Hi,
Apple is notorious for breaking development environments with OS
upgrades, so this is unfortunate but unsurprising. We've had to jump
through many hoops just to keep Amber compiling properly on OSX. I'm
not sure which if any devs currently have Mojave (I certainly don't),
so I don't really have a timeline for when this might get fixed.
However, regarding the 'C++11 not present' issue - this isn't really
an error, more a warning to let you know that the compiler doesn't
seem to support the C++11 stuff that the PME library (helPME) needs.
If you don't need PME support in cpptraj you can ignore this since no
other components of cpptraj care about it.
-Dan
On Tue, Oct 9, 2018 at 1:53 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> So just a reflection, since I have updated my OS and Xcode installation, is it not strange that I seem to have downgraded my c++ compiler?
>
> I used the exact same installation procedure before upgrading my OS without running into the "Testing C++11 support: Not present” CPPTRAJ error, so this used to work. Wonder why it stoped working,
>
> Best regards
> // Gustaf
>
>
> > On 8 Oct 2018, at 10:04, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> >
> > 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:
> > 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
> >
> > 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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Received on Tue Oct 09 2018 - 07:30:02 PDT
