I am on a Mac but I am not a Mac user. I need to run a make command (actually make makewisdom) to compile a software, but my compiler does not recognize some commands:
$ make makewisdom
gcc -I/Users/username/presto/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include -I -I/opt/local/include -DUSEFFTW -DUSEMMAP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wall -W -fPIC -O3 -ffast-math -Wno-unused-result -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -fopenmp -o makewisdom makewisdom.c -L/opt/local/lib -lfftw3f
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
make: *** [makewisdom] Error 1
I know the problem is with clang. I am reading lots of discussions (such this and this, and more), and trying to workaround the problem, but no luck yet. It maybe that I just need to set a different default compiler? (to, for example, gcc, whatever is the version I have installed):
$ gcc --version
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin18.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
Related
I am using MacOS Mojave version 10.14.16 and I am trying to install http://www.rpl2.net/index.php (a programming language using Reverse Polish Notation as found on some HP calculators like the 48GX), supposed to work on MacOSX (they say "MacOS X (Xcode 3.1.4 + gfortran 4.5)").
So I have downloaded the latest stable release, cd to the folder, and wanted to run
./configure
make
make install
But the ./configure is failing due to "configure: error: Can not find libgomp !". There is no libgomp package I can install with brew (I already installed gcc which comes with gfortran and thought it would provide libgomp but apparently not).
Could someone help a poor applied mathematician trying to install a software on its macbook?
Thanks
EDIT
in my config.log I have this, maybe it will help:
configure:7433: checking for vim
configure:7449: found /usr/bin/vim
configure:7461: result: yes
configure:7507: checking for main in -lm
configure:7526: gcc -o conftest -g -O2 -O2 -fno-strict-overflow conftest.c -lm >&5
configure:7526: $? = 0
configure:7535: result: yes
configure:7548: checking for pthread_mutex_init in -lc
configure:7573: gcc -o conftest -g -O2 -O2 -fno-strict-overflow conftest.c -lc -lm >&5
configure:7573: $? = 0
configure:7582: result: yes
configure:7687: checking for omp_get_num_procs in -lgomp
configure:7712: gcc -o conftest -g -O2 -O2 -fno-strict-overflow conftest.c -lgomp -lc -lm >&5
ld: library not found for -lgomp
clang: error: linker command failed with exit code 1 (use -v to see invocation)
configure:7712: $? = 1
You don't say how you installed GCC. If you did it using homebrew, and
brew install gcc
you should be able to see:
/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgomp.dylib
which would mean you need to compile with:
gcc ... -L /usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -l gomp ...
Failing that, you can always search for libgomp with:
find /usr -name "lib*gomp*lib"
You can test which gcc you are using with:
type gcc
I am trying to install OpenMP enabled xgboost on my mac. I installed gcc with no problem:
brew install gcc --without-multilib
then cloned git repository:
git clone --recursive https://github.com/dmlc/xgboost
cd xgboost; cp make/config.mk ./config.mk
but I get an error when I do
make -j4
Here is the error I get. I'd appreciate if you can help fixing this problem:
c++ -std=c++0x -Wall -O3 -msse2 -Wno-unknown-pragmas -funroll-loops -Iinclude -Idmlc-core/include -Irabit/include -fPIC -fopenmp -o xgboost build/cli_main.o build/learner.o build/logging.o build/c_api/c_api.o build/c_api/c_api_error.o build/common/common.o build/data/data.o build/data/simple_csr_source.o build/data/simple_dmatrix.o build/data/sparse_page_dmatrix.o build/data/sparse_page_raw_format.o build/data/sparse_page_source.o build/data/sparse_page_writer.o build/gbm/gblinear.o build/gbm/gbm.o build/gbm/gbtree.o build/metric/elementwise_metric.o build/metric/metric.o build/metric/multiclass_metric.o build/metric/rank_metric.o build/objective/multiclass_obj.o build/objective/objective.o build/objective/rank_obj.o build/objective/regression_obj.o build/tree/tree_model.o build/tree/tree_updater.o build/tree/updater_colmaker.o build/tree/updater_histmaker.o build/tree/updater_prune.o build/tree/updater_refresh.o build/tree/updater_skmaker.o build/tree/updater_sync.o dmlc-core/libdmlc.a rabit/lib/librabit.a -pthread -lm -fopenmp
