osx stuff for amber
Opened this issue · 2 comments
hainm commented
- donwload and install gfortran for osx: https://gcc.gnu.org/wiki/GFortranBinaries#MacOS
- cd $AMBERHOME
- export CXX='clang++ -stdlib=libstdc++'
- ./configure -macAccelerate clang
- cd $AMBERHOME/AmberTools/src
- make pytraj
hainm commented
can import pytraj with miniconda now. However, got
In [15]: pt.rmsd(traj)
python(98474,0x7fff7a73c000) malloc: ***
error for object 0x1045e6f40: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6hainm commented
the issue here is that
pytraj is linked to /usr/lib/libstdc++.6.dylib while libcpptraj is linked to /usr/local/gfortran/lib/libstdc++.6.dylib
This only happens in amber. For stand alone cpptraj version, no gfortran is used, so cpptraj is linked to
/usr/lib/libstdc++.6.dylib