After being able to build with GCC, I tried to add OpenMP support:
[root@login002 freesurfer-dev-20120106]# ./configure --enable-openmp -disable- all-apps --with-mni-dir=/export/minc-1.4/ --with-vxl-dir=/export/vxl-1.13.0 --prefix=/scratch/mtobias/freesurfer-dev-gcc-openmp ... (Note: Mac OS X doesn't use crypt) checking for nccreate in -lnetcdf... no configure: error: FATAL: netcdf lib not found. Set LDFLAGS or --with-mni-dir.
I don't believe there's a problem with the library:
[root@login002 freesurfer-dev-20120106]# ls /export/minc-1.4/lib libEBTKS.a libminc.a libnetcdf.a libvolume_io.la perl5 libEBTKS.la libminc.la libvolume_io.a mni_autoreg
[root@login002 freesurfer-dev-20120106]# nm /export/minc-1.4/lib/libnetcdf.a | grep nccreate 000000000000028d T nccreate
and if I eliminate the "--enable-openmp" flag it configures fine.
Depending on how well FreeSurfer is parallelized, OpenMP could be a great benefit for us here, but if it doesn't work too well, or isn't really supported, I can move on to try other things.
Cheers, Malcolm