Undefined Reference Error

[JT17]

Hi so I have installed everything according to the installation guide and there aren't any issues as far as I know. However, I cannot compile anything in C++ or import the library in python. When I try to import cuv_python I get an Import error:ImportError: /usr/local/lib/libtp_theano.so.0: undefined symbol: _ZN5boost6system

When I try to compile a simple program in C++ I get a whole list of errors which seem to indicate something inside cuv can't find some file in cuv: /tmp/ccxiUJdU.o: In function cuv::reference<int, cuv::host_memory_space>::operator int() const': program.cpp:(.text._ZNK3cuv9referenceIiNS_17host_memory_spaceEEcviEv[_ZNK3cuv9referenceIiNS_17host_memory_spaceEEcviEv]+0x1f): undefined reference toint cuv::detail::entryget(int const, unsigned long, cuv::host_memory_space)' /tmp/ccxiUJdU.o: In function cuv::reference<unsigned int, cuv::host_memory_space>::operator unsigned int() const': program.cpp:(.text._ZNK3cuv9referenceIjNS_17host_memory_spaceEEcvjEv[_ZNK3cuv9referenceIjNS_17host_memory_spaceEEcvjEv]+0x1f): undefined reference tounsigned int cuv::detail::entryget(unsigned int const, unsigned long, cuv::host_memory_space)' /tmp/ccxiUJdU.o: In function cuv::default_allocator::default_allocator()': program.cpp:(.text._ZN3cuv17default_allocatorC2Ev[_ZN3cuv17default_allocatorC5Ev]+0x1f): undefined reference tovtable for cuv::default_allocator' /tmp/ccxiUJdU.o: In function void cuv::sequence<float, cuv::dev_memory_space, cuv::row_major>(cuv::tensor<float, cuv::dev_memory_space, cuv::row_major>&)': program.cpp:(.text._ZN3cuv8sequenceIfNS_16dev_memory_spaceENS_9row_majorEEEvRNS_6tensorIT_T0_T1_EE[_ZN3cuv8sequenceIfNS_16dev_memory_spaceENS_9row_majorEEEvRNS_6tensorIT_T0_T1_EE]+0x22): undefined reference tovoid cuv::apply_0ary_functor<float, cuv::dev_memory_space>(cuv::tensor<float, cuv::dev_memory_space, cuv::row_major>&, cuv::NullaryFunctor const&)' /tmp/ccxiUJdU.o: In function cuv::reference<float, cuv::host_memory_space>::operator float() const': program.cpp:(.text._ZNK3cuv9referenceIfNS_17host_memory_spaceEEcvfEv[_ZNK3cuv9referenceIfNS_17host_memory_spaceEEcvfEv]+0x1f): undefined reference tofloat cuv::detail::entryget(float const, unsigned long, cuv::host_memory_space)' /tmp/ccxiUJdU.o: In function boost::enable_if_c<boost::is_convertible<long, unsigned int>::value, void>::type cuv::reference<unsigned int, cuv::host_memory_space>::operator=<long>(long const&)': program.cpp:(.text._ZN3cuv9referenceIjNS_17host_memory_spaceEEaSIlEEN5boost11enable_if_cIXsrNS4_14is_convertibleIT_jEE5valueEvE4typeERKS7_[_ZN3cuv9referenceIjNS_17host_memory_spaceEEaSIlEEN5boost11enable_if_cIXsrNS4_14is_convertibleIT_jEE5valueEvE4typeERKS7_]+0x2c): undefined reference tovoid cuv::detail::entryset(unsigned int, unsigned long, unsigned int, cuv::host_memory_space)' /tmp/ccxiUJdU.o: In function void cuv::fill<float, cuv::host_memory_space, cuv::row_major, int>(cuv::tensor<float, cuv::host_memory_space, cuv::row_major>&, int const&)': program.cpp:(.text._ZN3cuv4fillIfNS_17host_memory_spaceENS_9row_majorEiEEvRNS_6tensorIT_T0_T1_EERKT2_[_ZN3cuv4fillIfNS_17host_memory_spaceENS_9row_majorEiEEvRNS_6tensorIT_T0_T1_EERKT2_]+0x39): undefined reference tovoid