[gmx-users] installation trouble with mpi support
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