Re: [gmx-users] storage problem during a simulation
gmxcheck can still read your output files safely. :-) On Tue, Jul 23, 2013 at 10:26 PM, Francesco wrote: > the simulations are still running, they should end tomorrow afternoon. > > Fra > > On Tue, 23 Jul 2013, at 06:26 PM, Mark Abraham wrote: >> What does gmxcheck have to say about your output files? >> On Jul 23, 2013 12:17 PM, "Francesco" wrote: >> >> > Hi all, >> > This morning the gpu cluster that I'm using had some troubles with the >> > network connection between nodes that deny access to the storage. >> > Now, the simulations are still running and it seems that during the >> > "shut down" mdrun wrote a lot of checkpoints and restarted the >> > simulation once the communication was restored. >> > >> > Do you think that I will have distortions or errors in the final >> > results? >> > >> > this is a portion of the log file: >> > >> > BEGIN LOG >> > >> > ... >> > DD step 4680 vol min/aver 0.851 load imb.: force 18.2% >> > >> >Step Time Lambda >> >468193620.00.0 >> > >> >Energies (kJ/mol) >> > AngleProper Dih. Improper Dih. LJ-14 >> > Coulomb-14 >> > 3.29220e+043.94888e+042.06055e+031.69577e+04 >> > 1.50705e+05 >> > LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. >> > Potential >> > 3.28228e+05 -2.51293e+04 -3.04153e+068.44070e+03 >> > -2.48786e+06 >> > Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure >> > (bar) >> > 4.98840e+05 -1.98902e+063.10237e+02 -2.13738e+02 >> > -4.80807e+01 >> >Constr. rmsd >> > 2.76295e-05 >> > >> > Writing checkpoint, step 46813920 at Tue Jul 23 02:45:44 2013 >> > Writing checkpoint, step 46813960 at Tue Jul 23 09:48:22 2013 >> > Writing checkpoint, step 46814000 at Tue Jul 23 09:48:23 2013 >> > Writing checkpoint, step 46814040 at Tue Jul 23 09:48:24 2013 >> > Writing checkpoint, step 46814080 at Tue Jul 23 09:48:25 2013 >> > ... >> > Writing checkpoint, step 46814960 at Tue Jul 23 09:48:44 2013 >> > >> > >> > DD step 46814999 vol min/aver 0.865 load imb.: force 26.2% >> > >> >Step Time Lambda >> >4681500093630.00.0 >> > >> > Writing checkpoint, step 46815000 at Tue Jul 23 09:48:45 2013 >> > >> > >> >Energies (kJ/mol) >> > AngleProper Dih. Improper Dih. LJ-14 >> > Coulomb-14 >> > 3.28615e+043.93530e+041.99727e+031.70754e+04 >> > 1.51152e+05 >> > LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. >> > Potential >> > 3.30108e+05 -2.51173e+04 -3.04119e+068.48412e+03 >> > -2.48528e+06 >> > Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure >> > (bar) >> > 4.97562e+05 -1.98772e+063.09443e+02 -2.13533e+02 >> > 3.68992e+01 >> >Constr. rmsd >> > 2.70999e-05 >> > >> > Writing checkpoint, step 46815040 at Tue Jul 23 09:48:46 2013 >> > >> > END LOG >> > >> > thank you for your help >> > >> > cheers, >> > >> > Fra >> > -- >> > Francesco Carbone >> > PhD student >> > Institute of Structural and Molecular Biology >> > UCL, London >> > fra.carbone...@ucl.ac.uk >> > -- >> > gmx-users mailing listgmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > * Please search the archive at >> > 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 >> > >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> 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 > > > -- > Francesco Carbone > PhD student > Institute of Structural and Molecular Biology > UCL, London > fra.carbone...@ucl.ac.uk > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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-
Re: [gmx-users] storage problem during a simulation
