Hey Aref, it seems that eigen3 is downloaded and used.
What happens when you just 'import modshogun' within your python? Sergey On Sun, Jan 24, 2016 at 5:00 PM, Aref Nammari <[email protected]> wrote: > Hi, > > Here is the the cmake output and other details. > > Below is the cmake command issued. > > aref@aref-Inspiron-N5010:~/shogun-develop/release$ cmake > -DCMAKE_INSTALL_PREFIX="/usr/local" -DPythonModular=ON -DRModular=ON > -DBUNDLE_EIGEN=ON .. >>cmake_out.txt 2>&1 > aref@aref-Inspiron-N5010:~/shogun-develop/release$ > > > _______________________________________________________________________________________________________________ > > This is the build drectory after cmake > > aref@aref-Inspiron-N5010:~/shogun-develop/release$ ls > CMakeCache.txt cmake_out.txt doc Makefile > CMakeFiles CPackConfig.cmake Eigen3 src > cmake_install.cmake CPackSourceConfig.cmake examples > aref@aref-Inspiron-N5010:~/shogun-develop/release$ > > > ________________________________________________________________________________________________________________ > > This is the output of cmake written to file. > > > -- The C compiler identification is GNU 4.8.4 > -- The CXX compiler identification is GNU 4.8.4 > -- Check for working C compiler: /usr/bin/cc > -- Check for working C compiler: /usr/bin/cc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Found CCache: /usr/bin/ccache > -- Found SWIG: /usr/bin/swig2.0 (found suitable version "2.0.11", minimum > required is "2.0.5") > -- Performing Test _HAS_CXX11_FLAG > -- Performing Test _HAS_CXX11_FLAG - Success > -- Checking C++11 support for "__func__" > -- Checking C++11 support for "__func__": works > -- Checking C++11 support for "atomic" > -- Checking C++11 support for "atomic": works > -- Checking C++11 support for "auto" > -- Checking C++11 support for "auto": works > -- Checking C++11 support for "auto_ret_type" > -- Checking C++11 support for "auto_ret_type": works > -- Checking C++11 support for "class_override_final" > -- Checking C++11 support for "class_override_final": not supported > -- Checking C++11 support for "constexpr" > -- Checking C++11 support for "constexpr": works > -- Checking C++11 support for "cstdint" > -- Checking C++11 support for "cstdint": works > -- Checking C++11 support for "decltype" > -- Checking C++11 support for "decltype": works > -- Checking C++11 support for "initializer_list" > -- Checking C++11 support for "initializer_list": works > -- Checking C++11 support for "lambda" > -- Checking C++11 support for "lambda": works > -- Checking C++11 support for "long_long" > -- Checking C++11 support for "long_long": works > -- Checking C++11 support for "nullptr" > -- Checking C++11 support for "nullptr": works > -- Checking C++11 support for "regex" > -- Checking C++11 support for "regex": not supported > -- Checking C++11 support for "rvalue-references" > -- Checking C++11 support for "rvalue-references": works > -- Checking C++11 support for "sizeof_member" > -- Checking C++11 support for "sizeof_member": works > -- Checking C++11 support for "static_assert" > -- Checking C++11 support for "static_assert": works > -- Checking C++11 support for "variadic_templates" > -- Checking C++11 support for "variadic_templates": works > -- Looking for C++ include unordered_map > -- Looking for C++ include unordered_map - found > -- Using system's malloc > -- Looking for isfinite > -- Looking for isfinite - not found > -- Looking for isinf > -- Looking for isinf - found > -- Looking for isnan > -- Looking for isnan - found > -- Looking for signgam > -- Looking for signgam - found > -- Looking for fdopen > -- Looking for fdopen - found > -- Looking for log2 > -- Looking for log2 - found > -- Looking for powl > -- Looking for powl - found > -- Looking for lgammal > -- Looking for lgammal - found > -- Looking for sqrtl > -- Looking for sqrtl - found > -- Looking for finite > -- Looking for finite - found > -- Looking for isfinite > -- Looking for isfinite - not found > -- Looking for isinf > -- Looking for isinf - found > -- Looking for isnan > -- Looking for isnan - found > -- Performing Test HAVE_STD_ISINF > -- Performing Test HAVE_STD_ISINF - Success > -- Performing Test HAVE_STD_ISFINITE > -- Performing Test HAVE_STD_ISFINITE - Success > -- Performing Test HAVE_STD_ISNAN > -- Performing Test HAVE_STD_ISNAN - Success > -- Looking for xmmintrin.h > -- Looking for xmmintrin.h - found > -- Looking for emmintrin.h > -- Looking for emmintrin.h - found > -- Looking for arc4random > -- Looking for arc4random - not found > -- Found GDB: /usr/bin/gdb > -- Could NOT find MOSEK (missing: MOSEK_DIR MOSEK_INCLUDE_DIR > MOSEK_LIBRARY) > -- Looking for include file pthread.h > -- Looking for include file pthread.h - found > -- Looking for pthread_create > -- Looking for pthread_create - not found > -- Looking for