[gmx-users] problem with mpi configuration.
Mark.Abraham at anu.edu.au
Thu Mar 13 13:51:47 CET 2008
Dr. Niharendu Choudhury wrote:
> Dear Pohl,
> I think your prefix directory /usr/local/gromacs332 is not accesible for
> writting. Try to creat new directories with other names and use those in
First, they need to fix their typo in their configure command line, as
mentioned by another poster. Otherwise, it isn't known that the failure
to write these files is caused by permission issues, rather than their
> Have you setenv for the include and lib of the fftw files?
> (For instance, assume we have installed FFTW with --prefix=/home/joe/fftw.
> If your shell is tcsh, you set
> setenv CPPFLAGS -I/home/joe/fftw/include
> setenv LDFLAGS -L/home/joe/fftw/lib
> or, if you are using a bash shell:
> export CPPFLAGS=-I/home/joe/fftw/include
> export LDFLAGS=-L/home/joe/fftw/lib )
> If not do that.
This works, but it's superior to leave the environment alone and instead
to use "./configure CPPFLAGS=-I/home/joe/fftw/include
LDFLAGS=-L/home/joe/fftw/lib". Not only do you avoid having to get it
right for each shell, but you don't pollute your environment for this
shell (small point), and (more importantly) in config.log you will have
a record of the command line for any subsequent time you need to run
configure. When someone has to come back in 6 months to configure an MPI
or double-precision version, the record of what was done last time saves
on repeated detective work.
If you need multiple -I or -L flags, then enclosing them in quotes,
separated by spaces, works, i.e. "./configure LDFLAGS='-L/some/lib
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