Hi
This works for me :P, ymmv
macmini:~ tru$ cd ambertools19/
macmini:ambertools19 tru$ tar xjf ../AmberTools19.tar.bz2
macmini:ambertools19 tru$ type gcc; gcc -v ; type gfortran; gfortran -v
gcc is /usr/bin/gcc
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.0 (clang-1100.0.33.8)
Target: x86_64-apple-darwin19.0.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
gfortran is /usr/local/bin/gfortran
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/9.2.0_1/libexec/gcc/x86_64-apple-darwin19/9.2.0/lto-wrapper
Target: x86_64-apple-darwin19
Configured with: ../configure --build=x86_64-apple-darwin19 --prefix=/usr/local/Cellar/gcc/9.2.0_1 --libdir=/usr/local/Cellar/gcc/9.2.0_1/lib/gcc/9 --disable-nls --enable-checking=release --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-9 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --with-pkgversion='Homebrew GCC 9.2.0_1' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --disable-multilib --with-native-system-header-dir=/usr/include --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
Thread model: posix
gcc version 9.2.0 (Homebrew GCC 9.2.0_1)
macmini:~ tru$ brew info gcc
gcc: stable 9.2.0 (bottled), HEAD
GNU compiler collection
https://gcc.gnu.org/
/usr/local/Cellar/gcc/9.2.0_1 (1,462 files, 287.9MB) *
Poured from bottle on 2019-10-14 at 22:39:31
From:
https://github.com/Homebrew/homebrew-core/blob/master/Formula/gcc.rb
==> Dependencies
Required: gmp ✔, isl ✔, libmpc ✔, mpfr ✔
==> Options
--HEAD
Install HEAD version
==> Analytics
install: 108,250 (30 days), 252,909 (90 days), 974,587 (365 days)
install_on_request: 53,085 (30 days), 118,718 (90 days), 462,836 (365
days)
build_error: 0 (30 days)
macmini:~ tru$ brew list gcc
/usr/local/Cellar/gcc/9.2.0_1/bin/c++-9
/usr/local/Cellar/gcc/9.2.0_1/bin/cpp-9
/usr/local/Cellar/gcc/9.2.0_1/bin/g++-9
/usr/local/Cellar/gcc/9.2.0_1/bin/gcc-9
/usr/local/Cellar/gcc/9.2.0_1/bin/gcc-ar-9
/usr/local/Cellar/gcc/9.2.0_1/bin/gcc-nm-9
/usr/local/Cellar/gcc/9.2.0_1/bin/gcc-ranlib-9
/usr/local/Cellar/gcc/9.2.0_1/bin/gcov-9
/usr/local/Cellar/gcc/9.2.0_1/bin/gcov-dump-9
/usr/local/Cellar/gcc/9.2.0_1/bin/gcov-tool-9
/usr/local/Cellar/gcc/9.2.0_1/bin/gfortran
/usr/local/Cellar/gcc/9.2.0_1/bin/gfortran-9
/usr/local/Cellar/gcc/9.2.0_1/bin/x86_64-apple-darwin19-c++-9
/usr/local/Cellar/gcc/9.2.0_1/bin/x86_64-apple-darwin19-g++-9
/usr/local/Cellar/gcc/9.2.0_1/bin/x86_64-apple-darwin19-gcc-9
/usr/local/Cellar/gcc/9.2.0_1/bin/x86_64-apple-darwin19-gcc-9.2.0
/usr/local/Cellar/gcc/9.2.0_1/bin/x86_64-apple-darwin19-gcc-ar-9
/usr/local/Cellar/gcc/9.2.0_1/bin/x86_64-apple-darwin19-gcc-nm-9
/usr/local/Cellar/gcc/9.2.0_1/bin/x86_64-apple-darwin19-gcc-ranlib-9
/usr/local/Cellar/gcc/9.2.0_1/bin/x86_64-apple-darwin19-gfortran-9
/usr/local/Cellar/gcc/9.2.0_1/include/c++/ (787 files)
/usr/local/Cellar/gcc/9.2.0_1/lib/gcc/ (622 files)
/usr/local/Cellar/gcc/9.2.0_1/libexec/gcc/ (13 files)
/usr/local/Cellar/gcc/9.2.0_1/share/gcc-9.2.0/ (4 files)
/usr/local/Cellar/gcc/9.2.0_1/share/man/ (10 files)
