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TRIQS / triqs_0.x

DEPRECATED -- This is the repository of the older versions of TRIQS
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Installation error #81

Closed blueway39 closed 12 years ago

blueway39 commented 12 years ago

[root@hpc triqs_build]# cmake /home/joon/program/Triqs-source-boost/Triqs -DBOOST_SOURCE_DIR=/home/joon/program/Triqs-source-boost/boost_1_49_0 -DCMAKE_INSTALL_PREFIX=/home/joon/program/Triqs-source-boost/triqs_build/Triqs-Install -- Installation directory is /home/joon/program/Triqs-source-boost/triqs_build/Triqs-Install -- The C compiler identification is GNU 4.5.4 -- The CXX compiler identification is GNU 4.5.4 -- The Fortran compiler identification is GNU -- Check for working C compiler: /usr/local/bin/gcc -- Check for working C compiler: /usr/local/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/local/bin/c++ -- Check for working CXX compiler: /usr/local/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working Fortran compiler: /usr/local/bin/gfortran -- Check for working Fortran compiler: /usr/local/bin/gfortran -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /usr/local/bin/gfortran supports Fortran 90 -- Checking whether /usr/local/bin/gfortran supports Fortran 90 -- yes -- DYNAMIC Built -- CMAKE_GENERATOR: Unix Makefiles -- CMAKE_CL_64: -- CMAKE_SIZEOF_VOID_P: 8 -- CMAKE_GENERATOR: Unix Makefiles -- CMAKE_CL_64: -- Build type: Release -- Looking for rpc/rpc.h -- Looking for rpc/rpc.h - found -- Looking for stdarg.h -- Looking for stdarg.h - found -- Looking for sys/stat.h -- Looking for sys/stat.h - found -- Looking for sys/systeminfo.h -- Looking for sys/systeminfo.h - not found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for windows.h -- Looking for windows.h - not found -- Looking for C++ include valarray -- Looking for C++ include valarray - found -- Found MPI_C: /home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libmpi.so;/home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libopen-rte.so;/home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libopen-pal.so;/usr/lib64/libdl.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so
-- Found MPI_CXX: /home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libmpi_cxx.so;/home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libmpi.so;/home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libopen-rte.so;/home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libopen-pal.so;/usr/lib64/libdl.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so
-- Found MPI_Fortran: /home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libmpi_f90.so;/home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libmpi_f77.so;/home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libmpi.so;/home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libopen-rte.so;/home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libopen-pal.so;/usr/lib64/libdl.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so
-- MPI compiler was /home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/bin/mpicxx -- Found intel/mkl library -- Found FFTW: /usr/local/lib/libfftw3.a
-- Found HDF5: debug;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so;/usr/lib64/libhdf5_cpp.so;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so;/usr/lib64/libhdf5_cpp.so
-- HDF5 version found is 1.8.9 in /usr/include -- Python interpreter /opt/EPD/bin/python -- Python interpreter ok : version 2.7.3 -- PYTHON_INCLUDE_DIRS = /opt/EPD/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/EPD/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/EPD/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/EPD/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- Numpy include in /opt/EPD/lib/python2.7/site-packages/numpy/core/include -- HDF5_LIBRARIES = debug;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so;/usr/lib64/libhdf5_cpp.so;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so;/usr/lib64/libhdf5_cpp.so -- Triqs general lib detection ( but boost ) -- Adding definitions -D_LARGEFILE_SOURCE;-D_LARGEFILE64_SOURCE;-D_BSD_SOURCE;-D_FORTIFY_SOURCE=2;-D_LARGEFILE_SOURCE;-D_LARGEFILE64_SOURCE;-D_BSD_SOURCE;-D_FORTIFY_SOURCE=2 -- Adding include /home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/include;/usr/include;/opt/EPD/include/python2.7;/opt/EPD/lib/python2.7/site-packages/numpy/core/include -- Adding libs /home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libmpi_cxx.so;/home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libmpi.so;/home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libopen-rte.so;/home/sandia/mpi/intel-12.1.2/openmpi-1.4.4/lib/libopen-pal.so;/usr/lib64/libdl.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libpthread.so;debug;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so;/usr/lib64/libhdf5_cpp.so;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so;/usr/lib64/libhdf5_cpp.so;/opt/EPD/lib/python2.7/config/libpython2.7.a -- Adding library dir
-- Python modules will be installed in /home/joon/program/Triqs-source-boost/triqs_build/Triqs-Install/lib/python2.7/site-packages/pytriqs -- I am using boost sources from /home/joon/program/Triqs-source-boost/boost_1_49_0 to compile a mini boost_for_triqs -- BOOST_INCLUDE_DIR = /home/joon/program/Triqs-source-boost/boost_1_49_0 -- You are using mkl -- cblas header found at /opt/intel/mkl/10.2.5.035/include -- Found CBLAS: /opt/intel/mkl/10.2.5.035/include
-- Found Git: /usr/local/bin/git
-- Git hash 46c39ec1d3a4f187fa7ddbae7bbe9ec4444c6be1 -- Git branches :

-- Configuring incomplete, errors occurred! [root@hpc triqs_build]#

I use the 'Cent OS' and think all necessary things are installed.

