[gmx-users] P4_error for extending coarse grained MD simulations

Carsten Kutzner ckutzne at gwdg.de
Fri Jul 9 11:34:51 CEST 2010 

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 <ckutzne at 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.pku at 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.abraham at anu.edu.au>
>> 
>> 
>> 
>> ----- Original Message -----
>> From: 张春雷 <chunleizhang.pku at 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 at 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 <xwxnju at gmail.com>写道：
>> >  
>> > How about using the last .gro file to continue your simulation?
>> > 
>> > 
>> >  
>> > 2010/6/24 张春雷 <chunleizhang.pku at 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
>> > 
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> 
> 
> --
> 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
> 
> 
> 
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