c++ -std=c++0x -Wall -O3 -msse2 -Wno-unknown-pragmas -funroll-loops -Iinclude -Idmlc-core/include -Irabit/include -fPIC -fopenmp -shared -o lib/libxgboost.so build/learner.o build/logging.o build/c_api/c_api.o build/c_api/c_api_error.o build/common/common.o build/data/data.o build/data/simple_csr_source.o build/data/simple_dmatrix.o build/data/sparse_page_dmatrix.o build/data/sparse_page_raw_format.o build/data/sparse_page_source.o build/data/sparse_page_writer.o build/gbm/gblinear.o build/gbm/gbm.o build/gbm/gbtree.o build/metric/elementwise_metric.o build/metric/metric.o build/metric/multiclass_metric.o build/metric/rank_metric.o build/objective/multiclass_obj.o build/objective/objective.o build/objective/rank_obj.o build/objective/regression_obj.o build/tree/tree_model.o build/tree/tree_updater.o build/tree/updater_colmaker.o build/tree/updater_histmaker.o build/tree/updater_prune.o build/tree/updater_refresh.o build/tree/updater_skmaker.o build/tree/updater_sync.o dmlc-core/libdmlc.a rabit/lib/librabit.a -pthread -lm -fopenmp
clangclang: : warningwarning: : argument unused during compilation: '-pthread'argument unused during compilation: '-pthread'
ld: library not found for -lgomp
ld: library not found for -lgomp
clang: error: clanglinker command failed with exit code 1 (use -v to see invocation):
error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [lib/libxgboost.so] Error 1
make: *** Waiting for unfinished jobs....
make: *** [xgboost] Error 1
I have the same issue and solved it by:
brew install clang-omp
export CC=clang-omp
export CXX=clang-omp++
git clone --recursive https://github.com/dmlc/xgboost
cd xgboost; cp make/config.mk ./config.mk; make -j4
cd python-package
sudo python setup.py install
If you used pip to install xgboost before, then delete the previous installed xgboost from your project. Then use
pip install xgboost
to install it again.
A new versions of OSX has a Clang as a default c\c++ compiler. Therefore your c++ command refers to clang++.
You should define a CC\CXX environmental variables for your make command like this CC=gcc CXX=g++ make -j
Also you can build an OpenMP for clang OpenMPrt and customise your shell environment (I didn't try this by own)
(I have no mac at this moment to check this solution; just linux)
I am trying to install a python module (SPArse Modeling Software) but the install script doesn't seem to be able to find the system's default Python.framework. This is an almost new (no migration assistant) Mac OS 10.9.5 system with both the default system python and Anaconda installed. I briefly installed Enthought Canopy but removed it when I decided to go with Anaconda. /System/Library/Frameworks/Python.framework exists and seems to have all the files you would expect.
In terminal, this is what happens:
bash-3.2$ which python
//anaconda/bin/python
bash-3.2$ cd spams-python
bash-3.2$ python setup.py build
running build
running build_py
running build_ext
building '_spams_wrap' extension
gcc -fno-strict-aliasing -I//anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dictLearn -I//anaconda/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7/ -I//anaconda/include/python2.7 -c spams_wrap.cpp -o build/temp.macosx-10.5-x86_64-2.7/spams_wrap.o -DNDEBUG -DUSE_BLAS_LIB -fPIC -fopenmp -m32
clang: warning: argument unused during compilation: '-fopenmp'
#Omitting some irrelevant (I think) warnings#
4 warnings generated.
gcc -bundle -undefined dynamic_lookup -L//anaconda/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/spams_wrap.o -L//anaconda/lib -lstdc++ -lblas -llapack -o build/lib.macosx-10.5-x86_64-2.7/_spams_wrap.so -m32 -framework Python
ld: framework not found Python
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'gcc' failed with exit status 1
So, my question is, is my diagnosis of the problem correct? How can I tell GCC where Python.framework is? Is there some environment variable that isn't set correctly?
