StackExchange referenced twitter about libstdc++ and it's removal from
Xcode 10.0. The suggested work around was to install Xcode 9.4, and simply
copy the folders over:
cp
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk/usr/lib/libstdc++.*
/Applications/Xcode-beta.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk/usr/lib/
cp
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/usr/lib/libstdc++.*
/Applications/Xcode-beta.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/usr/lib/
"PSA: libstdc++ is gone from the iOS 12.0 SDK (it is present in the runtime
for binary compatibility). It's days are numbered on macOS as well. Migrate
over to libc++ if you haven't already. #WWDC2018 #cplusplus" @jeremyhu
https://stackoverflow.com/questions/50694822/xcode-10-ios-12-does-not-contain-libstdc6-0-9
https://twitter.com/jeremyhu/status/1003882060556062720
Andrew
On Wed, Oct 10, 2018 at 9:53 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> OK - I can try to assist with debugging but you'll have to bear with me.
>
> Create a file called testprogram.cpp with the following contents:
>
> #include <cstdio>
> #include <string>
> int main() {
> std::string temp("Testing");
> printf("%s\n", temp.c_str());
> return 0;
> }
>
> Then try to compile it like so:
>
> clang++ -O3 -o testp testprogram.cpp
>
> And report any output/error messages. If it works and you can execute
> the resulting program, try compiling again and add the following
> flags:
>
> 1) -std=c++11
> 2) -stdlib=libstdc++
>
> And let me know the results of that as well.
>
> Thanks,
>
> -Dan
> On Wed, Oct 10, 2018 at 2:01 AM Gustaf Olsson <gustaf.olsson.lnu.se>
> wrote:
> >
> > Sure thing an thank you for helping out
> >
> > fftw3 enabled.
> > fftw3 specified: /Users/guolaa/SOFTWARE/amber18
> > sanderlib specified: /Users/guolaa/SOFTWARE/amber18
> > netcdf specified: /Users/guolaa/SOFTWARE/amber18
> > arpack specified: /Users/guolaa/SOFTWARE/amber18
> > Testing C++11 support: Not present
> > Error: Could not link properly with clang++ on OSX
> >
> > I’m not sure that CPPTRAJ is what is stopping a successful compilation
> though it seems like it is what is breaking the configuration. The reported
> error is the only error received so far during configuration with clang.
> >
> > Best regards
> > // Gustaf
> >
> > > On 9 Oct 2018, at 17:45, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> > >
> > > 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
> > >>>>>
> > >>>>>
> > >>>>> _______________________________________________
> > >>>>> AMBER mailing list
> > >>>>> AMBER.ambermd.org
> > >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>
> > >>>> _______________________________________________
> > >>>> AMBER mailing list
> > >>>> AMBER.ambermd.org
> > >>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Andrew Schaub
949-877-9380 (cell)
aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
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Received on Thu Oct 11 2018 - 13:30:02 PDT
