECTED] wrote: Ok (you didn't say that in the first mail...). Does it also happen on one processor? I Haven't tested in d.p. After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. I energy minimized the system in d.p. and it is still running after 710 ps. No had stopped at 710 ps... Why is it then working with single precision? -Edvin it's difficult to say, it could be coincidence but could also be due to a problem in the software. is this 3.3.1? you are welcome to submit a bugzilla, but we would like to have a system that crashes in ten steps in DP but not in SP... -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
[EMAIL PROTECTED] wrote: Ok (you didn't say that in the first mail...). Does it also happen on one processor? I Haven't tested in d.p. After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. I energy minimized the system in d.p. and it is still running after 710 ps. No had stopped at 710 ps... Why is it then working with single precision? You have the possibility of observing different behaviour because the simulation is of a chaotic system. Small changes in starting conditions lead to radical differences later in time. If your starting configuration has some "unhappiness" that has to relax (as is normal for arbitrarily-solvated biomolecules) under one numerical regime it might explode instantly, under another it might start to relax but some resonant effect leads to problems later, and under yet another it finds the right equilibrium ensemble without breaking. The way to avoid this behaviour is to follow a regime like I recommended in the URL I gave last time. If that is not gentle enough to massage the system into good behaviour (when the topology is correct) then there are further degrees of gentleness you might apply. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
> >Ok (you didn't say that in the first mail...). > >Does it also happen on one processor? > > I Haven't tested in d.p. > > >After how many steps does it happen? (see Marks mail). > > after 30 steps, that is 600 ps. > > > I energy minimized the system in d.p. and it is still running after > 710 ps. > No had stopped at 710 ps... Why is it then working with single precision? -Edvin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
[EMAIL PROTECTED] wrote: Ok (you didn't say that in the first mail...). Does it also happen on one processor? I Haven't tested in d.p. After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. that means the trajectory is quite different from SP. I energy minimized the system in d.p. and it is still running after 710 ps. this also changes the trajectory, so the error need not be related to the precision. when it happens again please try to investigate what happened to the structure just before the crash. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error using double precision
>Ok (you didn't say that in the first mail...). >Does it also happen on one processor? I Haven't tested in d.p. >After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. I energy minimized the system in d.p. and it is still running after 710 ps. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
[EMAIL PROTECTED] wrote: edvin.erdtman at nat.oru.se wrote: I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: this usually means you have an unequilibrated system. But it worked with single precision! Or do I need to make a energy minimization first in DP? Ok (you didn't say that in the first mail...). Does it also happen on one processor? After how many steps does it happen? (see Marks mail). -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
[EMAIL PROTECTED] wrote: edvin.erdtman at nat.oru.se wrote: I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: this usually means you have an unequilibrated system. But it worked with single precision! Or do I need to make a energy minimization first in DP? Check out http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation MD simulations are chaotic, and from the same starting point (as measured to single precision) you will observe divergent behaviour, increasingly so as time progresses. The fact that only one of the simulations crash is likely just a numerical artefact. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error using double precision
>edvin.erdtman at nat.oru.se wrote: >> I installed both double and single precision gromacs on a new system. When >> running a membrane MD with double precision 8 processor mpi calc, this error >> appars in the error output file: > > >this usually means you have an unequilibrated system. But it worked with single precision! Or do I need to make a energy minimization first in DP? --- Fil. Mag. Edvin Erdtman Biofysikalisk kemi Naturvetenskapliga instutitionen Fakultetsgatan 1 Örebro Universitet S-701 82 Örebro, Sweden Tel: +46 19 30 36 69 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
[EMAIL PROTECTED] wrote: I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: this usually means you have an unequilibrated system. Error on node 4, will try to stop all the nodes Halting parallel program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]) on CPU 4 out of 8 --- Program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]), VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 1335. It should have been within [ 0 .. 1296 ] Please report this to the mailing list (gmx-users@gromacs.org) --- Thanx for Using GROMACS - Have a Nice Day Error on node 6, will try to stop all the nodes Halting parallel program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]) on CPU 6 out of 8 gcq#10922: Thanx for Using GROMACS - Have a Nice Day * MPI-error in rank 2 Routine MPI_Abort : Terminating after call to MPI_Abort * --- mpimon --- Aborting run after process-2 terminated abnormally Childprocess 17353 exited with exitcode 2 --- gcq#10922: Thanx for Using GROMACS - Have a Nice Day Thankful for some help. Edvin -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error using double precision
I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: Error on node 4, will try to stop all the nodes Halting parallel program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]) on CPU 4 out of 8 --- Program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]), VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 1335. It should have been within [ 0 .. 1296 ] Please report this to the mailing list (gmx-users@gromacs.org) --- Thanx for Using GROMACS - Have a Nice Day Error on node 6, will try to stop all the nodes Halting parallel program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]) on CPU 6 out of 8 gcq#10922: Thanx for Using GROMACS - Have a Nice Day * MPI-error in rank 2 Routine MPI_Abort : Terminating after call to MPI_Abort * --- mpimon --- Aborting run after process-2 terminated abnormally Childprocess 17353 exited with exitcode 2 --- gcq#10922: Thanx for Using GROMACS - Have a Nice Day Thankful for some help. Edvin --- Fil. Mag. Edvin Erdtman Biofysikalisk kemi Naturvetenskapliga instutitionen Fakultetsgatan 1 Örebro Universitet S-701 82 Örebro, Sweden Tel: +46 19 30 36 69 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
