Re: [AMBER] Amber Install on Mojave

From: David A Case <>
Date: Fri, 12 Oct 2018 08:13:45 -0400

On Mon, Oct 08, 2018, Andrew Schaub wrote:

> MacOS 10.14, XCode 10
> ./configure -macAccelerate -mpi gnu
> make install
> building 'parmed.amber._rdparm' extension
> creating build/temp.macosx-10.7-x86_64-2.7
> creating build/temp.macosx-10.7-x86_64-2.7/src
> clang -fno-strict-aliasing -I/opt/amber18/miniconda/include -arch x86_64
> -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
> -I/opt/amber18/AmberTools/src/parmed/src
> -I/opt/amber18/miniconda/include/python2.7 -c src/_rdparm.cpp -o
> build/temp.macosx-10.7-x86_64-2.7/src/_rdparm.o
> warning: include path for stdlibc++ headers not found; pass '-std=libc++'
> on the command line to use the libc++ standard library instead
> [-Wstdlibcxx-not-found]
> In file included from src/_rdparm.cpp:17:
> /opt/amber18/AmberTools/src/parmed/src/readparm.h:5:10: fatal error:
> 'locale' file not found
> #include <locale>

It's hard to see why the serial build worked (I think that is what you
reported) yet the above should fail...

As a workaround, try this: edit AMBERHOME/AmberTools/src/Makefile,
finding the line:

python_parallel:: parmed mmpbsa_py_parallel

Remove "parmed" from the above line, which will skip the building of
parmed when mpi is set at configure time. Let's see what else is


p.s. I'll try to install Mojave on some machine this weekend. But I
suspect that more c++ knowledge than I have may be needed here. And a
fix may involve the innards of miniconda, since it is using clang to
build parmed, even though you asked for gnu compilers at the configure

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Received on Fri Oct 12 2018 - 05:30:02 PDT
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