ld: library not found for -lgomp & clang: error: linker command failed with exit code 1

[KrisWu618]

Environment info

Operating System:
mac OS X Yosemite 10.10.5

Package used (python/R/jvm/C++):
python 3.5

$brew tap homebrew/boneyard
$brew install clang-omp
$brew reinstall gcc --without-multilib

$ gcc -v
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.5.0
Thread model: posix

$ clang -v
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.5.0
Thread model: posix

Below please find the steps and errors when I install xgboost.

$git clone --recursive https://github.com/dmlc/xgboost
$ cd xgboost;
$ cp make/config.mk ./config.mk;
$ make -j4

c++ -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -O3 -funroll-loops -msse2 -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/common/hist_util.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_fast_hist.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++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -O3 -funroll-loops -msse2 -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/common/hist_util.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_fast_hist.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
clang: warning: argument unused during compilation: '-pthread'
clang: warning: argument unused during compilation: '-pthread'
ld: library not found for -lgomp
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [lib/libxgboost.so] Error 1
make: *** Waiting for unfinished jobs....
ld: library not found for -lgomp
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [xgboost] Error 1

I have saw a couple of people having the same issues. But I am not clear about how to solve it.

#3
Here the solution mentioned I need to install OpenMP, which I already did. And it says I need to remove -fopenmp in Makefile, but I didn't find it in Makefile.

#29
Here the solution mentioned "See the build guide, in README.md you need to remove -fopenmp flag". But I didn't see -fopenmp in the README.md.

I have no idea about "ld: library not found for -lgomp; clang: error: linker command failed with exit code 1 (use -v to see invocation)". Can anybody help me?

Thank you very much.

[KrisWu618]

Problem solved! My case was a little complicated. I have tried installing xgboost last year but it did not work out. I gave up. Recently I wanted to reinstall it so that I can play with Kaggle. It took me three days to figure out all the issues. There were a couple of steps how I reinstall it.

First, I need to reinstall brew and install clang-omp. If you have compile issue, you may need to do it as well.

$brew tap homebrew/boneyard
$brew install clang-omp
$brew reinstall gcc --without-multilib

Second, I removed xgboost file I downloaded last year.

$cd
$ls 
$rm -rf xgboost

Then, I tried to reinstall xgboost.
$git clone --recursive https://github.com/dmlc/xgboost

Go to Makefile and make/config.mk. Replace the following code:
export CC = gcc
export CXX = g++

export CC = gcc-6
export CXX = g++-6

I still have issue with -fopenmp and -lgomp. I found the solution here #1839

The above issue was solved by the code:

cd xgboost; 
cp make/config.mk ./config.mk; 
make clean_all && make -j4

It worked out. I have tried install xgboost in python.
cd python-package; sudo python setup.py install
But it shows error that 'no such file'. I looked into the file and noticed my python-package was under xgboost file. So I change the path:
cd xgboost/python-package; sudo python setup.py install

Finally I can use xgboost!! Yay!

Reference:

1. https://xgboost.readthedocs.io/en/latest/build.html
2. https://www.ibm.com/developerworks/community/blogs/jfp/entry/Installing_XGBoost_on_Mac_OSX?lang=en
3. [mac] ld: symbol(s) not found for architecture x86_64 #1839