The Anaconda Python is not a Framework build of Python. If the module expects that it's not going to work. Commenting out commenting out "'-framework', 'Python'" in setup.py sounds like a good start, and if it works, then it probably is the right solution.
Compile it with gcc-5, and I successed.
Any suggestions for resolving the following error (unknown option passed to ld) will be highly appreciated. The "buildit" script is the one from http://libcxx.llvm.org/ with the line
export TRIPLE=-apple-
added to it.
Thanks in advance
System Version: Mac OS X 10.6.8 (10K549)
$ clang++ -v
clang version 3.4 (trunk 192978) (llvm/trunk 192977)
Target: x86_64-apple-darwin10.8.0
Thread model: posix
/usr/local/libcxx/lib: sudo ./buildit
for FILE in '../src/*.cpp'
clang++ -c -g -Os -arch i386 -arch x86_64 -nostdinc++ -std=c++11 -fstrict-aliasing -Wall -Wextra -Wshadow -Wconversion -Wpadded -Wstrict-aliasing=2 -Wstrict-overflow=4 -U__STRICT_ANSI__ -I../include ../src/algorithm.cpp
for FILE in '../src/*.cpp'
...
clang algorithm.o bind.o chrono.o condition_variable.o debug.o exception.o future.o hash.o ios.o iostream.o locale.o memory.o mutex.o new.o optional.o random.o regex.o shared_mutex.o stdexcept.o string.o strstream.o system_error.o thread.o typeinfo.o utility.o valarray.o -arch i386 -arch x86_64 -o libc++.1.dylib -dynamiclib -nodefaultlibs -current_version 1 -compatibility_version 1 -install_name /usr/lib/libc++.1.dylib -lSystem -Wl,-unexported_symbols_list,libc++unexp.exp /usr/lib/libc++abi.dylib -Wl,-reexported_symbols_list,libc++abi.exp -Wl,-force_symbols_not_weak_list,notweak.exp -Wl,-force_symbols_weak_list,weak.exp -nostdinc++ -std=c++11 -fstrict-aliasing -Wall -Wextra -Wshadow -Wconversion -Wpadded -Wstrict-aliasing=2 -Wstrict-overflow=4 -U__STRICT_ANSI__
clang: warning: argument unused during compilation: '-nostdinc++'
clang: warning: argument unused during compilation: '-std=c++11'
ld: unknown option: -reexported_symbols_list
clang: error: linker command failed with exit code 1 (use -v to see invocation)
I've been struggling for days with the same problem, but eventually got it compiled.
Before running the build script, try setting the following environment variables:
export TRIPLE=-apple-
export MACOSX_DEPLOYMENT_TARGET=10.6
I'm using GCC 4.7.2 and LD 2.23 but when I add -flto to my compile options my compile time increases by over 20%! The manual seems to indicate that -fuse-linker-plugin is needed for the optimization to work. It also says that it's enabled by default with -flto but when I add it explicitly I see the following error in the link command:
g++: error: -fuse-linker-plugin is not supported in this configuration
According to manual, it should be supported by LD 2.21 or greater. Any idea why I'm getting this error? For reference here are examples of my full compile commands:
g++ -Wall -pipe -O3 -flto -fno-strict-aliasing -mtune=generic --no-exceptions -fPIC -c some.cc
g++ -o exec -Xlinker some1.o some2.o -static some1.a some2.a -Wl,--wrap,open -flto -fuse-linker-plugin
Running 'ld --help | grep plugin' shows "-plugin" option so I don't understand why GCC is complaining:
-plugin PLUGIN Load named plugin
-plugin-opt ARG Send arg to last-loaded plugin
Link time optimizations aren't supposed to reduce compilation time, but optimize runtime of your program.
#options, just add "-flto -fuse-linker-plugin" to your CFLAGS(or CXXFLAGS for c++) and LDFLAGS and it should work just fine.
#gold: ld --version is probably gonna return gnu LD, to switch to gold, make ld symlink which ld point to which ld.gold
e.g. ln -s /usr/bin/ld.gold /usr/bin/ld