Hi,
If you comment out the cpptraj install, does the rest of Amber compile OK?
-Dan
On Thu, Apr 4, 2019 at 9:16 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> I agree, it has become one giant mess.
>
> One also need to remember that this current “workaround” with the header files (and commenting out libstdc++ ?) will break with the next major version release of Xcode (Xcode11) which will not come with the PKG installer for the deprecated header files.
>
> Meanwhile, as Virtualbox does not support APFS yet it took me a while to get a VM spun up to try different install alternatives than Homebrew. The discussed option using “binary” distributions does not work on macOS 10.14 in combination with Xcode 10.2 and it is not a solution for this particular combination of software, OS and compilers. Compilation breaks with the exakt same error:
>
>
> Tests-Mac:~ testos$ which gcc
> /usr/local/bin/gcc
> Tests-Mac:~ testos$ gcc --version
> gcc (GCC) 8.2.0
> Copyright © 2018 Free Software Foundation, Inc.
> Detta är fri programvara, se källkoden för kopieringsvillkor. Det
> finns INGEN garanti, inte ens för KÖP eller LÄMPLIGHET FÖR NÅGOT
> SPECIELLT ÄNDAMÅL.
>
> Tests-Mac:~ testos$ which g++
> /usr/local/bin/g++
> Tests-Mac:~ testos$ g++ --version
> g++ (GCC) 8.2.0
> Copyright © 2018 Free Software Foundation, Inc.
> Detta är fri programvara, se källkoden för kopieringsvillkor. Det
> finns INGEN garanti, inte ens för KÖP eller LÄMPLIGHET FÖR NÅGOT
> SPECIELLT ÄNDAMÅL.
>
> Tests-Mac:~ testos$ which gfortran
> /usr/local/bin/gfortran
> Tests-Mac:~ testos$ gfortran --version
> GNU Fortran (GCC) 8.2.0
> Copyright © 2018 Free Software Foundation, Inc.
> Detta är fri programvara, se källkoden för kopieringsvillkor. Det
> finns INGEN garanti, inte ens för KÖP eller LÄMPLIGHET FÖR NÅGOT
> SPECIELLT ÄNDAMÅL.
>
>
> Obtaining the gnu compiler suite versions, e.g.:
> gcc -v
> The C version is 8.2.0
> The Fortran version is ../gcc-8.2.0/configure
> 8.2.0
>
> Testing the gcc compiler:
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> OK
>
> Testing the g++ compiler:
> g++ -fPIC -o testp testp.cpp
> OK
>
> Testing the gfortran compiler:
> gfortran -fPIC -O0 -o testp testp.f
> OK
>
> Testing mixed C/Fortran compilation:
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
> gfortran -fPIC -O0 -c -o testp.f.o testp.f
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w
> OK
>
> Testing pointer size:
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c
> Detected 64 bit operating system.
>
> Testing flex: OK
>
> Checking NetCDF...
> Using bundled NetCDF library.
> Starting NetCDF build.
> Configuring NetCDF C interface (may be time-consuming)...
> Compiling the NetCDF C interface (may be time-consuming)...
> Configuring NetCDF Fortran interface (may be time-consuming)...
> Compiling the NetCDF Fortran interface (may be time-consuming)...
> NetCDF build succeeded.
>
> Checking for zlib: OK
>
> Checking for libbz2: OK
>
> Testing the g++ compiler with boost:
> g++ -fPIC testp.cpp -lboost_thread -lboost_system -o testp
>
> Warning: Could not link to boost. Ensure boost-thread, boost-system and boost headers are installed.
> Warning: Failed command:
> g++ -fPIC -lboost_thread -lboost_system -o testp testp.cpp
> Warning: Check boost.compile.err for error details.
> Warning: Memembed functionality in packmol_memgen not available.
>
> Configuring fftw-3.3 (may be time-consuming)...
>
> fftw-3.3 configure succeeded.
>
> Configuring XBLAS (may be time-consuming)...
>
> XBLAS configure succeeded.
>
> Configuring CPPTRAJ...complete.
>
> The configuration file, config.h, was successfully created.
>
>
>
> In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/sysctl.h:83,
> from StringRoutines.cpp:14:
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/ucred.h:94:2: fel: ”_Atomic” är inte namnet på en typ
> _Atomic u_long cr_ref; /* reference count */
> ^~~~~~~
> make[4]: *** [StringRoutines.o] Error 1
> make[3]: *** [install] Error 2
> make[2]: *** [build_cpptraj] Error 2
> make[1]: *** [serial] Error 2
> make: *** [install] Error 2
>
> As this affects both the binary gcc 8.2 distribution as well as the 8.3 and 7 that I tried from different sources, I don’t think switching to macports or any other source of binary distributions will solve the issue.
>
> Compiling gcc8 under macOS 10.14.4/Xcode 10.2 (yes I tried compiling gcc8.3 from source) breaks with the same error, so I don’t see any way of using gnu compilers to build amber18 on macOS (latest release OS and Xcode) until this gets resolved.
>
> Best regards
> // Gustaf
>
> On 3 Apr 2019, at 16:36, David A Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>> wrote:
>
> On Wed, Apr 03, 2019, Gustaf Olsson wrote:
>
> So this turned out to be more of a rant then I intended ....
>
> Before Mojave, one could use almost any gnu compiler (and almost any
> version > 4.6) and be as fine as one would be with Linux.
>
> Mojave caused lots of problems, and we were arguably slow in picking up
> on them, especially since a lot of developers (including me) had
> switched from macports/homebrew to clang.
>
> If you can be patient, we are working hard to get AmberTools19 (due out
> this month) to work with as many combinations of compilers and OSX
> variants as we can. I'll post info soon on getting release candidates for
> people to try out.
>
> [A part of the problem: just saying "mojave" or "macports" is no longer
> enough. Mojave systems may or may not have altered headers; macports
> has fixed some problems, so that one may need to get updated compilers,
> etc.]
>
> ....dac
>
>
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Received on Thu Apr 04 2019 - 07:00:03 PDT
