[gmx-users] grompp cpp pre-processor

[David van der Spoel]

On Mon, 2005-06-06 at 19:56 -0500, Nathan Moore wrote:
> This now works on the apple serial system I have, and the results I can
> generate there make sense.  That said, I'd like to run the code on a much
> larger production parallel system.  Is the grompp command a stand-alone
> executable?  I don't have access to the shell on the parallel system and
> am worried that it will fail there (I'll have to try tomorrow).
you can run grompp on your workstation and ship the tpr files to the
other machine.
> 
> In the same vein, different approach, Can I run the command,
>      grompp -f grompp.mdp -p topol.top -c conf.gro -o villin.tpr
> one one ppc32 architecture and use the resulting villin.tpr binary (osX)
> on a different ppc32 system (linux) with mdrun_d?  Is the binary file
> platform-specific?
> 
> thanks,  this list is an enormous help!
> 
> NT Moore
> 
> 
>  > On Mon, 2005-06-06 at 15:10 -0500, Nathan Moore wrote:
> >> I've installed GROMACS on an apple laptop running os X.  I installed the
> >> files, and making was simple this time.  I notice though that when I try
> >> the demo or the benchmarks, GROMACS fails at the stage of creating an
> >> .mdp
> >> binary for use in mdrun.
> >>
> >> Specifically, when I look at the villin example from the benchmarks:
> >>
> >>
> >> 3:06pm|nmoore at winesap> ls
> >> conf.gro  grompp.mdp  mdout.mdp  topol.top
> >> 3:06pm|nmoore at winesap> grompp -f grompp.mdp -p topol.top -c conf.gro -o
> >> villin.tpr
> >>
> >> ...
> >>
> >> calling /lib/cpp...
> >> sh: line 1: /lib/cpp: No such file or directory
> >> cpp exit code: 32512
> >> Tried to execute: '/lib/cpp  -I/usr/local/gromacs/share/top  topol.top >
> >> grompp9uh5Yn'
> >> The '/lib/cpp' command is defined in the .mdp file
> >> processing topology...
> >> processing coordinates...
> >> Fatal error: number of coordinates in coordinate file (conf.gro, 9389)
> >>              does not match topology (topol.top, 0)
> >>
> >>  - - -
> >>
> >> Now I can certainly add in the location of cpp with an include flag,
> >> 3:07pm|nmoore at winesap> which cpp
> >> /usr/bin/cpp
> >>
> >> but is this the only problem (and if so, what's the proper flag?)?
> >>
> >> the error "number of coordinates in coordinate file (conf.gro, 9389)
> >> does
> >> not match topology (topol.top, 0)" makes no sense at all as toplo.top
> >> has
> >> quite a bit of information within.
> >>
> >> Any suggestions would be welcomed.  It is exciting to get the package
> >> running!
> >>
> > remove the whole line from the mdp file or change it to
> > cpp = cpp
> > (works whenever cpp is in your path). We should change the default...
> >> NT Moore
> >>
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++