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
>>>>
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>>
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Received on Tue Oct 09 2018 - 23:30:02 PDT
