Workaround found…
I don’t know why though GNU GCC still links to Xcode on macOS 14 so trying a pure gcc compile fails with the ‘_Atomic’ has no type error as described previously.
Config files have changed since I put up the website however this procedure worked for me using Xcode 10.2, macOS 10.14.4 and gfortran 8.3 installed using homebrew.
Assuming you’ve already installed xcode and the command-line tools as well as the missing headers:
$ tar xvf AmberTools18.tar.bz2
$ export AMBERHOME=/[PATH]/[TO]/amber18
$ export PATH=${AMBERHOME}:$PATH
$ export MACOSX_DEPLOYMENT_TARGET=’10.14'
$ cd $AMBERHOME
$ vi $AMBERHOME/AmberTools/src/pytraj/setup.py
# Comment out lines:
2255 # # mac/clang
2256 # if [ "$skippython" = "no" ]; then
2257 # cpptrajcxxflags="-stdlib=libstdc++ $cpptrajcxxflags"
2258 # cpptrajldflags="-stdlib=libstdc++ -L/usr/lib/"
2259 # fi
$ vi AmberTools/src/pytraj/setup.py
# Comment out line:
142 # extra_compile_args.append('-stdlib=libstdc++')
$ ./configure -macAccelerate clang
Compilation worked and I am running tests as we speak. I’ll try to find time to update the website and also spin up my VM and try MacPorts and HPC gfortran, although any option for fortran with clang should work.
Have a wonderful weekend
// Gustaf
On 28 Mar 2019, at 16:21, Reza Esmaeeli <goldeagle.93.gmail.com<mailto:goldeagle.93.gmail.com>> wrote:
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<mailto: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 <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
______________________________
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Postdoktor
Linnéuniversitetet
Fakulteten för hälso- och livsvetenskap
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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<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 <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 <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 <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 <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
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Received on Fri Mar 29 2019 - 07:30:02 PDT