cuv::apply_0ary_functor<float, cuv::host_memory_space>(cuv::tensor<float, cuv::host_memory_space, cuv::row_major>&, cuv::NullaryFunctor const&, float const&)' /tmp/ccxiUJdU.o: In function cuv::reference<float, cuv::dev_memory_space>::operator float() const': program.cpp:(.text._ZNK3cuv9referenceIfNS_16dev_memory_spaceEEcvfEv[_ZNK3cuv9referenceIfNS_16dev_memory_spaceEEcvfEv]+0x1f): undefined reference tofloat cuv::detail::entryget(float const, unsigned long, cuv::dev_memory_space)' /tmp/ccxiUJdU.o: In function bool cuv::tensor<float, cuv::dev_memory_space, cuv::row_major>::copy_memory<cuv::host_memory_space, cuv::row_major>(cuv::tensor<float, cuv::host_memory_space, cuv::row_major> const&, bool, CUstream_st_)': program.cpp:(.text._ZN3cuv6tensorIfNS_16dev_memory_spaceENS_9row_majorEE11copy_memoryINS_17host_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st[_ZN3cuv6tensorIfNS_16dev_memory_spaceENS_9row_majorEE11copy_memoryINS_17host_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st]+0x19f): undefined reference tovoid cuv::detail::copy(float, float const, unsigned long, cuv::dev_memory_space, cuv::host_memory_space, CUstream_st)' program.cpp:(.text._ZN3cuv6tensorIfNS_16dev_memory_spaceENS_9row_majorEE11copy_memoryINS_17host_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st[_ZN3cuv6tensorIfNS_16dev_memory_spaceENS_9row_majorEE11copy_memoryINS_17host_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstreamst]+0x2a1): undefined reference to`void cuv::detail::copy2d<float, float>(float, float const_, unsigned long, unsigned long, unsigned long, unsigned long, cuv::dev_memory_space, cuv::host_memory_space, CUstreamst)' program.cpp:(.text._ZN3cuv6tensorIfNS_16dev_memory_spaceENS_9row_majorEE11copy_memoryINS_17host_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st[_ZN3cuv6tensorIfNS_16dev_memory_spaceENS_9row_majorEE11copy_memoryINS_17host_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstreamst]+0x3b1): undefined reference to `void cuv::detail::copy2d<float, float>(float, float const_, unsigned long, unsigned long, unsigned long, unsigned long, cuv::dev_memory_space, cuv::host_memory_space, CUstreamst)' program.cpp:(.text._ZN3cuv6tensorIfNS_16dev_memory_spaceENS_9row_majorEE11copy_memoryINS_17host_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st[_ZN3cuv6tensorIfNS_16dev_memory_spaceENS_9row_majorEE11copy_memoryINS_17host_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st]+0x4b9): undefined reference to `cuv::cuvAssertFailed(char const)' program.cpp:(.text._ZN3cuv6tensorIfNS_16dev_memory_spaceENS_9row_majorEE11copy_memoryINS_17host_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st[_ZN3cuv6tensorIfNS_16dev_memory_spaceENS_9row_majorEE11copy_memoryINS_17host_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstreamst]+0x4dc): undefined reference to`cuv::cuvAssertFailed(char const)' program.cpp:(.text._ZN3cuv6tensorIfNS_16dev_memory_spaceENS_9row_majorEE11copy_memoryINS_17host_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st[_ZN3cuv6tensorIfNS_16dev_memory_spaceENS_9row_majorEE11copy_memoryINS_17host_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstreamst]+0x54b): undefined reference to `void cuv::detail::copy2d<float, float>(float, float const_, unsigned long, unsigned long, unsigned long, unsigned