I already read issues on this web, but I can't handle my error.
How can I do? Please, help me.

mferrero commented 12 years ago

Hi! I see you are trying to link against the MKL blas and lapack. CMake has often troubles to find the good linking flags. You have to give manually the linking flags. In your case, you can try to run cmake like this:

cmake /home/joon/program/Triqs-source-boost/Triqs -DBOOST_SOURCE_DIR=/home/joon/program/Triqs-source-boost/boost_1_49_0 -DCMAKE_INSTALL_PREFIX=/home/joon/program/Triqs-source-boost/triqs_build/Triqs-Install -DBLAS_LIBRARY=-Wl,--start-group;/opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_intel_lp64.a;/opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_sequential.a;/opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_core.a;-Wl,--end-group -DLAPACK_LIBRARY=/opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_solver_lp64_sequential.a -DMKL_INCLUDE_DIR=/opt/intel/mkl/10.2.5.035/include

Let me know if this help!

blueway39 commented 12 years ago

[root@hpc triqs_build]# cmake /home/joon/program/Triqs-source-boost/Triqs -DBOOST_SOURCE_DIR=/home/joon/program/Triqs-source-boost/boost_1_49_0 -DCMAKE_INSTALL_PREFIX=/home/joon/program/Triqs-source-boost/triqs_build/Triqs-Install -DBLAS_LIBRARY=-Wl,--start-group;/opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_intel_lp64.a;/opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_sequential.a;/opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_core.a;-Wl,--end-group -DLAPACK_LIBRARY=/opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_solver_lp64_sequential.a -DMKL_INCLUDE_DIR=/opt/intel/mkl/10.2.5.035/include

 ( same before )

-- **** WARNING **** -- Wien2k users : after installation of TRIQS, copy the files from -- /home/joon/program/Triqs-source-boost/triqs_build/Triqs-Install/share/triqs/Wien2k_SRC_files/SRC_templates -- to your Wien2k installation WIENROOT/SRC_templates (Cf documentation).
-- This is not handled automatically by the installation process.

-- Preparing optional python module CTHyb -- Preparing python module CTHyb -- Making pytriqs/Solvers/HybridizationExpansion/pytriqs_Solver_HybridizationExpansion.py -- Preparing the various scripts -- Configuring done -- Generating done -- Build files have been written to: /home/joon/program/Triqs-source-boost/triqs_build bash: /opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_intel_lp64.a: Permission denied bash: /opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_sequential.a: Permission denied bash: /opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_core.a: Permission denied bash: -Wl,--end-group: command not found

[root@hpc triqs_build]# make -j12 Scanning dependencies of target triqs_Wien2k Scanning dependencies of target triqs_HubbardI Scanning dependencies of target dmftproj [ 1%] [ 1%] Scanning dependencies of target boost_for_triqs Generating vertex.so Generating hubbard_I.so See /home/joon/program/Triqs-source-boost/triqs_build/pytriqs/Wien2k/F90/f2pyBuild.log for logs See /home/joon/program/Triqs-source-boost/triqs_build/pytriqs/Solvers/HubbardI/F90/f2pyBuild.log for logs [ 1%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/modules.f.o [ 1%] [ 2%] [ 2%] [ 3%] [ 3%] [ 3%] [ 4%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/outband.f.o Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/outbwin.f.o Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/orthogonal_wannier.f.o Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/rot_dens.f.o [ 4%] [ 5%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/outputqmc.f.o Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/density.f.o Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/symmetrize_mat.f.o Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/rot_projectmat.f.o Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/orthogonal.f.o [ 5%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/set_projections.f.o [ 5%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/read_k_list.f.o [ 6%] [ 6%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/timeinv.f.o Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/set_rotloc.f.o [ 7%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/setsym.f.o [ 7%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/set_ang_trans.f.o [ 7%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/readcomline.f.o make[2]: * No rule to make target -Wl,--start-group', needed bypytriqs/Wien2k/dmftproj/dmftproj'. Stop. make[2]: * Waiting for unfinished jobs.... [ 8%] Building Fortran object pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/dmftproj.f.o [ 8%] Built target triqs_Wien2k [ 9%] [ 9%] [ 9%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/home/joon/program/Triqs-source-boost/boost_1_49_0/libs/serialization/src/archive_exception.cpp.o [ 10%] [ 10%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/home/joon/program/Triqs-source-boost/boost_1_49_0/libs/serialization/src/basic_archive.cpp.o Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/home/joon/program/Triqs-source-boost/boost_1_49_0/libs/serialization/src/basic_iarchive.cpp.o Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/home/joon/program/Triqs-source-boost/boost_1_49_0/libs/serialization/src/basic_iserializer.cpp.o Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/home/joon/program/Triqs-source-boost/boost_1_49_0/libs/serialization/src/basic_oarchive.cpp.o [ 11%] Building CXX 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foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/home/joon/program/Triqs-source-boost/boost_1_49_0/libs/serialization/src/stl_port.cpp.o [ 19%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/home/joon/program/Triqs-source-boost/boost_1_49_0/libs/serialization/src/text_iarchive.cpp.o [ 20%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/home/joon/program/Triqs-source-boost/boost_1_49_0/libs/serialization/src/text_oarchive.cpp.o [ 20%] Building CXX object foreignlibs/boost/CMakeFiles/boost_for_triqs.dir/home/joon/program/Triqs-source-boost/boost_1_49_0/libs/serialization/src/text_wiarchive.cpp.o make[1]: * [pytriqs/Wien2k/dmftproj/CMakeFiles/dmftproj.dir/all] Error 2 make[1]: * Waiting for unfinished jobs.... 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boost_for_triqs make: *\ [all] Error 2 [root@hpc triqs_build]#

