Re: [AMBER] Error installing amber macOS M1

From: Rodrigo da Silva Bitzer <bitzer.iq.ufrj.br>
Date: Tue, 5 Oct 2021 18:56:19 +0000

Hi David,

I gave up trying to use homebrew on M1 to build amber.
Now, I am using cmake and gfortran installed from their repositories.
However, I have new errors at this moment:

[ 26%] Linking Fortran executable sander.LES
Undefined symbols for architecture arm64:
  "___builtin___clear_cache", referenced from:
      ___rism3d_closure_c_MOD_ljcorrection_int_ionic in librism.a(rism3d_closure_c.F90.o)
ld: symbol(s) not found for architecture arm64
collect2: error: ld returned 1 exit status
make[2]: *** [AmberTools/src/sander/sander.LES] Error 1
make[1]: *** [AmberTools/src/sander/CMakeFiles/sander.LES.dir/all] Error 2
make: *** [all] Error 2

Can you help me?

I have applied the required updates (no error using ./update_amber --update).

--
Rodrigo S. Bitzer
Professor Adjunto A (Assistant Professor)
Molecular Modeling, Computational Catalysis and Supramolecular Chemistry
Departamento de Físico-Química, Instituto de Química
Universidade Federal do Rio de Janeiro, Brazil
bitzer.iq.ufrj.br; rodrigobitzer.gmail.com
https://www.iq.ufrj.br/
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Friday, October 1, 2021 9:13 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Error installing amber macOS M1
On Thu, Sep 30, 2021, Rodrigo da Silva Bitzer wrote:
>
>Using /usr/bin/patch, I could run make install until the following error:
>
>[ 96%] Linking CXX executable metatwist
>Undefined symbols for architecture arm64:
>  "boost::iostreams::detail::bzip2_base::end(bool, std::nothrow_t)", referenced from:
>      boost::iostreams::symmetric_filter<boost::iostreams::detail::bzip2_decompressor_impl<std::__1::allocator<char> >, std::__1::allocator<char> >::symmetric_filter<bool>(long, bool const&) in metatwist.cpp.o
I'm guessing that you may be the first person to try to use homebrew on M1
to build Amber.  Try adding -DFORCE_INTERNAL_LIBS="boost" to the options
in your run_cmake script.  This should compile boost locally, and not rely
on the installed library.
....dac
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Received on Tue Oct 05 2021 - 12:00:02 PDT