long, cuv::dev_memory_space, cuv::host_memory_space, CUstreamst)' /tmp/ccxiUJdU.o: In function bool cuv::tensor<float, cuv::host_memory_space, cuv::row_major>::copy_memory<cuv::dev_memory_space, cuv::row_major>(cuv::tensor<float, cuv::dev_memory_space, cuv::row_major> const&, bool, CUstream_st*)': program.cpp:(.text._ZN3cuv6tensorIfNS_17host_memory_spaceENS_9row_majorEE11copy_memoryINS_16dev_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st[_ZN3cuv6tensorIfNS_17host_memory_spaceENS_9row_majorEE11copy_memoryINS_16dev_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st]+0x19f): undefined reference tovoid cuv::detail::copy(float, float const, unsigned long, cuv::host_memory_space, cuv::dev_memory_space, CUstreamst)' program.cpp:(.text._ZN3cuv6tensorIfNS_17host_memory_spaceENS_9row_majorEE11copy_memoryINS_16dev_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st[_ZN3cuv6tensorIfNS_17host_memory_spaceENS_9row_majorEE11copy_memoryINS_16dev_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstreamst]+0x2a1): undefined reference to `void cuv::detail::copy2d<float, float>(float, float const_, unsigned long, unsigned long, unsigned long, unsigned long, cuv::host_memory_space, cuv::dev_memory_space, CUstreamst)' program.cpp:(.text._ZN3cuv6tensorIfNS_17host_memory_spaceENS_9row_majorEE11copy_memoryINS_16dev_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st[_ZN3cuv6tensorIfNS_17host_memory_spaceENS_9row_majorEE11copy_memoryINS_16dev_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st]+0x3b1): undefined reference to void cuv::detail::copy2d<float, float>(float*, float const*, unsigned long, unsigned long, unsigned long, unsigned long, cuv::host_memory_space, cuv::dev_memory_space, CUstream_st*)' program.cpp:(.text._ZN3cuv6tensorIfNS_17host_memory_spaceENS_9row_majorEE11copy_memoryINS_16dev_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st[_ZN3cuv6tensorIfNS_17host_memory_spaceENS_9row_majorEE11copy_memoryINS_16dev_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st]+0x4b9): undefined reference tocuv::cuvAssertFailed(char const_)' program.cpp:(.text._ZN3cuv6tensorIfNS_17host_memory_spaceENS_9row_majorEE11copy_memoryINS_16dev_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st[_ZN3cuv6tensorIfNS_17host_memory_spaceENS_9row_majorEE11copy_memoryINS_16dev_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstreamst]+0x4dc): undefined reference to `cuv::cuvAssertFailed(char const)' program.cpp:(.text._ZN3cuv6tensorIfNS_17host_memory_spaceENS_9row_majorEE11copy_memoryINS_16dev_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st[_ZN3cuv6tensorIfNS_17host_memory_spaceENS_9row_majorEE11copy_memoryINS_16dev_memory_spaceES2_EEbRKNS0_IfT_T0_EEbP11CUstream_st]+0x54b): undefined reference to void cuv::detail::copy2d<float, float>(float*, float const*, unsigned long, unsigned long, unsigned long, unsigned long, cuv::host_memory_space, cuv::dev_memory_space, CUstream_st*)' /tmp/ccxiUJdU.o: In functionboost::enable_if_c<boost::is_convertible<unsigned long, int>::value, void>::type cuv::reference<int, cuv::host_memory_space>::operator=(unsigned long const&)': program.cpp:(.text._ZN3cuv9referenceIiNS_17host_memory_spaceEEaSImEEN5boost11enable_if_cIXsrNS4_14is_convertibleITiEE5valueEvE4typeERKS7[_ZN3cuv9referenceIiNS_17host_memory_spaceEEaSImEEN5boost11enable_if_cIXsrNS4_14is_convertibleITiEE5valueEvE4typeERKS7]+0x2c): undefined