TRIQS / triqs_0.x

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Undefined references to cblas calls during make #95

Closed vkv-zz closed 11 years ago

vkv-zz commented 11 years ago

Dear users,

After the TRIQS build (which throws out a few warnings), I get the following errors, among others, when trying to "make -j4":

... CMakeFiles/a_x_ty_nopy.dir/a_x_ty.cpp.o: In function `void triqs::arrays::triqs_arrays_assign_delegation > >(triqs::arrays::matrix_view >&, triqs::arrays::a_x_ty_lazy >, triqs::arrays::vector_view > > const&)': a_x_ty.cpp:(.text._ZN5triqs6arrays30triqs_arrays_assign_delegationINS0_11matrix_viewIdNS0_6Option7optionsINS0_3Tag7FortranENS5_12shared_blockENS5_12NoBoundCheckEvEEEEEEvRT_RKNS0_11a_x_ty_lazyIdNS0_11vector_viewIdNS4_INS5_1CES7_S8_vEEEESH_EE[_ZN5triqs6arrays30triqs_arrays_assign_delegationINS0_11matrix_viewIdNS0_6Option7optionsINS0_3Tag7FortranENS5_12shared_blockENS5_12NoBoundCheckEvEEEEEEvRT_RKNS0_11a_x_ty_lazyIdNS0_11vector_viewIdNS4_INS5_1CES7_S8_vEEEESH_EE]+0x401): undefined reference to`cblas_dger' collect2: error: ld returned 1 exit status make[2]: **\* [triqs/arrays/test/C++/a_x_ty_nopy] Error 1 make[1]: **\* [triqs/arrays/test/C++/CMakeFiles/a_x_ty_nopy.dir/all] Error 2 I believe most of the dependencies have the required versions on my machine (Suse 12.2). Any suggestions on debugging this error will be appreciated. Thanks, Vipin P.S: The build-time warnings (possibly irrelevant), among others, are: ... CMake Warning at cmake/FindPythonModuleEmbeddingTool.cmake:19 (add_library): Cannot generate a safe runtime search path for target _pytriqs_Solver_HybridizationExpansion because files in some directories may conflict with libraries in implicit directories: ``` runtime library [libhdf5.so.7] in /usr/lib64 may be hidden by files in: /usr/lib64/mpi/gcc/openmpi/lib64 runtime library [libhdf5_hl.so.7] in /usr/lib64 may be hidden by files in: /usr/lib64/mpi/gcc/openmpi/lib64 ``` Some of these libraries may not be found correctly. Call Stack (most recent call first): cmake/FindPythonModuleEmbeddingTool.cmake:37 (python_build_module) pytriqs/Solvers/HybridizationExpansion/CMakeLists.txt:55 (python_build_module_optional) -- Generating done -- Build files have been written to: /users/varma/Desktop/Applications_Libraries/triqs_build
parcollet commented 11 years ago

Hi,

1 )You need to install the cblas library. How depends on your distribution ...

@mferrero : we have to stop the cmake if this lib is not present, it will be a lot clearer...

2) The warning : you seem to have several hdf5 on your machine, which is not recommended...

vkv-zz commented 11 years ago

Hi,

Thanks for the reply.

It seems I do have cblas. This is what yast gives:

/usr/include/cblas.h /usr/include/cblas_f77.h /usr/lib64/libcblas.a /usr/lib64/libcblas.so /usr/lib64/libcblas_pic.a /usr/share/doc/packages/cblas-devel /usr/share/doc/packages/cblas-devel/README The result of 'locate cblas' is: /usr/include/gsl/gsl_cblas.h /usr/lib/debug/usr/lib64/python2.7/site-packages/scipy/lib/blas/cblas.so.debug /usr/lib/debug/usr/lib64/python2.7/site-packages/scipy/linalg/cblas.so.debug /usr/lib/debug/usr/lib64/python3.2/site-packages/scipy/lib/blas/cblas.cpython-32mu.so.debug /usr/lib/debug/usr/lib64/python3.2/site-packages/scipy/linalg/cblas.cpython-32mu.so.debug /usr/lib64/libgslcblas.so /usr/lib64/libgslcblas.so.0 /usr/lib64/libgslcblas.so.0.0.0 /usr/lib64/python2.7/site-packages/scipy/lib/blas/cblas.so /usr/lib64/python2.7/site-packages/scipy/linalg/cblas.so /usr/lib64/python3.2/site-packages/scipy/lib/blas/cblas.cpython-32mu.so /usr/lib64/python3.2/site-packages/scipy/linalg/cblas.cpython-32mu.so /usr/local/maple9/bin.IBM_INTEL_LINUX/libcblas.so /usr/local/maple9/bin.IBM_INTEL_LINUX/libcblasmp.so /usr/src/debug/scipy-0.11.0/build/py3k/build/src.linux-x86_64-3.2/build/src.linux-x86_64-3.2/scipy/lib/blas/cblasmodule.c /usr/src/debug/scipy-0.11.0/build/py3k/build/src.linux-x86_64-3.2/build/src.linux-x86_64-3.2/scipy/linalg/cblasmodule.c /usr/src/debug/scipy-0.11.0/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/lib/blas/cblasmodule.c /usr/src/debug/scipy-0.11.0/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/linalg/cblasmodule.c As you say, there are multiple hdf5 installed. Do you think this might cause this error or any other known problems? Regards, Vipin
mferrero commented 11 years ago

Hi, I think we will need more information. Can you provide:

1) The full output and arguments you used for the cmake command 2) The CMakeCache.txt file somewhere on gist 3) The output of the make command

This will help us figure out what is going wrong. It looks like the cmake could find the cblas header but not the library. You might have to specify it by hand.

vkv-zz commented 11 years ago

Hi,

I have uploaded the inputs and outputs of make and cmake, and the entire CMakeCache.txt at https://gist.github.com/4126920

Any suggestions will be greatly appreciated.

