Re: [AMBER] Installing AmberTools16 on OSX 10.11

From: Jason Swails <>
Date: Tue, 10 May 2016 11:57:31 -0400

On Tue, May 10, 2016 at 10:48 AM, Adams, John E. <>

> Although the configure process associated with installing AmberTools16 on
> my Mac (OS X 10.11) appears to proceed normally, “make install” eventually
> terminates with the following message.
> running build_ext
> building 'pytraj.c_dict' extension
> creating build/temp.macosx-10.11-intel-2.7
> creating build/temp.macosx-10.11-intel-2.7/pytraj
> gcc -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g
> -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX
> -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv
> -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe
> -I/Users/JEAdams/amber16/AmberTools/src/cpptraj/src
> -I/Users/JEAdams/amber16/AmberTools/src/pytraj/pytraj/
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
> -c pytraj/c_dict.cpp -o build/temp.macosx-10.11-intel-2.7/pytraj/c_dict.o
> -O0 -ggdb
> gcc: error: unrecognized command line option '-Wshorten-64-to-32'
> error: command 'gcc' failed with exit status 1
> make[2]: *** [pytraj] Error 1
> make[1]: *** [serial] Error 2
> make: *** [install] Error 2
> My compiler is gcc4.9, and I have python2.7. (The output from the
> configuration step indicated no issues.) A quick search of the internet
> indicates that ‘-Wshorten-64-to-32’ is not recognized by gcc. Any
> suggestions for working around the above error?

​There are a couple simple solutions:

. Re-run configure specifying the "clang" compiler instead of "gnu".
2. Run the $AMBERHOME/AmberTools/src/configure_python script to install a
compatible Python inside $AMBERHOME
3. Comment-out the pytraj installation in
$AMBERHOME/AmberTools/src/Makefile (obviously if you want pytraj or need to
use it, this option won't work).

As an aside, to help us figure out how to fix this, can you give us the
configure command you used in addition to the config.h file that was
generated? If you are using the standard system Python, step 1 is probably
the easiest.


Jason M. Swails
AMBER mailing list
Received on Tue May 10 2016 - 09:00:04 PDT
Custom Search