Re: [AMBER] Amber Installation Problem on Mac: me too

From: Mooers, Blaine H.M. (HSC) <"Mooers,>
Date: Fri, 4 Oct 2019 22:29:15 +0000

I use Mac OS 10.14, too.
I had failed to compile AMBER18 two weeks ago with macports python2.7.
I succeeded by using the miniconda python. I think miniconda installed clang in the environment that I used.

A week ago I became aware of the missing MacOSX10.14.sdk file while reinstalling numpy.
I was prompted by DAC's past to try installing amber18 with macports python3.7.
It worked in spite of an error during the run of ./configure.

 ./configure -macAccelerate --with-python=/opt/local/bin/python3.7 clang

Error: Boost compile failed.
       Check /Users/blaine/software/amber18/src/boost_config.log
       memembed and moft will not be built

The "make install" and "make test" seemed to go well:

Finished serial test suite for Amber 18 at Fri Oct 4 13:51:44 CDT 2019.

     162 file comparisons passed
       0 file comparisons failed ( 0 ignored)
       0 tests experienced errors
Test log file saved as /Users/blaine/software/amber18/logs/test_amber_serial/2019-10-04_13-47-55.log
No test diffs to save!

Summary of AmberTools serial tests:

    2418 file comparisons passed
       3 file comparisons failed ( 2 ignored)
       9 tests experienced errors
Test log file saved as /Users/blaine/software/amber18/logs/test_at_serial/2019-10-04_11-46-09.log
Test diffs file saved as /Users/blaine/software/amber18/logs/test_at_serial/2019-10-04_11-46-09.diff

The problem may come from Mac clang using libc++ where it previously used libstdc++.

Best regards,


Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

From: David A Case []
Sent: Friday, October 04, 2019 11:17 AM
To: AMBER Mailing List
Subject: [EXTERNAL] Re: [AMBER] Amber Installation Problem on Mac: update

On Fri, Oct 04, 2019, David Case wrote:
>One part of the problem is that gcc from macports seems to be looking
>for an include path that was removed from XCode11. You could try this:
>cd /Applications/
>If there is not a soft link from MacOSX10.14.sdk -> MacOSX.sdk, you can
>create one;

I take this back: creating such a soft link solves some problems but not

My best guess now: gcc from macports is expecting to find the
MacOSX10.14.sdk to get its header files. But Xcode11 is only providing
a MacOSX10.15.sdk. It looks to me like Xcode11 is really designed to go
with OSX10.15, even though Apple pushed out the Xcode upgrade before
announcing any public availability for Catalina (aka OSX10.15).

Even after Catalina is released, we will have to wait for Macports (or
HomeBrew) to upgrade their releases, so that the compilers will look for
the headers Apple is now providing.

For me, for Amber:

1. Xcode11 with OSX10.14 seems fine if I use clang.

2. Xcode10.3 with OSX10.4 and macports gcc8 seems fine.

("seems fine" may be misleading, since there may be glitches I am


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Received on Fri Oct 04 2019 - 15:30:02 PDT
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