[gmx-users] problem with mpi configuration.

Mark Abraham 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 
> prefix.

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 
malformed filename.

> 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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