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RabbitBio / RabbitTClust

RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches
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Could NOT find OpenMP_C #9

Open shenweima opened 8 months ago

shenweima commented 8 months ago

I have install openmp,but an errors.

(masw_conda) bash>$ ./install.sh 
++ cd RabbitSketch
++ mkdir -p build
++ cd build
++ cmake -DCXXAPI=ON -DCMAKE_INSTALL_PREFIX=. ..
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /share/home/yzbsl_masw/.conda/envs/masw_conda/bin/x86_64-conda_cos6-linux-gnu-cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /share/home/yzbsl_masw/.conda/envs/masw_conda/bin/x86_64-conda_cos6-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /share/home/yzbsl_masw/software/RabbitTClust_v.2.2.1/RabbitSketch/build
++ make -j8
Scanning dependencies of target rabbitsketch_static
Scanning dependencies of target rabbitsketch
[  5%] Building CXX object CMakeFiles/rabbitsketch_static.dir/src/HyperLogLog.cpp.o
[ 11%] Building CXX object CMakeFiles/rabbitsketch_static.dir/src/MinHash.cpp.o
[ 16%] Building CXX object CMakeFiles/rabbitsketch.dir/src/HyperLogLog.cpp.o
[ 22%] Building CXX object CMakeFiles/rabbitsketch_static.dir/src/MurmurHash3.cpp.o
[ 38%] Building CXX object CMakeFiles/rabbitsketch.dir/src/MinHash.cpp.o
[ 38%] Building CXX object CMakeFiles/rabbitsketch_static.dir/src/OrderMinHash.cpp.o
[ 44%] Building CXX object CMakeFiles/rabbitsketch.dir/src/MurmurHash3.cpp.o
[ 44%] Building CXX object CMakeFiles/rabbitsketch.dir/src/OrderMinHash.cpp.o
[ 55%] Building CXX object CMakeFiles/rabbitsketch_static.dir/src/WeightedMinHash.cpp.o
[ 55%] Building CXX object CMakeFiles/rabbitsketch.dir/src/WeightedMinHash.cpp.o
[ 61%] Building CXX object CMakeFiles/rabbitsketch.dir/src/histoSketch.cpp.o
[ 66%] Building CXX object CMakeFiles/rabbitsketch_static.dir/src/histoSketch.cpp.o
[ 77%] Building CXX object CMakeFiles/rabbitsketch.dir/src/kssd.cpp.o
[ 77%] Building CXX object CMakeFiles/rabbitsketch_static.dir/src/kssd.cpp.o
[ 88%] Building C object CMakeFiles/rabbitsketch_static.dir/src/xxhash.c.o
[ 88%] Building C object CMakeFiles/rabbitsketch.dir/src/xxhash.c.o
[100%] Linking CXX shared library librabbitsketch.so
[100%] Linking CXX static library librabbitsketch_static.a
/share/home/yzbsl_masw/.conda/envs/masw_conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: skipping incompatible /share/home/yzbsl_masw/.conda/envs/masw_conda/lib/libgcc_s.so.1 when searching for libgcc_s.so.1
/share/home/yzbsl_masw/.conda/envs/masw_conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: skipping incompatible /share/home/yzbsl_masw/.conda/envs/masw_conda/lib/libgcc_s.so.1 when searching for libgcc_s.so.1
[100%] Built target rabbitsketch_static
[100%] Built target rabbitsketch
++ make install
[ 50%] Built target rabbitsketch_static
[100%] Built target rabbitsketch
Install the project...
-- Install configuration: ""
-- Installing: /share/home/yzbsl_masw/software/RabbitTClust_v.2.2.1/RabbitSketch/build/lib/librabbitsketch.so
-- Installing: /share/home/yzbsl_masw/software/RabbitTClust_v.2.2.1/RabbitSketch/build/lib/librabbitsketch_static.a
-- Installing: /share/home/yzbsl_masw/software/RabbitTClust_v.2.2.1/RabbitSketch/build/include/Sketch.h
-- Installing: /share/home/yzbsl_masw/software/RabbitTClust_v.2.2.1/RabbitSketch/build/include/robin_hood.h
-- Installing: /share/home/yzbsl_masw/software/RabbitTClust_v.2.2.1/RabbitSketch/build/include/MinHash.h
-- Installing: /share/home/yzbsl_masw/software/RabbitTClust_v.2.2.1/RabbitSketch/build/include/hash.h
-- Installing: /share/home/yzbsl_masw/software/RabbitTClust_v.2.2.1/RabbitSketch/build/include/histoSketch.h
-- Installing: /share/home/yzbsl_masw/software/RabbitTClust_v.2.2.1/RabbitSketch/build/include/HyperLogLog.h
++ cd ../../
++ cd RabbitFX
++ mkdir -p build
++ cd build
++ cmake -DCMAKE_INSTALL_PREFIX=. ..
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /share/home/yzbsl_masw/.conda/envs/masw_conda/bin/x86_64-conda_cos6-linux-gnu-cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /share/home/yzbsl_masw/.conda/envs/masw_conda/bin/x86_64-conda_cos6-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Error at /share/home/yzbsl_masw/.conda/envs/masw_conda/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:165 (message):
  Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
Call Stack (most recent call first):
  /share/home/yzbsl_masw/.conda/envs/masw_conda/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:458 (_FPHSA_FAILURE_MESSAGE)
  /share/home/yzbsl_masw/.conda/envs/masw_conda/share/cmake-3.18/Modules/FindOpenMP.cmake:529 (find_package_handle_standard_args)
  CMakeLists.txt:5 (find_package)

-- Configuring incomplete, errors occurred! See also "/share/home/yzbsl_masw/software/RabbitTClust_v.2.2.1/RabbitFX/build/CMakeFiles/CMakeOutput.log". See also "/share/home/yzbsl_masw/software/RabbitTClust_v.2.2.1/RabbitFX/build/CMakeFiles/CMakeError.log".

ZekunYin commented 8 months ago

Hi, It seems that your environment lacks support for openmp. We use openmp for multithreading in this project. I think you need to check whether the openmp is correctly installed. If the issue still occurs, please feel free to contact us.

Best, Zekun