*facepalm*
One more reason not to try to solve problems in a rush…
So as for now configuration still breaks if the files
> $AMBERHOME/AmberTools/src/configure2
> $AMBERHOME/AmberTools/src/pytraj/setup.py
are not modified replacing libstdc++ with libc++ or commenting out affected lines.
Configuring CPPTRAJ...
CPPTRAJ configure failed. Check ‘/amber18/AmberTools/src/cpptraj_config.log' for details.
Configure failed due to the errors above!
Testing C++11 support: Not present
Error: Could not link properly with clang++ on OSX
However, making these changes and remembering the
> export MACOSX_DEPLOYMENT_TARGET=10.14
Compilation using clang works.
Trying the -mpi compilation also works however when configuring -openmp I get an error complaining about open-mpi not being compatible with clang (?)
Best regards
// Gustaf
> On 18 Apr 2019, at 15:47, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> Hi
>
> You can try
>
> export MACOSX_DEPLOYMENT_TARGET=10.14
>
> and “make install” again.
>
> Hai
>
> On Thu, Apr 18, 2019 at 4:20 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
>> So, today I came to the office just to find that my laptop had
>> autoupdated, amongst other things, XCode which is now Version 10.2.1
>> (10E1001).
>>
>> Having a moment of honest panic I tried to recompile the AmberTools18
>> package and yes, once again I cannot compile… This is not using the gnu gcc
>> (which still, however, does not work and fails with the “_Atomic” error).
>> This issue is still persistent and has not been fixed by the developers or
>> by apple and diskussions are seemingly ongoing on how to handle this
>> problem. I did exactly what worked on the last version and what is outlined
>> in the latest confirmed install procedure on the website though it fails
>> with the same parmed error as last time.
>>
>> …
>> …
>> copying parmed/modeller/data/standard_residues.lib ->
>> build/lib.macosx-10.7-x86_64-2.7/parmed/modeller/data
>> UPDATING build/lib.macosx-10.7-x86_64-2.7/parmed/_version.py
>> set build/lib.macosx-10.7-x86_64-2.7/parmed/_version.py to
>> '3.0.0+57.g74a84d30'
>> running build_ext
>> building 'parmed.amber._rdparm' extension
>> creating build/temp.macosx-10.7-x86_64-2.7
>> creating build/temp.macosx-10.7-x86_64-2.7/src
>> clang -fno-strict-aliasing
>> -I/Users/guolaa/SOFTWARE/amber18/miniconda/include -arch x86_64 -DNDEBUG -g
>> -fwrapv -O3 -Wall -Wstrict-prototypes
>> -I/Users/guolaa/SOFTWARE/amber18/AmberTools/src/parmed/src
>> -I/Users/guolaa/SOFTWARE/amber18/miniconda/include/python2.7 -c
>> src/_rdparm.cpp -o build/temp.macosx-10.7-x86_64-2.7/src/_rdparm.o
>> warning: include path for stdlibc++ headers not found; pass
>> '-stdlib=libc++' on the command line to use the libc++ standard library
>> instead [-Wstdlibcxx-not-found]
>> In file included from src/_rdparm.cpp:17:
>> /Users/guolaa/SOFTWARE/amber18/AmberTools/src/parmed/src/readparm.h:5:10:
>> fatal error: 'locale' file not found
>> #include <locale>
>> ^~~~~~~~
>> 1 warning and 1 error generated.
>> error: command 'clang' failed with exit status 1
>> make[2]: *** [parmed] Error 1
>> make[1]: *** [serial] Error 2
>> make: *** [install] Error 2
>>
>> I have commented out the libstdc++ lines as described and done a
>> search/replace (:%s/libstdc++/libc++/g) to make sure I did not miss a new
>> line or something else however it still does not work and fails with the
>> same error. These are the files modified:
>> $AMBERHOME/AmberTools/src/configure2
>> $AMBERHOME/AmberTools/src/pytraj/setup.py
>>
>> Are there any more files referencing the now deprecated c++ stuff from
>> Xcode that I am unaware of?
>>
>> (( Maybe it’s just time to give up and dual-boot as it at least seems that
>> Apple is hellbent on breaking cross platform compatibility ))
>>
>> Best regards
>> // Gustaf
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Sun Apr 21 2019 - 04:00:02 PDT
