I see. Thank you for your kind support despite being busy.
Hope everything goes well.
Thanks,
Reza
> On Mar 28, 2019, at 7:48 PM, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> So, installing the headers solved the fortran linking issue though apple Clang still/again fails to configure CPTRAJ which breaks configuration and makes installing impossible.
>
> As I don’t have time to solve this issue right now I ran the process using HOMEBREW GCC-8
>
> ln -s /usr/local/bin/gcc-8 /usr/local/bin/gcc
> ln -s /usr/local/bin/g++-8 /usr/local/bin/g++
> ln -s /usr/local/bin/c++-8 /usr/local/bin/c++
>
> export AMBERHOME=/[PATH]/[TO]/amber18
> export PATH=${AMBERHOME}:$PATH
> export MACOSX_DEPLOYMENT_TARGET='10.14'
> cd $AMBERHOME
>
>
> ./configure -macAccelerate gnu
> make install
>
> The compilation broke with:
>
> 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: error: '_Atomic' does not name a type
> _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
>
> I’ll try to work this out though it will take a few days...
>
> On 28 Mar 2019, at 15:58, Gustaf Olsson <gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se><mailto:gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se>>> wrote:
>
> So, reinstalling the “header files”
>
> $ open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>
> Solved the fortran issue. Though now I am right back at
>
> Configuring CPPTRAJ...
> CPPTRAJ configure failed. Check '/Users/guolaa/SOFTWARE/amber18/AmberTools/src/cpptraj_config.log' for details.
> Configure failed due to the errors above!
>
> $vi /amber18/AmberTools/src/cpptraj_config.log
>
> Error: Could not link properly with clang++ on OSX
>
> So back to square one I suppose. Additionally, config files seems to have changed meaning that I’ll have ot update the website as soon as I figure out how to get this running on my own system.
>
> Med vänlig hälsning
> Gustaf Olsson
> ______________________________
> Gustaf Olsson, fil.dr
> Postdoktor
>
> Linnéuniversitetet
> Fakulteten för hälso- och livsvetenskap
> 391 82 Kalmar
>
> 0772-28 80 00 Växel
> 0480-44 62 07 Direkt
> 0725-94 94 46 Mobil
> 0480-44 62 62 Fax
> gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se><mailto:gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se>><mailto:gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se>>
> Lnu.se <http://lnu.se/><http://lnu.se/ <http://lnu.se/>>
>
> Utmanande utbildningar. Framstående forskning. Linnéuniversitetet – ett modernt, internationellt universitet i Småland.
>
> On 28 Mar 2019, at 15:08, Gustaf Olsson <gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se><mailto:gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se>><mailto:gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se>>> wrote:
>
> Seems that some update of Xcode/macOS or GNU compilers seems to have broken clang compilation again.
>
> Testing mixed C/Fortran compilation:
> clang -fPIC -DUSE_AMBER_C9XCOMPLEX -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
> clang -fPIC -DUSE_AMBER_C9XCOMPLEX -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -L/usr/local/Cellar/gcc/8.3.0/lib/gcc/8/gcc/x86_64-apple-darwin18.2.0/8.3.0/../../../ -lgfortran -w -framework Accelerate -lmc
> ld: library not found for -lmc
> clang: error: linker command failed with exit code 1 (use -v to see invocation)
> ./configure2: line 2609: ./testp: No such file or directory
> Error: Unable to compile mixed C/Fortran code.
> Please check your compiler settings and configure flags.
> Configure failed due to the errors above!
>
> So I don’t know when I have enough time to dig into this though as soon as I have a solution/workaround I’ll update the post and mailing list.
>
> // Gustaf
>
>
> On 28 Mar 2019, at 12:32, Gustaf Olsson <gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se><mailto:gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se>><mailto:gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se>><mailto:gustaf.olsson.lnu.se <mailto: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>><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:
>
> 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>><mailto:gustaf.olsson.lnu.se <mailto:gustaf.olsson.lnu.se>><mailto: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>> <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>> <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>><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>><mailto:AMBER.ambermd.org <mailto:AMBER.ambermd.org>><mailto:AMBER.ambermd.org <mailto:AMBER.ambermd.org>>
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org<mailto:AMBER.ambermd.org><mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 - 08:30:02 PDT
