Re: [AMBER] New compile-issue macOS, CPPTRAJ

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Thu, 4 Apr 2019 13:54:53 +0000

Using only the GNU compilers?

I’ll put it on the agenda for tomorrow.

// Gustaf

> On 4 Apr 2019, at 15:30, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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 - 07:00:04 PDT
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