[gmx-users] grompp cpp pre-processor

[Nathan Moore]

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).

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
>>
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> --
> 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
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