[AMBER] Testing C++11 support: Not present

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Mon, 8 Oct 2018 08:04:12 +0000

Good morning

In an effort to cause myself the maximum amount of headache I decided to update my Apple machine to Mojave OS X version 10.14 realising that this would likely break several things and to the shock of no-one, it did. Using Homebrew and trying to use the parameters set by “brew” i am compiling using the Mac clang compiler and the “brew” gfortran compiler. This has worked well for a good long while now.

Trying to compile I got an error regarding files missing and some other things, though I found this email in my inbox posted to the list by Andrew Schaub:

        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:

        There is a .pkg file (
        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,


What this means is running:

        open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

Since the PKG is already downloaded. However, this feature will go away and needs a modification on the developer side. This did, however, not solve the compilation issues using clang! I received the following logged message from CPPTRAJ during configuration:

        Testing C++11 support: Not present

So this did not work using the "./configure -macAccelerate clang” configuration. I then forced a switch to using the Homebrew gcc-8 version and configuring using "./configure -macAccelerate gnu”, configuration went fine but compilation broke with error:

        ld: symbol(s) not found for architecture x86_64
        collect2: error: ld returned 1 exit status
        make[2]: *** [/Users/guolaa/SOFTWARE/amber18//bin/sander] Error 1
        make[1]: *** [serial] Error 2
        make: *** [install] Error 2

So as it is looking right now, there is no easy way to compile amber on OS X Mojave using the Homebrew package manager using either GCC or CLANG. I’ll keep trying to get a version to compile or just wait until an update of CPPTRAJ fixes the compiler issue.

Best regards
// Gustaf

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Received on Mon Oct 08 2018 - 01:30:02 PDT
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