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? Justin Zhang 在 2010年7月9日 下午4:00,Carsten Kutzner <ckut...@gwdg.de>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 <chunleizhang....@gmail.com>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 <mark.abra...@anu.edu.au> >> >> >>> >>> ----- Original Message ----- >>> From: 张春雷 <chunleizhang....@gmail.com> >>> 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 <gmx-users@gromacs.org> >>> >>> > 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 <xwx...@gmail.com>写道: >>> >>>> > >>>> > How about using the last .gro file to continue your simulation? >>>> > >>>> > >>>> > >>>> > 2010/6/24 张春雷 <chunleizhang....@gmail.com> >>>> >>>>> > 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 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/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/mailing_lists/users.php >>>>> >>>> > >>>> > >>>> > -- >>>> > 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/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/mailing_lists/users.php >>>> >>> > >>> > -- >>> > gmx-users mailing list gmx-users@gromacs.org >>> > 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 gmx-users-requ...@gromacs.org. >>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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