Hi,
you could try a make clean, and then configure again with --enable-threads.
It seems for some reason you only build the serial mdrun version.
Carsten
On Mar 24, 2011, at 1:51 PM, Adam Herbst wrote:
> Dear GROMACS users,
> I successfully installed GROMACS 4.5.1 several months ago on a Mac Pro with
> 12 CPUs, and the "mdrun" command (not "mpirun mdrun_mpi") allows parallel
> simulations--it automatically uses multiple processors, while the number of
> processors can be manually specified as N with the flag "mdrun -nt N". I
> understand that this is a feature of GROMACS 4 and later. Now I am making
> minor changes to the mdrun source code, and I want to recompile such that the
> parallel version of mdrun is updated with my changes. But when I run:
>
> make mdrun (or just make)
> make install-mdrun (or just make install)
>
> from the top-level source directory, the only executables that are updated
> are the ones with the _mpi suffix, such as mdrun_mpi. The version of mdrun
> in src/kernel/ is updated, but this one has no -nt flag and cannot seem to
> run on multiple processors. And when I run
>
> mpirun -np N mdrun_mpi [options],
>
> the same simulation is started separately on each processor, leading to a
> crash. If I use
>
> mpirun -np 1 -cpus-per-proc N mdrun_mpi [options],
>
> I get an error message that this is not supported on my computer ("An attempt
> to set processor affinity has failed").
>
> I can't configure the input .tpr file for parallel because grompp doesn't
> have the -np flag in GROMACS 4.
>
> How can I update the parallel-capable "mdrun" executable with my changes?
> Thanks in advance,
>
> Adam
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
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