On Jul 9, 2010, at 11:29 AM, 张春雷 wrote: > Hi Carsten, > > The error message I post is got on a single core with MPI. > > p0_6991: p4_error: interrupt SIGSEGV: 11 > > So it states p0_xxxx. > > I dont think the error is due to the MPI progrom. > Am I right? Yes, but there must be some more diagnostic information from mdrun about what has gone wrong. Please check stderr / stdout output files as well as md.log.
Carsten > > Justin Zhang > > 在 2010年7月9日 下午4:00，Carsten Kutzner <[email protected]>写道： > Hi Justin, > > what kind of error message do you get if you run this system > on a single core without MPI? > > Carsten > > > On Jul 8, 2010, at 9:36 PM, 张春雷 wrote: > >> Dear all, >> >> I have post this question about a two weeks ago. During these days, I >> followed suggestions from Mark and weixin, but did not fix it. Here, I >> repeat it again to seek more help. >> >> I attempt to extend MD simulation for a coarse-grained system. CG models are >> in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07. >> >> I tried to use check point file state.cpt to extend my simulation. The mdrun >> program can read to the check file. But it reported error like this: >> >> Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 >> >> Loaded with Money >> >> starting mdrun 'Protein in POPE bilayer' >> 24000000 steps, 720000.0 ps (continuing from step 12000000, 360000.0 ps). >> step 12000000, remaining runtime: 0 s >> p0_6991: p4_error: interrupt SIGSEGV: 11 >> >> I check the state.cpt file using gmxdump and compare it with other >> checkpoint files that can be used for extending All-atom simulations. I >> found that in the CG check point file, some sections are missing: box-v >> (3x3) and thermostat-integral. >> I am not sure whether this missing sections cause my run crash. If it is, >> could any one tell me possible reasons that result in the loss of box-v and >> thermostat-integral and how to fix the problem? >> >> Your suggestions are greatly helpful and appreciated. >> >> Justin Zhang >> >> >> >> 在 2010年6月25日 下午4:45，张春雷 <[email protected]>写道： >> Information shown by gmxcheck: >> >> Checking file state.cpt >> >> # Atoms 9817 >> Last frame -1 time 360000.000 >> >> >> Item #frames Timestep (ps) >> Step 1 >> Time 1 >> Lambda 1 >> Coords 1 >> Velocities 1 >> Forces 0 >> Box 1 >> >> Checking file state_prev.cpt >> >> # Atoms 9817 >> Last frame -1 time 359010.000 >> >> >> Item #frames Timestep (ps) >> Step 1 >> Time 1 >> Lambda 1 >> Coords 1 >> Velocities 1 >> Forces 0 >> Box 1 >> >> Checking file md_360ns.trr >> trn version: GMX_trn_file (double precision) >> Reading frame 0 time 0.000 >> # Atoms 9817 >> Reading frame 2000 time 300000.000 >> >> >> Item #frames Timestep (ps) >> Step 2401 150 >> Time 2401 150 >> Lambda 2401 150 >> Coords 2401 150 >> Velocities 2401 150 >> Forces 0 >> Box 2401 150 >> >> Is anything wrong? >> >> >> 2010/6/25 Mark Abraham <[email protected]> >> >> >> >> ----- Original Message ----- >> From: 张春雷 <[email protected]> >> Date: Friday, June 25, 2010 16:46 >> Subject: Re: [gmx-users] P4_error for extending coarse grained MD simulations >> To: Discussion list for GROMACS users <[email protected]> >> >> > The last .gro file only provides coordinates of the system. No velocity is >> > recorded. Actually, what I attempt to achieve is a binary identical >> > trajectory. So I think the velocity from the last step is critical. >> > >> > I have tried another approach in which the checkpoint file is neglected. >> > >> > $mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g >> > md_720ns.log >> > >> > It works. So the checkpoint file appears to contain some error. But it is >> > generated by a normally finished production simulation. >> >> What does gmxcheck say about all the files involved? >> >> Mark >> >> >> > Have you encountered similar things? >> > >> > Thank you for your suggestions! >> > >> > >> > >> > 在 2010年6月25日 上午9:16，weixin <[email protected]>写道： >> > >> > How about using the last .gro file to continue your simulation? >> > >> > >> > >> > 2010/6/24 张春雷 <[email protected]> >> > Dear GMX-users, >> > >> > This is Justin. >> > I am performing coarse-grained simulation on a protein-lipid bilayer >> > system. This is a MARTINI CG model. >> > I have successfully completed a 360ns simulation, during which the time >> > step is 30 fs. >> > >> > I would like to extend the simulation to 1micro-second. The commands I >> > used are: >> > >> > $tpbconv_mpi_d -s md_360ns.tpr -extend 360000 -o md_720ns.tpr >> > >> > $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g >> > md_360ns.log -cpi state.cpt >> > >> > However, I received the following message: >> > >> > Checkpoint file is from part 1, new output files will be suffixed part0002. >> > Getting Loaded... >> > Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) >> > >> > Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 >> > >> > Loaded with Money >> > >> > starting mdrun 'Protein in POPE bilayer' >> > 24000000 steps, 720000.0 ps (continuing from step 12000000, 360000.0 ps). >> > step 12000000, remaining runtime: 0 s >> > p0_6991: p4_error: interrupt SIGSEGV: 11 >> > >> > I have searched the mail-list, but found no similar report. I also search >> > through google, but no answer seems satisfactory. >> > >> > I once performed extending simulation for all atom simulation, and the >> > method mentioned above worked. >> > >> > Is anyone familiar with MARTINI CG simulation? >> > Could you give me some suggestions? >> > >> > Many thanks! >> > >> > Justin >> > >> > -- >> > gmx-users mailing list [email protected] >> > http://lists.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 mailing list [email protected] >> > http://lists.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 mailing list [email protected] >> > http://lists.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 mailing list [email protected] >> http://lists.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 mailing list [email protected] >> http://lists.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 > > > -- > Dr. Carsten Kutzner > Max Planck Institute for Biophysical Chemistry > Theoretical and Computational Biophysics > Am Fassberg 11, 37077 Goettingen, Germany > Tel. +49-551-2012313, Fax: +49-551-2012302 > http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne > > > > > > -- > gmx-users mailing list [email protected] > http://lists.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 mailing list [email protected] > http://lists.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
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