Undefined reference to `dsyev_' and friends when compiling from source

[akastrin]

I try to compile tsne-cuda from source using the following procedure:

export PATH=/opt/cuda-9.0/bin:$PATH
export LD_LIBRARY_PATH=/opt/cuda-9.0/lib64:$LD_LIBRARY_PATH
git clone https://github.com/CannyLab/tsne-cuda.git
git submodule init
git submodule update 
cd ./build
cmake  .. -DBUILD_PYTHON=TRUE -DWITH_MKL=FALSE -DCMAKE_C_COMPILER=gcc-6 -DCMAKE_CXX_COMPILER=g++-6
make -j10

However, the process stops with the following error:

Scanning dependencies of target tsne
[ 89%] Building CXX object CMakeFiles/tsne.dir/third_party/faiss/gpu/GpuResources.cpp.o
[ 89%] Building CXX object CMakeFiles/tsne.dir/third_party/faiss/gpu/GpuAutoTune.cpp.o
[ 90%] Building CXX object CMakeFiles/tsne.dir/third_party/faiss/gpu/IndexProxy.cpp.o
[ 90%] Building CXX object CMakeFiles/tsne.dir/third_party/faiss/gpu/StandardGpuResources.cpp.o
[ 90%] Building CXX object CMakeFiles/tsne.dir/third_party/faiss/gpu/GpuClonerOptions.cpp.o
[ 90%] Building CXX object CMakeFiles/tsne.dir/third_party/faiss/gpu/impl/RemapIndices.cpp.o
[ 91%] Building CXX object CMakeFiles/tsne.dir/third_party/faiss/gpu/utils/DeviceMemory.cpp.o
[ 91%] Building CXX object CMakeFiles/tsne.dir/third_party/faiss/gpu/utils/DeviceUtils.cpp.o
[ 91%] Building CXX object CMakeFiles/tsne.dir/third_party/faiss/gpu/utils/MemorySpace.cpp.o
[ 92%] Building CXX object CMakeFiles/tsne.dir/third_party/faiss/gpu/utils/StackDeviceMemory.cpp.o
[ 92%] Building CXX object CMakeFiles/tsne.dir/third_party/faiss/gpu/utils/Timer.cpp.o
[ 92%] Building CXX object CMakeFiles/tsne.dir/third_party/faiss/gpu/utils/WorkerThread.cpp.o
[ 92%] Linking CXX executable tsne
ld: lib/libfaiss.so: undefined reference to `dsyev_'
ld: lib/libfaiss.so: undefined reference to `sgeqrf_'
ld: lib/libfaiss.so: undefined reference to `sorgqr_'
ld: lib/libfaiss.so: undefined reference to `sgesvd_'
make[2]: *** [CMakeFiles/tsne.dir/build.make:1574: tsne] Error 1
make[1]: *** [CMakeFiles/Makefile2:249: CMakeFiles/tsne.dir/all] Error 2
make: *** [Makefile:171: all] Error 2]

I use Arch Linux with CUDA 9.0, CMake 3.18; further details are provided here and here.

Any advice is appreciated. Thanks.

[DavidMChan]

It looks like FAISS is not linking correctly against lapack/openblas (probably because you have a newer version than the older FAISS code). You can try the version on the develop/ branch (which should be more up to date), or try to track down the LAPACK linking errors.

[DavidMChan]

This should be resolved as of the new installation instructions in 3.0.0!