pthread_create in pthreads > -- Looking for pthread_create in pthreads - not found > -- Looking for pthread_create in pthread > -- Looking for pthread_create in pthread - found > -- Found Threads: TRUE > -- Try OpenMP C flag = [-fopenmp] > -- Performing Test OpenMP_FLAG_DETECTED > -- Performing Test OpenMP_FLAG_DETECTED - Success > -- Try OpenMP CXX flag = [-fopenmp] > -- Performing Test OpenMP_FLAG_DETECTED > -- Performing Test OpenMP_FLAG_DETECTED - Success > -- Found OpenMP: -fopenmp > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.26") > -- Looking for dgemm_ > -- Looking for dgemm_ - found > -- A library with BLAS API found. > -- Looking for cheev_ > -- Looking for cheev_ - found > -- A library with LAPACK API found. > -- Looking for clapack_dpotrf in /usr/lib/atlas-base/liblapack_atlas.so.3 > -- Looking for clapack_dpotrf in /usr/lib/atlas-base/liblapack_atlas.so.3 > - found > -- Could NOT find ATLAS (missing: ATLAS_INCLUDES) > -- Found CBLAS: /usr/lib/libcblas.so.3 > -- Looking for cblas_dsyrk in /usr/lib/libcblas.so.3 > -- Looking for cblas_dsyrk in /usr/lib/libcblas.so.3 - found > -- Found GLPK: /usr/lib/x86_64-linux-gnu/libglpk.so > -- Could NOT find CPLEX (missing: CPLEX_LIBRARY CPLEX_INCLUDE_DIR) > -- Found Arpack : /usr/lib/libarpack.so > -- Could NOT find OPENCL (missing: OPENCL_INCLUDE_DIR) > -- Could NOT find ViennaCL (missing: VIENNACL_INCLUDE_DIR > OPENCL_INCLUDE_DIRS OPENCL_LIBRARIES) (Required is at least version "1.5.0") > -- checking for one of the modules 'libColPack>=1.0.9;ColPack>=1.0.9' > -- Could NOT find NLOPT (missing: NLOPT_LIBRARY NLOPT_INCLUDE_DIR) > -- Could NOT find LPSOLVE (missing: LPSOLVE_LIBRARIES > LPSOLVE_INCLUDE_DIR) > -- Could NOT find ColPack (missing: COLPACK_LIBRARIES COLPACK_LIBRARY_DIR > COLPACK_INCLUDE_DIR) > -- Could NOT find ARPREC (missing: ARPREC_LIBRARIES ARPREC_INCLUDE_DIR) > -- Found Doxygen: /usr/bin/doxygen (found suitable version "1.8.6", > minimum required is "1.8.6") > -- Found PythonInterp: /usr/bin/python (found version "2.7.6") > -- checking for one of the modules 'libjson>=0.11;json>=0.11;json-c>=0.11' > -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version > "2.9.1") > -- Found HDF5: > /usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so > > -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version > "7.35.0") > -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8") > -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version > "1.0.6") > -- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so > -- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so - > found > -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so > -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so - > found > -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so > -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so - > found > -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so > -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so - > found > -- Found LibLZMA: /usr/include (found version "5.1.0") > -- Could NOT find SNAPPY (missing: SNAPPY_LIBRARIES SNAPPY_INCLUDE_DIR) > -- Lzo includes and libraries NOT found. > -- Spinlock support found > -- Found PROTOBUF: /usr/lib/x86_64-linux-gnu/libprotobuf.so > -- Supported backend(s) for linear algebra NOT FOUND/NOT ENABLED > -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found > version "2.7.6") > -- Found NumPy: version "1.8.2" > /usr/lib/python2.7/dist-packages/numpy/core/include > -- Found R: /usr/bin/R > -- > =================================================================================================================== > -- Summary of Configuration Variables > -- > -- The following OPTIONAL packages have been found: > > * CCache > * GDB > * OpenMP > * BLAS > * LAPACK > * CBLAS > * GLPK > * ARPACK > * Doxygen (required version >= 1.8.6) > * LibXml2 > * HDF5 > * CURL > * ZLIB > * BZip2 > * LibLZMA > * Spinlock > * Threads > * Protobuf > > -- The following REQUIRED packages have been found: > > * SWIG (required version >= 2.0.5) > * PythonLibs > * PythonInterp > * NumPy > * R > > -- The following OPTIONAL packages have not been found: > > * Mosek > * Atlas > * CPLEX > * ViennaCL (required version >= 1.5.0) > * NLopt > * LpSolve > * ColPack > * ARPREC > * SNAPPY > * LZO > > -- The following REQUIRED packages have not been found: > > * OpenCL > > -- > =================================================================================================================== > -- Enabled Integration > -- OpenCV Integration is OFF - enable with -DOpenCV=ON > -- > =================================================================================================================== > -- Enabled Interfaces > -- libshogun is ON > -- python modular is ON > -- octave modular is OFF - enable with -DOctaveModular=ON > -- java modular is OFF - enable with -DJavaModular=ON > -- perl modular is OFF - enable with -DPerlModular=ON > -- ruby modular is OFF - enable with -DRubyModular=ON > -- csharp modular is OFF - enable with -DCSharpModular=ON > -- R modular is ON > -- lua modular is OFF - enable with -DLuaModular=ON > -- > -- Enabled legacy interfaces > -- cmdline static is OFF - enable with -DCmdLineStatic=ON > -- python static is OFF - enable with -DPythonStatic=ON > -- octave static is OFF - enable with -DOctaveStatic=ON > -- matlab static is OFF - enable with -DMatlabStatic=ON > -- R static is OFF - enable with -DRStatic=ON > -- > =================================================================================================================== > -- To compile shogun type > -- make > -- > -- To install shogun to /usr/local type > -- make install > -- > -- or to install to a custom directory > -- make install DESTDIR=/my/special/path > -- (or rerun cmake with -DCMAKE_INSTALL_PREFIX=/my/special/path) to just > change the prefix > -- > =================================================================================================================== > -- Configuring done > -- Generating done > -- Build files have been written to: /home/aref/shogun-develop/release > > On Sun, Jan 24, 2016 at 6:07 AM, Aref Nammari <[email protected]> > wrote: > >> I am not sure what do you mean by "cake output". I removed the >> LaplacianInferenceMethod from the import statement (it wasn't even used in >> the rest of the script) and everything works. I tried all the examples in >> the modular_python graphical including eigenfaces.py and everything seems >> to work--I had to modify some things because some of the examples used >> functions that were changed or renamed and LaplacianInferenceMethod could >> be one of those. Am I right to believe that there is not an issue with >> Eigen but rather the issue us with the examples not following recent >> changes in shogun 4.0.0? >> >> On Sun, Jan 24, 2016 at 3:31 AM, Heiko Strathmann < >> [email protected]> wrote: >> >>> Hi >>> >>> Ok, that's one down. Can you post your cake output? Seems like Eigen >>> wasn't detected >>> >>> H >>> >>> >>> On Saturday, 23 January 2016, Aref Nammari <[email protected]> >>> wrote: >>> >>>> Hi Heiko, >>>> >>>> I downloaded and built the latest git develop branch and got the same >>>> results. It is the "from modshogun import LaplacianInferenceMethod " that >>>> is the source of the error--cannot import error. >>>> >>>> Aref >>>> >>>> On Fri, Jan 22, 2016 at 8:42 AM, Aref Nammari <[email protected]> >>>> wrote: >>>> >>>>> Hello Heiko, >>>>> >>>>> Thank you for the reply. >>>>> I believe the problem is not related to Eigen3. I took a look at the >>>>> script I was trying to run and tried to see where the error was. I >>>>> narrowed >>>>> it down to an import statement " from modshogun import >>>>> LaplacianInferenceMethod ". This import causes a not found error. The >>>>> exception in the script returns 'Eigen3 needed for Gaussian Processes' >>>>> which led me to believe that there was a problem in the build. I think the >>>>> build is OK. However, I am not quite sure why the import does not work. >>>>> The >>>>> example I was trying to run is in >>>>> examples/undocumented/python_modular/graphical/classifier_gaussian_process_binary_classification.py >>>>> I will try the latest version in git and see if the problem persists. >>>>> >>>>> >>>>> Thanks, >>>>> Aref >>>>> >>>>> On Fri, Jan 22, 2016 at 3:52 AM, Heiko Strathmann < >>>>> [email protected]> wrote: >>>>> >>>>>> Hi Aref, >>>>>> >>>>>> This is weird, can you post a gist with the cmake output somewhere? >>>>>> >>>>>> Also, could you try to do the same thing again with the latest git >>>>>> version of shogun? >>>>>> >>>>>> H >>>>>> >>>>>> 2016-01-21 20:14 GMT+00:00 Aref Nammari <[email protected]>: >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> >>>>>>> >>>>>>> I have installed shogun-toolbox version 4.0.0 downloaded from >>>>>>> shogun-toolbox.org. I installed python –modular and RModular. No >>>>>>> errors were reported during the build process. I tried several examples >>>>>>> and >>>>>>> they seem to work with the exception of examples requiring Eigen3. >>>>>>> During >>>>>>> the build process I have turned BUNDLE_EIGEN ON and the package appears >>>>>>> to >>>>>>> have been downloaded but when I try some of the examples requiring >>>>>>> Eigen3 >>>>>>> (such Gaussian_processe examples) I get an error “Gaussian processes >>>>>>> require Eigen3 be installed). I am not sure what the problem is or how >>>>>>> to >>>>>>> solve it. Any help in this area is appreciated. I am running python >>>>>>> 2.7.6 >>>>>>> and also have Anaconda installed. The OS is Ubuntu 14.04 LTS. >>>>>>> >>>>>>> >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Aref >>>>>>> >>>>>> >>>>>> >>>>> >>>> >> >