the simulations are still running, they should end tomorrow afternoon. Fra On Tue, 23 Jul 2013, at 06:26 PM, Mark Abraham wrote: > What does gmxcheck have to say about your output files? > On Jul 23, 2013 12:17 PM, "Francesco" wrote: > > > Hi all, > > This morning the gpu cluster that I'm using had some troubles with the > > network connection between nodes that deny access to the storage. > > Now, the simulations are still running and it seems that during the > > "shut down" mdrun wrote a lot of checkpoints and restarted the > > simulation once the communication was restored. > > > > Do you think that I will have distortions or errors in the final > > results? > > > > this is a portion of the log file: > > > > BEGIN LOG > > > > ... > > DD step 4680 vol min/aver 0.851 load imb.: force 18.2% > > > >Step Time Lambda > >468193620.00.0 > > > >Energies (kJ/mol) > > AngleProper Dih. Improper Dih. LJ-14 > > Coulomb-14 > > 3.29220e+043.94888e+042.06055e+031.69577e+04 > > 1.50705e+05 > > LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > > Potential > > 3.28228e+05 -2.51293e+04 -3.04153e+068.44070e+03 > > -2.48786e+06 > > Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure > > (bar) > > 4.98840e+05 -1.98902e+063.10237e+02 -2.13738e+02 > > -4.80807e+01 > >Constr. rmsd > > 2.76295e-05 > > > > Writing checkpoint, step 46813920 at Tue Jul 23 02:45:44 2013 > > Writing checkpoint, step 46813960 at Tue Jul 23 09:48:22 2013 > > Writing checkpoint, step 46814000 at Tue Jul 23 09:48:23 2013 > > Writing checkpoint, step 46814040 at Tue Jul 23 09:48:24 2013 > > Writing checkpoint, step 46814080 at Tue Jul 23 09:48:25 2013 > > ... > > Writing checkpoint, step 46814960 at Tue Jul 23 09:48:44 2013 > > > > > > DD step 46814999 vol min/aver 0.865 load imb.: force 26.2% > > > >Step Time Lambda > >4681500093630.00.0 > > > > Writing checkpoint, step 46815000 at Tue Jul 23 09:48:45 2013 > > > > > >Energies (kJ/mol) > > AngleProper Dih. Improper Dih. LJ-14 > > Coulomb-14 > > 3.28615e+043.93530e+041.99727e+031.70754e+04 > > 1.51152e+05 > > LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > > Potential > > 3.30108e+05 -2.51173e+04 -3.04119e+068.48412e+03 > > -2.48528e+06 > > Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure > > (bar) > > 4.97562e+05 -1.98772e+063.09443e+02 -2.13533e+02 > > 3.68992e+01 > >Constr. rmsd > > 2.70999e-05 > > > > Writing checkpoint, step 46815040 at Tue Jul 23 09:48:46 2013 > > > > END LOG > > > > thank you for your help > > > > cheers, > > > > Fra > > -- > > Francesco Carbone > > PhD student > > Institute of Structural and Molecular Biology > > UCL, London > > fra.carbone...@ucl.ac.uk > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > 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 > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > 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 -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] storage problem during a simulation
What does gmxcheck have to say about your output files? On Jul 23, 2013 12:17 PM, "Francesco" wrote: > Hi all, > This morning the gpu cluster that I'm using had some troubles with the > network connection between nodes that deny access to the storage. > Now, the simulations are still running and it seems that during the > "shut down" mdrun wrote a lot of checkpoints and restarted the > simulation once the communication was restored. > > Do you think that I will have distortions or errors in the final > results? > > this is a portion of the log file: > > BEGIN LOG > > ... > DD step 4680 vol min/aver 0.851 load imb.: force 18.2% > >Step Time Lambda >468193620.00.0 > >Energies (kJ/mol) > AngleProper Dih. Improper Dih. LJ-14 > Coulomb-14 > 3.29220e+043.94888e+042.06055e+031.69577e+04 > 1.50705e+05 > LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > Potential > 3.28228e+05 -2.51293e+04 -3.04153e+068.44070e+03 > -2.48786e+06 > Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure > (bar) > 4.98840e+05 -1.98902e+063.10237e+02 -2.13738e+02 > -4.80807e+01 >Constr. rmsd > 2.76295e-05 > > Writing checkpoint, step 46813920 at Tue Jul 23 02:45:44 2013 > Writing checkpoint, step 46813960 at Tue Jul 23 09:48:22 2013 > Writing checkpoint, step 46814000 at Tue Jul 23 09:48:23 2013 > Writing checkpoint, step 46814040 at Tue Jul 23 09:48:24 2013 > Writing checkpoint, step 46814080 at Tue Jul 23 09:48:25 2013 > ... > Writing checkpoint, step 46814960 at Tue Jul 23 09:48:44 2013 > > > DD step 46814999 vol min/aver 0.865 load imb.: force 26.2% > >Step Time Lambda >4681500093630.00.0 > > Writing checkpoint, step 46815000 at Tue Jul 23 09:48:45 2013 > > >Energies (kJ/mol) > AngleProper Dih. Improper Dih. LJ-14 > Coulomb-14 > 3.28615e+043.93530e+041.99727e+031.70754e+04 > 1.51152e+05 > LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > Potential > 3.30108e+05 -2.51173e+04 -3.04119e+068.48412e+03 > -2.48528e+06 > Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure > (bar) > 4.97562e+05 -1.98772e+063.09443e+02 -2.13533e+02 > 3.68992e+01 >Constr. rmsd > 2.70999e-05 > > Writing checkpoint, step 46815040 at Tue Jul 23 09:48:46 2013 > > END LOG > > thank you for your help > > cheers, > > Fra > -- > Francesco Carbone > PhD student > Institute of Structural and Molecular Biology > UCL, London > fra.carbone...@ucl.ac.uk > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > 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 > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
[gmx-users] storage problem during a simulation
Hi all, This morning the gpu cluster that I'm using had some troubles with the network connection between nodes that deny access to the storage. Now, the simulations are still running and it seems that during the "shut down" mdrun wrote a lot of checkpoints and restarted the simulation once the communication was restored. Do you think that I will have distortions or errors in the final results? this is a portion of the log file: BEGIN LOG ... DD step 4680 vol min/aver 0.851 load imb.: force 18.2% Step Time Lambda 468193620.00.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 3.29220e+043.94888e+042.06055e+031.69577e+04 1.50705e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.28228e+05 -2.51293e+04 -3.04153e+068.44070e+03 -2.48786e+06 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 4.98840e+05 -1.98902e+063.10237e+02 -2.13738e+02 -4.80807e+01 Constr. rmsd 2.76295e-05 Writing checkpoint, step 46813920 at Tue Jul 23 02:45:44 2013 Writing checkpoint, step 46813960 at Tue Jul 23 09:48:22 2013 Writing checkpoint, step 46814000 at Tue Jul 23 09:48:23 2013 Writing checkpoint, step 46814040 at Tue Jul 23 09:48:24 2013 Writing checkpoint, step 46814080 at Tue Jul 23 09:48:25 2013 ... Writing checkpoint, step 46814960 at Tue Jul 23 09:48:44 2013 DD step 46814999 vol min/aver 0.865 load imb.: force 26.2% Step Time Lambda 4681500093630.00.0 Writing checkpoint, step 46815000 at Tue Jul 23 09:48:45 2013 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 3.28615e+043.93530e+041.99727e+031.70754e+04 1.51152e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.30108e+05 -2.51173e+04 -3.04119e+068.48412e+03 -2.48528e+06 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 4.97562e+05 -1.98772e+063.09443e+02 -2.13533e+02 3.68992e+01 Constr. rmsd 2.70999e-05 Writing checkpoint, step 46815040 at Tue Jul 23 09:48:46 2013 END LOG thank you for your help cheers, Fra -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
