There was a similar problem for a user that was compiling AFNI last year from source code. He resolved the problem by updating gcc.
[
afni.nimh.nih.gov]
It looks like the problem comes about with 3dAllineate with its OMP library calls. Would you report the version information with
afni -ver
and just to be sure this 3dAllineate is in the same directory as the afni binary.
which 3dAllineate
which afni
I would expect that 3dAllineate would fail immediately with just "3dAllineate -help". You might try one of the other AFNI binaries (like macosx_10.5_Intel_64icc).