> > export CC=/opt/openmpi.gcc/bin/mpicc > > export CPP=/opt/openmpi.gcc/bin/mpicxx > > ./configure --with-ncbi=/home/share/src/ncbi --prefix=/opt/local > --with-mpi=/opt/openmpi.gcc I think you should do: export CC=mpicc export CXX=mpicxx and, in my Makefile, I noticed that variable CPP was set to 'mpicc -E',like this: CPP= mpicc -E XU Zhao