Re: [AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Mon, 8 Oct 2018 14:54:11 +0000

This is the same error that I am receiving using Hombrew GNU compilers, it does not make a difference if -macAccelerate is included or omitted

Best regards
// Gustaf

On 8 Oct 2018, at 15:09, Andrew Schaub <aschaub.uci.edu<mailto:aschaub.uci.edu>> wrote:

Ok, I was able to get the serial version working on MacOS Mojave. It failed
when I tried to do mpi. It might have something to do with the /usr/include
I have AMBER on my workstation and other laptop. I'm just playing around
with trying to get it work on a new laptop.

$ ./configure -mpi -macAccelerate gnu
$ make install

It failed during the parmed installation:

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>
        ^~~~~~~~
1 warning and 1 error generated.
error: command 'clang' failed with exit status 1
make[2]: *** [parmed] Error 1
make[1]: *** [parallel] Error 2
make: *** [install] Error 2

Best Regards,

Andrew

On Sun, Oct 7, 2018 at 8:02 PM Andrew Schaub <aschaub.uci.edu<mailto:aschaub.uci.edu>> wrote:

Good Evening,

I just thought I would mention this on the listserv in case anyone else
has similar issues. When trying to install on Mojave, I was getting the
following error message:

ld: library not found for -lmc

It turns out it the compiler was looking for the /usr/include folder
which no longer exists with the most recent version of XCode Developer
Tools and Mojave. In order to get the installation to work, just install
the include folder from the following link instructions:
https://developer.apple.com/documentation/xcode_release_notes/xcode_10_release_notes

There is a .pkg file (
https://developer.apple.com/documentation/xcode_release_notes/xcode_10_release_notes)
which will install the include folder into the /usr/ folder like previous
versions of MacOS and XCode.

Afterwards I was able to get AMBER to work, using gcc5
./configure -macAccelerate gnu

Best Regards,

Andrew



--
Andrew Schaub
949-877-9380<tel:949-877-9380> (cell)
aschaub.uci.edu<mailto:aschaub@uci.edu>  <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
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Received on Mon Oct 08 2018 - 08:00:02 PDT
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