reference to void cuv::detail::entry_set<int>(int*, unsigned long, int, cuv::host_memory_space)' /tmp/ccxiUJdU.o: In functionvoid cuv::memory<float, cuv::dev_memory_space>::copy2d_from<float, cuv::host_memoryspace>(float const, unsigned long, unsigned long, unsigned long, unsigned long, cuv::host_memory_space, CUstreamst)': program.cpp:(.text._ZN3cuv6memoryIfNS_16dev_memory_spaceEE11copy2d_fromIfNS_17host_memory_spaceEEEvPKT_mmmmT0_P11CUstream_st[_ZN3cuv6memoryIfNS_16dev_memory_spaceEE11copy2d_fromIfNS_17host_memory_spaceEEEvPKT_mmmmT0_P11CUstream_st]+0x51): undefined reference to void cuv::detail::copy2d<float, float>(float*, float const*, unsigned long, unsigned long, unsigned long, unsigned long, cuv::dev_memory_space, cuv::host_memory_space, CUstream_st*)' /tmp/ccxiUJdU.o: In functionvoid cuv::memory<float, cuv::host_memory_space>::copy2d_from<float, cuv::dev_memoryspace>(float const, unsigned long, unsigned long, unsigned long, unsigned long, cuv::dev_memory_space, CUstreamst)': program.cpp:(.text._ZN3cuv6memoryIfNS_17host_memory_spaceEE11copy2d_fromIfNS_16dev_memory_spaceEEEvPKT_mmmmT0_P11CUstream_st[_ZN3cuv6memoryIfNS_17host_memory_spaceEE11copy2d_fromIfNS_16dev_memory_spaceEEEvPKT_mmmmT0_P11CUstream_st]+0x51): undefined reference to void cuv::detail::copy2d<float, float>(float*, float const*, unsigned long, unsigned long, unsigned long, unsigned long, cuv::host_memory_space, cuv::dev_memory_space, CUstream_st*)' /tmp/ccxiUJdU.o: In functionvoid cuv::linear_memory<unsigned int, cuv::host_memory_space>::copy_from<unsigned int, cuv::host_memory_space>(cuv::linear_memory<unsigned int, cuv::host_memory_space> const&, CUstreamst) const': program.cpp:(.text._ZNK3cuv13linear_memoryIjNS_17host_memory_spaceEE9copy_fromIjS1_EEvRKNS0_IT_T0_EEP11CUstream_st[_ZNK3cuv13linear_memoryIjNS_17host_memory_spaceEE9copy_fromIjS1_EEvRKNS0_IT_T0_EEP11CUstreamst]+0x54): undefined reference to `void cuv::detail::copy(unsigned int, unsigned int const_, unsigned long, cuv::host_memory_space, cuv::host_memory_space, CUstreamst)' /tmp/ccxiUJdU.o: In function void cuv::memory<float, cuv::dev_memory_space>::copy_from<float, cuv::host_memory_space>(float const*, unsigned long, cuv::host_memory_space, CUstream_st*)': program.cpp:(.text._ZN3cuv6memoryIfNS_16dev_memory_spaceEE9copy_fromIfNS_17host_memory_spaceEEEvPKT_mT0_P11CUstream_st[_ZN3cuv6memoryIfNS_16dev_memory_spaceEE9copy_fromIfNS_17host_memory_spaceEEEvPKT_mT0_P11CUstream_st]+0x38): undefined reference tovoid cuv::detail::copy(float, float const, unsigned long, cuv::dev_memory_space, cuv::host_memory_space, CUstreamst)' /tmp/ccxiUJdU.o: In function void cuv::memory<float, cuv::host_memory_space>::copy_from<float, cuv::dev_memory_space>(float const_, unsigned long, cuv::dev_memory_space, CUstream_st_)': program.cpp:(.text._ZN3cuv6memoryIfNS_17host_memory_spaceEE9copy_fromIfNS_16dev_memory_spaceEEEvPKT_mT0_P11CUstream_st[_ZN3cuv6memoryIfNS_17host_memory_spaceEE9copy_fromIfNS_16dev_memory_spaceEEEvPKT_mT0_P11CUstream_st]+0x38): undefined reference tovoid cuv::detail::copy(float, float const, unsigned long, cuv::host_memory_space, cuv::dev_memory_space, CUstreamst)' collect2: error: ld returned 1 exit status

