[gmx-users] P4_error for extending coarse grained MD simulations
张春雷
chunleizhang.pku at gmail.com
Fri Jul 9 11:29:11 CEST 2010
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 <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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>>>> >
>>>> >
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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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