Did you use "./configure gnu"?
If yes, the issue here is that the default gcc is actually clang.
Either:
- Try again "./configure -macAcclerate clang"
or
- export CC=/path/to/the/real/GCC CXX=/path/to/the/real/G++
- ./configure gnu
Hope this help
Hai
On Wed, Nov 2, 2016 at 9:32 AM, Ruth Helena Tichauer <rhtichau.laas.fr>
wrote:
> Dear Amber users,
>
> I’ve been trying to install AmberTools and Amber 16 on my mac OS El
> Capitan (version 10.11.6) but I keep getting the following error during the
> ./configure step:
>
> Checking for updates...
> Checking for available patches online. This may take a few seconds...
>
> Available AmberTools 16 patches:
>
> No patches available
>
> Available Amber 16 patches:
>
> No patches available
>
> Compatible Python found! Using /usr/bin/python
>
> Obtaining the gnu compiler suite versions, e.g.:
> gcc -v
> The C version is 7.3.0
> The Fortran version is ../gcc-6.1.0/configure
> 6.1.0
>
> Testing the gcc compiler:
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> testp.c
> OK
>
> Testing the g++ compiler:
> g++ -fPIC -o testp testp.cpp
> OK
>
> Testing the gfortran compiler:
> gfortran -fPIC -O0 -o testp testp.f
> OK
>
> Testing mixed C/Fortran compilation:
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o
> testp.c.o testp.c
> gfortran -fPIC -O0 -c -o testp.f.o testp.f
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> testp.c.o testp.f.o -lgfortran -w
> ld: library not found for -lgfortran
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> ./configure2: line 2347: ./testp: No such file or directory
> Error: Unable to compile mixed C/Fortran code.
> Please check your compiler settings and configure flags.
> Configure failed due to the errors above!
>
> I’ve googled this error and followed the instructions in this thread:
> http://archive.ambermd.org/201405/0347.html, including delating macports
> and reinstalling it but I’m still getting the same error.
>
> The output of gcc -v is:
>
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/usr/include/c++/4.2.1
> Apple LLVM version 7.3.0 (clang-703.0.31)
> Target: x86_64-apple-darwin15.6.0
> Thread model: posix
> InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin
>
> Any suggestion on how to solve this issue will be highly appreciated.
>
> Sincerely,
>
> Ruth
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Nov 02 2016 - 07:30:02 PDT
