Re: [AMBER] AmberTools20 comilation on macOS

From: David A Case <>
Date: Tue, 5 May 2020 08:58:58 -0400

On Tue, May 05, 2020, Gustaf Olsson wrote:

> "boost::re_detail_107200::raw_storage::insert(unsigned long, unsigned long)", referenced from:
> boost::re_detail_107200::basic_regex_parser<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::parse_repeat(unsigned long, unsigned long) in metatwist.cpp.o
> ....
> ....
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see invocation)
> make[2]: *** [AmberTools/src/moft/metatwist] Error 1
> make[1]: *** [AmberTools/src/moft/CMakeFiles/metatwist.dir/all] Error 2
> make: *** [all] Error 2
>This is using the built in (xcode) compilers.

Boy, I'm not real sure how to reproduce this. I'm guessing you may(?)
have boost installed somewhere on your machine (via homebrew? conda?).
Is that a possibility?

Try adding -DFORCE_EXTERNAL_LIBS=boost, if you indeed have another boost

Does your build report provide any clues? (This is at the bottom of the
cmake.log file). Posting that might help us figure out what is going

To skip metatwist/moft, set -DDISABLE_TOOLS=moft in your run_cmake file,
and see if other problems are arising.

>Applications/ is not present by default. Hence this test "fails"
>and sets cmake=cmake. Using a package manager (for me homebrew) I have
>cmake in /usr/local/bin/.

I doubt that this would lead to the problems you report. I've used
cmake from both kitware and macports, without any problems. What
compiler was used to build cmake should be irrelevant, as far as I can
>During the configuration stage, I also notice that the script does
>not find open-mpi or mkl libraries, even if these are installed. I
>assume there might be a need for some "hands on" convincing regarding

It's worth your while to visit the common options page:

and to read the section in the manual about MKL and MPI (if you have not
already done so.) In brief, MKL is "opt-in": you have to ask for it.
The MPI stack that is used is the one in your PATH: if that is openmpi,
then it should be used. But in my experience, you have to compile your
own MPI to use clang + gfortran.

>On another note, is there any way to define which compilers to use on the
>CLI (like before with configure gnu)?

If you have the gnu compilers in your path, just set -DCOMPILER=GNU,
(instead of CLANG), and you'll get the gnu compilers. A homebrew or
macports setup ought to work.

...good luck....dac

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Received on Tue May 05 2020 - 06:00:02 PDT
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