[gmx-users] continuation

[Berk Hess]

If you need a fix now, it is one line in src/gmxlib/checkpoint.c:
-                       outputfiles[i].offset = ( ((off_t) offset_high) << 32 ) | ( (off_t) offset_low );
+                       outputfiles[i].offset = ( ((off_t) offset_high) << 32 ) | ( (off_t) offset_low & mask );

Berk

> Date: Mon, 31 Aug 2009 15:39:05 +0200
> From: alexander.herz at mytum.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] continuation
> 
> Hi,
> 
> yes, the trr is 7GB.
> 
> Alex
> 
> Berk Hess schrieb:
> > Hi,
> >
> > -append yes is incorrect, it should be -append without the yes.
> > In this case this error has no effect though.
> >
> > Is your trr file larger than 2 GB?
> > We have fixed a bug with this in the upcoming 4.0.6 release.
> >
> > Berk
> >
> > > Date: Fri, 28 Aug 2009 16:48:07 +0200
> > > From: alexander.herz at mytum.de
> > > To: gmx-users at gromacs.org
> > > Subject: [gmx-users] continuation
> > >
> > > Hi,
> > >
> > > I'm trying to continue a sim using:
> > >
> > > old cmd line + -cpi state.cpt -append yes
> > >
> > > where old cmd line =
> > > mpirun -np 1 $GROMACS_T37/mdrun -s shear -c shear_final -g shear_final
> > > -o shear
> > >
> > > All files exist.
> > >
> > > and I get:
> > >
> > > -------------------------------------------------------
> > > Program mdrun, VERSION 4.0.5
> > > Source code file: checkpoint.c, line: 1248
> > >
> > > Fatal error:
> > > Truncation of file shear.trr failed.
> > > -------------------------------------------------------
> > >
> > > What's the problem??
> > >
> > > Thx,
> > > Alex
> > > _______________________________________________
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