Before removing the symlinks:
(Note that HomeBrew installs the GNU everything at /usr/local/Cellar/gcc/8.3.0/, so I modified the symlink commands accordingly.)
which gcc:
/usr/local/bin/gcc
(Note that HomeBrew installs the GNU at /usr/local/Cellar/gcc/8.3.0/, so I modified the symlink commands)
gcc --version:
gcc (Homebrew GCC 8.3.0) 8.3.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
which clang:
/usr/bin/clang
clang --version:
Apple LLVM version 9.1.0 (clang-902.0.39.1)
Target: x86_64-apple-darwin18.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
which gfortran:
/usr/local/bin/gfortran
gfortran --version:
GNU Fortran (GCC) 8.2.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
after removing the symlinks I get the same output for clang and gfortran but the following for gcc:
which gcc:
/usr/bin/gcc
(Note that HomeBrew installs the GNU at /usr/local/Cellar/gcc/8.3.0/, so I modified the symlink commands)
gcc --version:
Apple LLVM version 9.1.0 (clang-902.0.39.1)
Target: x86_64-apple-darwin18.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
Thank you very much. I’m not actually in a lot of hurry but I’ll keep watching the mailing list and the instruction post for updates.
Thanks again,
Reza
> On Mar 28, 2019, at 4:02 PM, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> Well, I don’t think updating will solve anything as it has only broken things for me in the past.
>
> What is the output of commands:
>
> which gcc
> which clan
> which gfortran
>
> gcc --version
> clang --version
> gfortran --version
>
> I am quite busy today so tomorrow afternoon I will be “more available”. If it does not work out, do contact me privately and we can try to identify the cause of the issue.
>
> Best regards
> // Gustaf
>
> On 28 Mar 2019, at 07:59, Reza Esmaeeli <goldeagle.93.gmail.com <mailto:goldeagle.93.gmail.com><mailto:goldeagle.93.gmail.com <mailto:goldeagle.93.gmail.com>>> wrote:
>
> Xcode 9.3 (9E145) and macOS 10.14.4.
> I installed CLT and the SDK headers as you instructed. Also gfortran 8.2 from GitHub <https://github.com/fxcoudert/gfortran-for-macOS/releases <https://github.com/fxcoudert/gfortran-for-macOS/releases>>.
>
> I removed the symlinks following David’s email and tried compiling with clang but I get two warnings and a similar error but for gfortran:
>
> Testing the clang compiler:
> clang -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> ld: warning: URGENT: building for OSX, but linking against dylib (/usr/lib/libSystem.dylib) built for (unknown). Note: This will be an error in the future.
> OK
>
> Testing the clang++ compiler:
> clang++ -fPIC -o testp testp.cpp
> ld: warning: ld: warning: URGENT: building for OSX, but linking against dylib (/usr/lib/libSystem.dylib) built for (unknown). Note: This will be an error in the future.URGENT: building for OSX, but linking against dylib (/usr/lib/libc++.dylib) built for (unknown). Note: This will be an error in the future.
>
> OK
>
> Testing the gfortran compiler:
> gfortran -fPIC -O0 -o testp testp.f
> ld: malformed file
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd:4:18: error: unknown enumerated scalar
> platform: zippered
> ^~~~~~~~
> file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd'
> collect2: error: ld returned 1 exit status
> ./configure2: line 2573: ./testp: No such file or directory
> Error: Unable to compile a Fortran program using gfortran -fPIC -O0
> Please check your compiler settings and configure flags.
> Configure failed due to the errors above!
>
> I suppose I should upgrade to latest Xcode first and try again?
>
> Thanks,
> Reza
>
>
> On Mar 28, 2019, at 11:11 AM, Gustaf Olsson <gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se><mailto:gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se>>> wrote:
>
> Which version of Xcode are you using?
>
> Which version of macOS ar you currently on?
>
> If you are on Xcode10 (10.0) and macOS 10.14, did you install the missing header files as instructed?
>
> I recently had an update of Xcode and CLT and I have not yet confirmed that compilation using GNU GCC (or clang for that matter) still works. I won’t be able to do so until next week either unfortunately. In the meanwhile, you can always try removing the symlinks for home-brew versions and configure using
>
> ./configure -macAccelerate clang
>
> This should use homebrew gfortran version and macOS clang version. If this also fails I assume that this is an apple issue.
>
> Best Regards
> Gustaf Olsson
>
> On 27 Mar 2019, at 19:48, Reza Esmaeeli <goldeagle.93.gmail.com <mailto:goldeagle.93.gmail.com><mailto:goldeagle.93.gmail.com <mailto:goldeagle.93.gmail.com>> <mailto:goldeagle.93.gmail.com <mailto:goldeagle.93.gmail.com>><mailto:goldeagle.93.gmail.com <mailto:goldeagle.93.gmail.com> <mailto:goldeagle.93.gmail.com <mailto:goldeagle.93.gmail.com>>>> wrote:
>
> Dear Amber Users!
>
> I have been trying to install AmberTools18 according to the HomeBrew method as described by Gustaf Olsson <https://www.ovetande.se/software/amber/installation/ <https://www.ovetande.se/software/amber/installation/> <https://www.ovetande.se/software/amber/installation/ <https://www.ovetande.se/software/amber/installation/>>>. I have installed GNU via HomeBrew and created the symlinks. But after running
>
> ./configure -macAccelerate gnu
>
> I get the following error:
>
> Obtaining the gnu compiler suite versions, e.g.:
> gcc -v
> The C version is 8.3.0
> 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
> ld: malformed file
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd:4:18: error: unknown enumerated scalar
> platform: zippered
> ^~~~~~~~
> file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd'
> collect2: error: ld returned 1 exit status
> ./configure2: line 2527: ./testp: No such file or directory
> Error: Unable to compile a C program using gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> Please check your compiler settings or configure flags.
> Configure failed due to the errors above!
>
> Any Ideas what may be the issue?
>
> Thanks,
> Reza
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org><mailto:AMBER.ambermd.org <mailto:AMBER.ambermd.org>> <mailto:AMBER.ambermd.org <mailto:AMBER.ambermd.org>><mailto:AMBER.ambermd.org <mailto:AMBER.ambermd.org><mailto:AMBER.ambermd.org <mailto:AMBER.ambermd.org>>>
> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber> <http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org><mailto:AMBER.ambermd.org <mailto:AMBER.ambermd.org>> <mailto:AMBER.ambermd.org <mailto:AMBER.ambermd.org>>
> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber> <http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org><mailto:AMBER.ambermd.org <mailto:AMBER.ambermd.org>>
> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 28 2019 - 07:30:04 PDT
