Hi,
Can you post '/amber18/AmberTools/src/cpptraj_config.log' in it's
entirety? Thanks,
-Dan
On Tue, Oct 9, 2018 at 10:35 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> Hi Dan, nice to hear from you agan.
>
> So, this is indeed good new since it would allow an installation that is no longer possible with homebrew gnu package.
>
> The issue I can’t solve is that since the configuration of CPPTRAJ fails
>
> Configuring CPPTRAJ...
> CPPTRAJ configure failed. Check '/amber18/AmberTools/src/cpptraj_config.log' for details.
> Configure failed due to the errors above!
>
> I cannot execute “make install” as the configuration did not complete:
>
> Makefile:4: config.h: No such file or directory
> make: *** No rule to make target `config.h'. Stop.
>
> I am assuming I can “force” or “skip” something here though I’n not really seeing what or how.
>
> Best regards
> // Gustaf
>
> > On 9 Oct 2018, at 16:17, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > 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
> >>>
> >>>
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> >>
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Received on Tue Oct 09 2018 - 09:00:02 PDT