macmini:amber18 tru$ ls -l /Library/Developer/CommandLineTools/*
/Library/Developer/CommandLineTools/Library:
total 0
drwxr-xr-x 3 root admin 96 Aug 16 14:39 Developer
drwxr-xr-x 3 root wheel 96 Sep 6 05:47 Frameworks
drwxr-xr-x 3 root admin 96 Aug 16 15:04 Perl
drwxr-xr-x 3 root wheel 96 Sep 6 05:47 PrivateFrameworks
/Library/Developer/CommandLineTools/SDKs:
total 0
lrwxr-xr-x 1 root wheel 15 Oct 9 17:32 MacOSX.sdk -> MacOSX10.15.sdk
drwxr-xr-x 7 root wheel 224 Jul 16 02:44 MacOSX10.14.sdk
drwxr-xr-x 8 root wheel 256 Aug 30 08:48 MacOSX10.15.sdk
/Library/Developer/CommandLineTools/usr:
total 0
drwxr-xr-x 124 root wheel 3968 Oct 9 17:29 bin
drwxr-xr-x 5 root wheel 160 Sep 6 05:47 include
drwxr-xr-x 44 root wheel 1408 Oct 9 17:29 lib
drwxr-xr-x 6 root admin 192 Sep 6 05:51 libexec
drwxr-xr-x 7 root admin 224 Oct 9 17:32 share
macmini:amber18 tru$ sw_vers
ProductName: Mac OS X
ProductVersion: 10.15
BuildVersion: 19A583
macmini:amber18 tru$
macmini:amber18 tru$ pwd
/Users/tru/ambertools19/amber18
macmini:amber18 tru$ export AMBERHOME=/Users/tru/ambertools19/amber18
macmini:amber18 tru$ ./configure clang | tee configure-clang.log
...
<patches>
<miniconda>
/Library/Developer/CommandLineTools/SDKs:
total 0
lrwxr-xr-x 1 root wheel 15 Oct 9 17:32 MacOSX.sdk -> MacOSX10.15.sdk
drwxr-xr-x 7 root wheel 224 Jul 16 02:44 MacOSX10.14.sdk
drwxr-xr-x 8 root wheel 256 Aug 30 08:48 MacOSX10.15.sdk
macmini:amber18 tru$ pwd
/Users/tru/ambertools19/amber18
macmini:amber18 tru$ export AMBERHOME=/Users/tru/ambertools19/amber18
macmini:amber18 tru$ ./configure clang | tee configure-clang.log
...
<patches>
<miniconda>
...
Configuring CPPTRAJ...complete.
The configuration file, config.h, was successfully created.
--------------------------------------------------------------------------------
Environment resource files are provided to set the proper environment
variables to use AMBER and AmberTools. This is required to run any Python
programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
/Users/tru/ambertools19/amber18/amber.sh file in your shell. Consider adding the line
test -f /Users/tru/ambertools19/amber18/amber.sh && source /Users/tru/ambertools19/amber18/amber.sh
to your startup file (e.g., ~/.bashrc)
If you use a C shell (e.g., csh, tcsh), source the
/Users/tru/ambertools19/amber18/amber.csh file in your shell. Consider adding the line
test -f /Users/tru/ambertools19/amber18/amber.csh && source /Users/tru/ambertools19/amber18/amber.csh
to your startup file (e.g., ~/.cshrc)
NOTE: MacOS users might need to add the content to ~/.bash_profile file
(You need to do the above before running 'make install')
--------------------------------------------------------------------------------
The next step is to source the amber.sh or amber.csh file
(if needed, see above), and then to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.
macmini:amber18 tru$ test -f /Users/tru/ambertools19/amber18/amber.sh && source /Users/tru/ambertools19/amber18/amber.sh
macmini:amber18 tru$ nice make install
...
