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
>
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Received on Wed Oct 10 2018 - 07:00:02 PDT
