Hi everyone,
sorry for restating what may be obvious for many on the list, but at least
I learn something new anytime I build Amber ;-) I think I figured it out
now (thanks to Dave). This is what I did to compile parallel Amber11 on my
Fedora11 Pentium 4 machine with the Intel compilers:
get OpenMPI-1.3.3 from the web
Configure it while specifying:
./configure --prefix=[...] CC=icc CXX=icpc F77=ifort FC=ifort
it's necessary to specify the compilers explicitly because most systems
will have gcc and gfortran, which are then made the defaults.
Make sure my PATH contains only the newly compiled mpirun&mpicc. Then,
make parallel works (including netcdf and parallel ptraj, which failed
before).
When I reconfigure the lam-MPI that comes with amber to use the intel
compilers, I still cant get netcdf parallel configured, with the same
error as before:
> configure:5490: error: mpi implementation does not support MPI-IO
but configuring amber with -nobintraj and skipping the parallel ptraj step
gives me a running version of sander.MPI using LAM.
So I guess the conclusion is that you cant have LAM-MPI if you want to
have netcdf and parallel ptraj, right?
Thanks to all repliers,
Regards,
Thomas
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu Sep 17 2009 - 05:00:02 PDT
