Re: [AMBER] Installation of AmberTools18 in macOS Mojave

From: David Case <david.case.rutgers.edu>
Date: Thu, 28 Mar 2019 02:02:52 +0000

On Wed, Mar 27, 2019, Reza Esmaeeli wrote:

>
>Testing the gcc compiler:
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
>ld: malformed file
>/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd:4:18: error: unknown enumerated scalar
>platform: zippered
> ^~~~~~~~
> file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd'
>collect2: error: ld returned 1 exit status

This has nothing to do with Amber. The configure script is trying to
compile a simple, three-line C-program, and getting the errors that you
see above. Somehow, your compiler installation is faulty: it is
unlikely that you could compile *any* C program.

A first thing to check: what does "which gcc" return? The way you
installed homebrew may somehow be faulty.

What I do, and what we recommend, is to use the clang C/C++ compilers
provided by Apple, and to install a fortran compiler using the link
provided here: http://ambermd.org/Installation.php.

...hope this helps....dac


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Received on Wed Mar 27 2019 - 19:30:02 PDT
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