.John
(add to Jason's options).
pytraj does not support clang compiler in OSX (yet), so you need to use
real GNU compiler if you want to use pytraj.
Force your mac to use real GNU compiler by export CC and CXX environment.
Here is my case, (install gcc5.3 by homebrew.)
*export CC=/usr/local/bin/gcc-5*
*export CXX=/usr/local/bin/g++-5*
then
*cd $AMBERHOME./configure gnu*
*# make sure you can install pytrajcd AmberTools/src/*
*make pytraj*
If things go well, go back to your normal AMBER install. (cd $AMBERHOME;
make install)
If above does not work, try to install miniconda (Jason's 2nd option), then
repeart above step.
cheers
Hai
On Tue, May 10, 2016 at 11:57 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, May 10, 2016 at 10:48 AM, Adams, John E. <AdamsJE.missouri.edu>
> wrote:
>
> > 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:
>
> 1
> . 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.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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>
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Received on Tue May 10 2016 - 10:00:03 PDT
