[gmx-users] installation trouble with mpi support

Senthil Kandasamy senthilk at engin.umich.edu
Sat Mar 30 16:49:17 CET 2002

Thanks for all your help folks. Now I have GROMACS installed on my small 
cluster and also on the University's linux cluster.
On my cluster, I had both mpich and lam installed. So I just changed the 
default mpi to lam and it worked like a charm.

On the University's machine, It was a bit trickier. I talked to the 
sys-admins and they told me that mpich was the standard and they did not 
want lam on the system because pbs was configured to run with mpich. I am 
not a computer scientist and I did not understand it completely. But I 
figured that they did not want to waste any time working on configuring pbs 
to work with both mpich and lam on the cluster. Also, they suggested that I 
install both fftw and gromacs in my home directory since I was possible the 
only user of GROMACS.

So I just installed fftw in my home directory using mpich. For this step, I 
had to set the environment variables LDFLAGS and CPPFLAGS to be  mpich's 
lib and include directories. I basically followed the how-to on fftw 
installation. This worked fine.  Then I set the appropriate LIBS and MPICC 
variables. Then, I tried to configure gromacs, but  it did not work well. 
During configuration, it complained that it did not find the fftw 
libraries. So I changed the LDFLAGS and CPPFLAGS variables to that of the 
/home/senthilk/fftw/lib and include directories. Now it complained that it 
could not  find the C compiler (presumable not able to link to the mpich 
libraries.). So I just copied all the /usr/local/mpich/lib files to 
/home/senthilk/fftw/lib directory and the /usr/local/mpich/include files to 
/home/senthilk/fftw/include directory, set the LDFLAGs and CPPFLAGS 
variables to the fftw/lib and fftw/include  directory, and it worked fine.

So there basically seems to be a problem during configuration when
1.I need to use mpich
2.  fftw is installed in a non-standard directory.
I am not sure if I did the right thing by copying the mpich files to the 
fftw directory, but it seemed to work.

  Thanks again for all your help (esp. David)

Now that installation is complete, I can start bugging the list with some 
real GROMACS questions.


More information about the gromacs.org_gmx-users mailing list