Any idea how to fix this? I'm thinking the python issue is missing a linking library to boost in the Makefile but I don't know how to fix that. I have no idea about the second error

[temporaer]

regarding the cuv_python error, I cannot reproduce it. can you add system to the boost library list in cuv_python/CMakeLists.txt and try again?

[temporaer]

regarding the second error, can you paste the program you're writing and how you tried to compile/link?

[JT17]

g++ -I /usr/local/cuda-6.0/ program.cpp -lboost_system

include

using namespace cuv;

int main(void){ tensor<float,host_memory_space> h(extents[8][5]); tensor<float,dev_memory_space> d(extents[8][5]); h=0; d=h; sequence(d); h=d; for(int i=0; i<h.size(); i++){ assert(d[i]==h[i]);
} return 0; }

[JT17]

Sorry this might be a stupid question but for the python fix would it be changing these lines? SET(CPACK_DEBIAN_PACKAGE_DEPENDS "libboost-dev, libblas-dev, libpng-dev, libjpeg-dev" ) SET(CPACK_DEBIAN_PACKAGE_SUGGESTS "cimg-dev, python-dev, libboost-python-dev" ) in CMakeLists.txt?

[temporaer]

if you want to compile a c++ program using cuv, you have to link to cuv as well. Try: g++ -I /usr/local/cuda-6.0/ program.cpp -lcuv

[temporaer]

The debian package dependencies are irrelevant for your problem I believe. Did you try adding system to the line I described?

[JT17]

Okay thanks the C++ code compiles now. As for adding system the Boost_LIBRARIES line is commented out in the TARGET_LINK_LIBRARIES line of the makefile. Could that be the issue?

[temporaer]

good point. The reason it is commented is that cuv is already linked to all of the boost libraries. Since cuv_python is linked to cuv, no further linking with boost should be necessary. It still weird. You can check which libraries it actually tries to link by running make VERBOSE=1 cuv_python (you may have to touch some .cpp file in cuv_python directory to force a rebuild). Could you post the line which does the linking here?

[JT17]

ah okay. as far as I can tell these are the linked libraries (boost_system is not one from what I can see) -lboost_date_time -lboost_python -lboost_date_time -lboost_python -lpython2.7 /usr/local/cuda-6.0/lib64/libcublas.so -lf77blas -latlas -lX11 -lpthread -lpng -lz ../3rd_party/cudaconv2/libtp_cudaconv2.so.0.9 -lcblas ../3rd_party/cuda_ndarray/libtp_theano.so.0.9 /usr/local/cuda-6.0/lib64/libcudart.so -lcuda -lpng -lpython2.7 -lf77blas -latlas -Wl,-rpath,/home/mobile/Downloads/CUV/build/debug/src/cuv:/usr/local/cuda-6.0/lib64:/home/mobile/Downloads/CUV/build/debug/src/3rd_party/cudaconv2:/home/mobile/Downloads/CUV/build/debug/src/3rd

[temporaer]

Are you sure boost.system is installed on your system?

[JT17]

yeah I've used it in the past and the C++ version of CUV compiles now

[temporaer]

What happens if you copy the linker line, add boost system, and run it? I understand this would only be a temporary fix, but just to ensure that this works...

[JT17]

I might have done it wrong but when I tried to just run that linker line it doesn't compile correctly because all of the .o files are missing

[temporaer]

you're probably not in the correct directory, when you run make it tells you a line like "Entering directory ...." before the command you copied. Please switch to that directory before running the modified command.

