[gmx-users] grompp cpp pre-processor
nmoore at physics.umn.edu
Tue Jun 7 02:56:43 CEST 2005
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
thanks, this list is an enormous help!
> 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
>> 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
>> 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 >
>> 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
>> 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)
>> not match topology (topol.top, 0)" makes no sense at all as toplo.top
>> quite a bit of information within.
>> Any suggestions would be welcomed. It is exciting to get the package
> 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 van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
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