Regards, Vipin

mferrero commented 11 years ago

You might want to try this:

cmake /users/varma/Desktop/Applications_Libraries/TRIQS-master -DLAPACK_LIBRARY="/usr/lib64/liblapack.so;/usr/lib64/libpthread.so" -DBLAS_LIBRARY="/usr/lib64/libcblas.so" -DBOOST_SOURCE_DIR=/users/varma/Desktop/Applications_Libraries/boost_1_49_0
vkv-zz commented 11 years ago

I started a new cmake and make with the above command, but strangely now the make process fails at an earlier point, with "undefined reference to zgemm_" while building dmftproj. The errors are:

Scanning dependencies of target triqs_HubbardI Scanning dependencies of target dmftproj Scanning dependencies of target triqs_Wien2k Scanning dependencies of target boost_for_triqs [ 1%] [ 1%] Generating hubbard_I.so See /users/varma/Desktop/Applications_Libraries/triqs_buildII/pytriqs/Solvers/HubbardI/F90/f2pyBuild.log for logs Generating vertex.so See /users/varma/Desktop/Applications_Libraries/triqs_buildII/pytriqs/Wien2k/F90/f2pyBuild.log for logs [ 1%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/modules.f.o [ 1%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/outband.f.o [ 2%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/outbwin.f.o [ 2%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/outputqmc.f.o [ 2%] Built target triqs_Wien2k [ 3%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/orthogonal_wannier.f.o [ 3%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/rot_dens.f.o [ 3%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/symmetrize_mat.f.o [ 4%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/density.f.o [ 4%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/archive_exception.cpp.o [ 4%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_archive.cpp.o [ 4%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/rot_projectmat.f.o [ 5%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_iarchive.cpp.o [ 5%] Built target triqs_HubbardI [ 6%] [ 6%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/orthogonal.f.o Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/set_projections.f.o [ 6%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/read_k_list.f.o [ 7%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/timeinv.f.o [ 7%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_iserializer.cpp.o [ 8%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_oarchive.cpp.o [ 8%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/set_rotloc.f.o [ 8%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_oserializer.cpp.o [ 8%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_pointer_iserializer.cpp.o [ 9%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_pointer_oserializer.cpp.o [ 9%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_serializer_map.cpp.o [ 10%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/setsym.f.o [ 10%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_text_iprimitive.cpp.o [ 10%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/set_ang_trans.f.o [ 10%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/readcomline.f.o [ 11%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/dmftproj.f.o [ 12%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_text_oprimitive.cpp.o [ 12%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_text_wiprimitive.cpp.o [ 13%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_text_woprimitive.cpp.o [ 13%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/basic_xml_archive.cpp.o [ 13%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/binary_iarchive.cpp.o [ 14%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/binary_oarchive.cpp.o Linking Fortran executable dmftproj /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: CMakeFiles/dmftproj.dir/orthogonal_wannier.f.o: undefined reference to symbol 'zgemm_' /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: note: 'zgemm_' is defined in DSO /usr/lib64/libblas.so.3 so try adding it to the linker command line /usr/lib64/libblas.so.3: could not read symbols: Invalid operation collect2: error: ld returned 1 exit status make[2]: **\* [pytriqs/Wien2k/dmftproj/dmftproj] Error 1 make[1]: **\* [pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/all] Error 2 make[1]: **\* Waiting for unfinished jobs.... [ 14%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/binary_wiarchive.cpp.o [ 15%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/binary_woarchive.cpp.o [ 15%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/codecvt_null.cpp.o [ 15%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/extended_type_info.cpp.o [ 16%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/extended_type_info_no_rtti.cpp.o [ 16%] [ 17%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/extended_type_info_typeid.cpp.o Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/polymorphic_iarchive.cpp.o [ 17%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/polymorphic_oarchive.cpp.o [ 17%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/shared_ptr_helper.cpp.o [ 18%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/stl_port.cpp.o [ 18%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/text_iarchive.cpp.o [ 18%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/text_oarchive.cpp.o [ 19%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/text_wiarchive.cpp.o [ 19%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/text_woarchive.cpp.o [ 20%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/users/varma/Desktop/Applications_Libraries/boost_1_49_0/libs/serialization/src/utf8_codecvt_facet.cpp.o [ 20%] Building CXX object 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mferrero commented 11 years ago

I see. Well, we're getting there. Let's try this then

cmake /users/varma/Desktop/Applications_Libraries/TRIQS-master -DLAPACK_LIBRARY="/usr/lib64/liblapack.so;/usr/lib64/libpthread.so" -DBLAS_LIBRARY="/usr/lib64/libcblas.so;/usr/lib64/libblas.so" -DBOOST_SOURCE_DIR=/users/varma/Desktop/Applications_Libraries/boost_1_49_0
vkv-zz commented 11 years ago

Update: I had to add "/usr/lib64/libblas.so" as well to the -DBLAS_LIBRARY option and everything's gone through now. Thanks for the help.

Vipin

mferrero commented 11 years ago

Telepathy at work...