[gmx-users] error in a parallel job
spoel at xray.bmc.uu.se
Sat Nov 15 10:04:00 CET 2003
On Sat, 2003-11-15 at 04:14, Lanyuan Lu wrote:
> A micelle in CO2. The only particular feature I can think about is that
> I used dummy atoms to produce the linear rigid model of CO2. Can
> this be a reason? I guess when the gromacs devided the box into 2,
> it broke some bonds. maybe that's the reason I got the error for
> SHAKE. The input file is like:
> [ moleculetype ]
> ; Name nrexcl
> CO2 3
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 CO 1 CO2 CO 1 0.6512
> 2 OO 1 CO2 OO 1 - 0.3256
> 3 OO 1 CO2 OO 1 - 0.3256
> 4 RM 1 CO2 RM 1 0.0
> 5 RM 1 CO2 RM 1 0.0
> 1 4 5 1 0.5
> 2 4 5 1 -0.0862
> 3 4 5 1 1.0862
> [ constraints ]
> 4 5 1 0.196
> 1 2 3 4 5
> 2 1 3 4 5
> 3 1 2 4 5
> I calculated the same micelle with single point CO2 model without problem.
> But for this 3-site CO2, It breaks often.
I don't see anything wrong with the topology off hand. You can make
testing a bit easier by first trying a small box with only CO2 (an odd
number of molecules!). If that crashes as well on two processors, you
may send me your input files and I'll have a look.
> Lanyuan Lu
> ----- Original Message -----
> From: "David" <spoel at xray.bmc.uu.se>
> To: <gmx-users at gromacs.org>
> Sent: Friday, November 14, 2003 2:30 PM
> Subject: Re: [gmx-users] error in a parallel job
> > On Fri, 2003-11-14 at 20:24, lulanyuan wrote:
> > > In short. For a certain system A I can calculate it using 1 processor but can not using 2. For other systems I can use any
> > > number of processors (1,2,4 etc) as I like. So what's the problem about system A?
> > > The error message I got was shake didn't converge. I din't change any condition other than number of processors.
> > > Thanks.
> > > Lanyuan
> > either your starting conformation or something peculiar about system A.
> > so what is system A?
> > > >Hello, everyone. I got a strange problem when I simulated
> > > >a system using two processors. The job is ok with one processor.
> > > >But when I try to calculate it using two, I got it broken in
> > > >the middle. In the log file I found a lot of error message saying shake was not converged in 1000 steps.
> > > >For other simulations, I got no problem for parallel jobs.
> > > >Can anyone give me a clue?
> > > >not without more information.
> > >
> > > >Thank you very much.
> > > >Lanyuan Lu
> > > ______________________________________
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> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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