[JT17]

Oh good point. It still doesn't work though. I ran this: /usr/bin/c++ -fPIC -fPIC -g -shared -Wl,-soname,_cuv_python.so -o _cuv_python.so CMakeFiles/cuv_python.dir/python_bindings.cpp.o CMakeFiles/cuv_python.dir/export_tensor.cpp.o CMakeFiles/cuv_python.dir/export_cuda_array.cpp.o CMakeFiles/cuv_python.dir/export_matrix_ops.cpp.o CMakeFiles/cuv_python.dir/export_tensor_ops.cpp.o CMakeFiles/cuv_python.dir/export_random.cpp.o CMakeFiles/cuv_python.dir/export_convolution_ops.cpp.o CMakeFiles/cuv_python.dir/export_image_ops.cpp.o CMakeFiles/cuv_python.dir/export_tools.cpp.o CMakeFiles/cuv_python.dir/export_libs_rbm.cpp.o CMakeFiles/cuv_python.dir/export_libs_kmeans.cpp.o CMakeFiles/cuv_python.dir/export_libs_kernels.cpp.o CMakeFiles/cuv_python.dir/export_libs_cimg.cpp.o ../cuv/libcuv.so.0.9 -lboost_date_time -lboost_python -lboost_date_time -lboost_python -lboost_system -lpython2.7 /usr/local/cuda-6.0/lib64/libcublas.so -lf77blas -latlas -lX11 -lpthread -lpng -lz ../3rd_party/cudaconv2/libtp_cudaconv2.so.0.9 -lcblas ../3rd_party/cuda_ndarray/libtp_theano.so.0.9 /usr/local/cuda-6.0/lib64/libcudart.so -lcuda -lpng -lpython2.7 -lf77blas -latlas -Wl,-rpath,/home/mobile/Downloads/CUV/build/debug/src/cuv:/usr/local/cuda-6.0/lib64:/home/mobile/Downloads/CUV/build/debug/src/3rd_party/cudaconv2:/home/mobile/Downloads/CUV/build/debug/src/3rd_party/cuda_ndarray:

but when I try import cuv_python I get /usr/local/lib/libtp_theano.so.0: undefined symbol: _ZN5boost6system15system_categoryEv

Could it be that my theano is broken not CUV?

[temporaer]

ok, that sounds like a promising idea. Can you please try the following:

in src/3rd_party/cuda_ndarray, edit CMakeLists.txt and add ${Boost_LIBRARIES} to the TARGET_LINK_LIBRARIES directive?

[JT17]

unfortunately that did not work either

[temporaer]

is boost_system part of the link command for tp_theano,so?

[JT17]

I'm not sure. Where is that defined? In CUV or in theano?

[temporaer]

cuv includes a copy of theano's cuda_ndarray source code in src/3rd_party. The link command is also there. By the way, when you try whether a change works, do you also install/copy to /usr/local? It seems you load your libraries from there...

[JT17]

I think I'm reinstalling the /usr/local copy every time. I have run make clean and rebuilt everything for most of the fixes. That should rebuild the /usr/local copy right?

[temporaer]

a make clean should not be necessary, cmake detects when linker commands have changes and should redo only those. a build does not imply an install, so I suspect you're using outdated versions. Can you make sure by looking at the modification time of the libs you use, i.e. by ls -al /usr/local/lib/libcuv.so.0.9 ?

[JT17]

Oh yeah you're right it is not an updated version that was really dumb of me. Do I need to run make install every time or is there a faster way?

[temporaer]

no, you just have to tell your programs where to look for the libraries.

• For compiling c++ programs, you need to add -L path-to-libcuv.so (most likely cuv/build/src/cuv),
• For running the program lateron, set LD_LIBRARY_PATH to the location of libcuv.so (same as above).
• To import cuv_python from python, set PYTHONPATH to the directory to the directory /above/ the one containing _cuv_python.so (most likely cuv/build/src)

[JT17]

Okay that worked thank you so much sorry for not realizing that earlier

[temporaer]

No problem. I'll push the fix later today.