/bin/mv cestats /Users/tru/ambertools19/amber18/bin
(cd nfe-umbrella-slice && /Library/Developer/CommandLineTools/usr/bin/make install)
[NFE] CXX umbrella.cc
[NFE] CXX dimension.cc
[NFE] CXX utils.cc
[NFE] CXX main.cc
[NFE] CXX nfe-umbrella-slice
(if [ "no" = "no" ]; then \
/Library/Developer/CommandLineTools/usr/bin/make python_serial ;\
fi;\
)
(cd parmed && PYTHONPATH=/Users/tru/ambertools19/amber18/lib/python2.7/site-packages /Users/tru/ambertools19/amber18/bin/amber.python setup.py install -f --prefix=/Users/tru/ambertools19/amber18 > build.log)
warning: no files found matching 'versioneer.py'
warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
In file included from src/_rdparm.cpp:17:
/Users/tru/ambertools19/amber18/AmberTools/src/parmed/src/readparm.h:5:10: fatal error: 'locale' file not found
#include <locale>
^~~~~~~~
1 warning and 1 error generated.
error: command 'clang' failed with exit status 1
make[2]: *** [parmed] Error 1
make[1]: *** [serial] Error 2
make: *** [install] Error 2
macmini:amber18 tru$
That was "fixed" by adding a line in /Users/tru/ambertools19/amber18/AmberTools/src/parmed/setup.py
parmed/setup.py:
..
27 def prepare_env_for_osx():
28 """ Prepares the environment for OS X building """
29 darwin_major_to_osx_map = {
30 '11': '10.7',
31 '12': '10.8',
32 '13': '10.9',
33 '14': '10.10',
34 '15': '10.11',
35 '16': '10.12',
36 '17': '10.13',
37 '18': '10.14',
38 '19': '10.14',
39 }
...
macmini:amber18 tru$ make
....
(cd pytraj && AMBERHOME=/Users/tru/ambertools19/amber18 AMBER_PREFIX=/Users/tru/ambertools19/amber18 PYTHONPATH=/Users/tru/ambertools19/amber18/lib/python2.7/site-packages /Users/tru/ambertools19/amber18/bin/amber.python setup.py install -f --prefix=/Users/tru/ambertools19/amber18 --disable-openmp > build.log )
warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
pytraj/topology/topology.cpp:636:10: fatal error: 'ios' file not found
#include "ios"
^~~~~
1 warning and 1 error generated.
error: command 'clang' failed with exit status 1
make[2]: *** [pytraj] Error 1
make[1]: *** [serial] Error 2
make: *** [install] Error 2
macmini:amber18 tru$
The same "fix" applied to pytraj/setup.py allows "make" to complete.
AmberTools/src/pytraj/setup.py:
...
140 def prepare_env_for_osx():
141 # Copied from ParmEd
142 #
https://github.com/ParmEd/ParmEd/blob/8ea11835cacbb986d76439f56bb529c83d34aa1f/setup.py#L28
143 """ Prepares the environment for OS X building """
144 darwin_major_to_osx_map = {
145 '11': '10.7',
146 '12': '10.8',
147 '13': '10.9',
148 '14': '10.10',
149 '15': '10.11',
150 '16': '10.12',
151 '17': '10.13',
152 '18': '10.14',
153 '19': '10.14',
154 }
...
The osx tuned version also works:
$ ./configure -macAccelerate clang && make install
Next step: try to replace the line '19': '10.14' by '19': '10.15'.
Cheers
Tru
--
Tru Huynh (PhD) | mailto:tru.pasteur.fr | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
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Received on Tue Oct 15 2019 - 03:30:02 PDT