Thank you for your comment. I tried it again, but got error.

As you can see, I use root account. I don't know why 'Permission denied' is printed.

When I put 'make -j12' ignored this message, there is error and stop.

What should I do for compiling successfully?

Thank you.

mferrero commented 12 years ago

Maybe you have to put quotes for the options. Try this:

cmake /home/joon/program/Triqs-source-boost/Triqs -DBOOST_SOURCE_DIR=/home/joon/program/Triqs-source-boost/boost_1_49_0 -DCMAKE_INSTALL_PREFIX=/home/joon/program/Triqs-source-boost/triqs_build/Triqs-Install -DBLAS_LIBRARY="-Wl,--start-group;/opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_intel_lp64.a;/opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_sequential.a;/opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_core.a;-Wl,--end-group" -DLAPACK_LIBRARY=/opt/intel/mkl/10.2.5.035/lib/em64t/libmkl_solver_lp64_sequential.a -DMKL_INCLUDE_DIR=/opt/intel/mkl/10.2.5.035/include

Can you then post the content of the file CMakeCache.txt somewhere on https://gist.github.com

Then I can see how the variables where set.

blueway39 commented 12 years ago

[root@hpc triqs_build]# make -j12

[ 58%] Building CXX object triqs/CMakeFiles/triqs.dir/gf_local/TailGF.cpp.o Linking CXX shared module mpi.so [ 58%] Built target mpi Linking CXX shared library libtriqs.so /usr/bin/ld: /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.5.4/../../../libfftw3.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.5.4/../../../libfftw3.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: * [triqs/libtriqs.so] Error 1 make[1]: * [triqs/CMakeFiles/triqs.dir/all] Error 2 make: *\ [all] Error 2

You're right. Thank you.

'make -j12' shows error above(bottom part). Should I recompile the fftw with -fpic or any others?

CMakeCache.txt file post on https://gist.github.com/3654507

Thanks again.

mferrero commented 12 years ago

Yes, all your libraries must be compiled with -fpic. So you should try to recompile fftw with -fpic and see how it goes.

We're making progress!

parcollet commented 12 years ago

Maybe we should add a if (NOT BLAS_LIBRARY) Warning(FATAL_ERROR "Blas not found") endif in the cmakelist. The first error would have been shorter and clearer...

blueway39 commented 12 years ago

[root@hpc triqs_build]# make test

          .
          .
          .

98% tests passed, 2 tests failed out of 104

Total Test time (real) = 61.07 sec

The following tests FAILED: 17 - group_indices_nopy (Failed) 54 - group_indices_wpy (Failed) Errors while running CTest make: *\ [test] Error 8 [root@hpc triqs_build]#

I got this error message. ('make -jN' is complied successfully.)

But last procedure 'make -jN install' is complied well.

Is it fine that I ignore the error message in 'make test'?

mferrero commented 12 years ago

I think it is fine to ignore these two errors. For some reason sometimes compilers return -0 instead of 0. Because we compare outputs, these two strings are different and the test fails, even though the numbers really mean the same. This is a bug that we need to fix.

In any case, it looks like you managed to install the code, great!

blueway39 commented 12 years ago

Your comments are very helpful for me.

Thank you again.

mferrero commented 12 years ago

@blueway39 I think I fixed the tests. You can try to get the latest version, compile and run the tests again. I think now everything should pass fine. Let me know!

blueway39 commented 12 years ago

Dear Michel Ferrero.

All in 'make test' are fine. 100% pass!

Thank you for telling me it.