Dear all,
I'm trying to build ALPS 2.1.1 with the Intel compiler on a HPC, but I get errors when I run cmake.
1) I run cmake with the command C=icc CXX=icpc cmake -D Boost_ROOT_DIR:PATH=/home/boeris/lib/boost-1.49.0 -DCMAKE_INSTALL_PREFIX=/home/boeris/lib/alps-2.1.1 -D MPI_C=mpicc -D MPI_CXX=mpicxx -D MPI_C_LIBRARIES=/opt/software/intel/impi/5.0.1.035/lib64/lib/libmpi.a -D MPI_CXX_LIBRARIES=/opt/software/intel/impi/5.0.1.035/lib64/libmpicxx.so -D FFTW_LIBRARIES=/opt/software/libraries/fftw3/3.3.4/lib/libfftw3.a -D FFTW_INCLUDE_DIR=/opt/software/libraries/fftw3/3.3.4/include -D HDF5_hdf5_LIBRARY_DEBUG= -D HDF5_hdf5_hl_LIBRARY_DEBUG= -D HDF5_m_LIBRARY_DEBUG= -D HDF5_rt_LIBRARY_DEBUG= -D HDF5_z_LIBRARY_DEBUG= -D SZIP_LIBRARIES=/opt/software/libraries/szip/2.1/lib/libsz.so -D SZIP_INCLUDE_DIRS=/opt/software/libraries/szip/2.1/include -D LAPACK_64_BIT=ON /home/boeris/lib/alps-2.1.1-r6176-src-with-boost/alps I set variables like HDF5_hdf5_LIBRARY_DEBUG to empty strings to avoid errors, as recommended in a previous post (https://lists.phys.ethz.ch/pipermail/comp-phys-alps-users/2013/002300.html)
2) I get errors telling me that variables like MPI_C_LIBRARIES or SZIP_LIBRARIES are missing, even if I tried to define them in the command above. The full output of cmake is copied at the end of the message.
I would really appreciate some help ! Regards.
------------ CMAKE OUTPUT ------------
CMake Error: Could not open file for write in copy operation /CMakeSystem.cmake.tmp CMake Error: : System Error: Permission denied CMake Error at /usr/share/cmake/Modules/CMakeDetermineSystem.cmake:182 (configure_file): configure_file Problem configuring file Call Stack (most recent call first): CMakeLists.txt:110 (include)
-- The C compiler identification is Intel 15.0.0.20140723 -- The CXX compiler identification is Intel 15.0.0.20140723 -- Check for working C compiler: /opt/software/intel/composer_xe_2015.0.090/bin/intel64/icc -- Check for working C compiler: /opt/software/intel/composer_xe_2015.0.090/bin/intel64/icc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /opt/software/intel/composer_xe_2015.0.090/bin/intel64/icpc -- Check for working CXX compiler: /opt/software/intel/composer_xe_2015.0.090/bin/intel64/icpc -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Build type: Release -- Python interpreter /opt/software/tools/python/2.7.8/bin/python -- Python interpreter ok : version 2.7.8 -- PYTHON_INCLUDE_DIRS = /opt/software/tools/python/2.7.8/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/software/tools/python/2.7.8/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- ALPS version: 2.1.1 -- 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 -- Looking for Boost Source -- Found Boost Source: /home/boeris/lib/boost-1.49.0 -- Boost Version: 1_49_0 -- Could NOT find MPI_C (missing: MPI_C_LIBRARIES) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIBRARIES) -- MPI compiler was -- The Fortran compiler identification is Intel -- Check for working Fortran compiler: /opt/software/intel/composer_xe_2015.0.090/bin/intel64/ifort -- Check for working Fortran compiler: /opt/software/intel/composer_xe_2015.0.090/bin/intel64/ifort -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /opt/software/intel/composer_xe_2015.0.090/bin/intel64/ifort supports Fortran 90 -- Checking whether /opt/software/intel/composer_xe_2015.0.090/bin/intel64/ifort supports Fortran 90 -- yes Falling back to CMake provied LAPACK/BLAS detection. -- 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 -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- A library with BLAS API found. -- A library with BLAS API found. -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- A library with LAPACK API found. -- SQLite Library: not found -- Found FFTW: /opt/software/libraries/fftw3/3.3.4/lib/libfftw3.a -- LPSolve Library: not found -- Found ZLIB: /usr/lib64/libz.so -- Could NOT find SZIP (missing: SZIP_LIBRARIES SZIP_INCLUDE_DIRS) -- Found HDF5: debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so -- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND -- Python interpreter /opt/software/tools/python/2.7.8/bin/python -- Python interpreter ok : version 2.7.8 -- PYTHON_INCLUDE_DIRS = /opt/software/tools/python/2.7.8/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/software/tools/python/2.7.8/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- Numpy include in /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- ALPS XML dir is /home/boeris/lib/alps-2.1.1/lib/xml -- Adding Boost dir: /home/boeris/lib/boost-1.49.0 -- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND;HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND CMake Warning (dev) at src/alps/CMakeLists.txt:85 (target_link_libraries): Link library type specifier "debug" is followed by specifier "optimized" instead of a library name. The first specifier will be ignored. This warning is for project developers. Use -Wno-dev to suppress it.
-- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND;HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND -- tebd will not be built -- Configuring incomplete, errors occurred! See also "/home/boeris/lib/build-alps/CMakeFiles/CMakeOutput.log". See also "/home/boeris/lib/build-alps/CMakeFiles/CMakeError.log".
Dear Guilhem Boeris,
It seems that you are executing cmake in a place where you have no write permission.
CMAKE OUTPUT
CMake Error: Could not open file for write in copy operation /CMakeSystem.cmake.tmp CMake Error: : System Error: Permission denied
Please run cmake in an appropriate directory, such as $HOME/build, in which you have full permission for file operations.
Best, Synge
On Jan 29, 2015, at 22:36, Guilhem Boeris guilhemboeris@yahoo.fr wrote:
Dear all,
I'm trying to build ALPS 2.1.1 with the Intel compiler on a HPC, but I get errors when I run cmake.
I run cmake with the command C=icc CXX=icpc cmake -D Boost_ROOT_DIR:PATH=/home/boeris/lib/boost-1.49.0 -DCMAKE_INSTALL_PREFIX=/home/boeris/lib/alps-2.1.1 -D MPI_C=mpicc -D MPI_CXX=mpicxx -D MPI_C_LIBRARIES=/opt/software/intel/impi/5.0.1.035/lib64/lib/libmpi.a -D MPI_CXX_LIBRARIES=/opt/software/intel/impi/5.0.1.035/lib64/libmpicxx.so -D FFTW_LIBRARIES=/opt/software/libraries/fftw3/3.3.4/lib/libfftw3.a -D FFTW_INCLUDE_DIR=/opt/software/libraries/fftw3/3.3.4/include -D HDF5_hdf5_LIBRARY_DEBUG= -D HDF5_hdf5_hl_LIBRARY_DEBUG= -D HDF5_m_LIBRARY_DEBUG= -D HDF5_rt_LIBRARY_DEBUG= -D HDF5_z_LIBRARY_DEBUG= -D SZIP_LIBRARIES=/opt/software/libraries/szip/2.1/lib/libsz.so -D SZIP_INCLUDE_DIRS=/opt/software/libraries/szip/2.1/include -D LAPACK_64_BIT=ON /home/boeris/lib/alps-2.1.1-r6176-src-with-boost/alps
I set variables like HDF5_hdf5_LIBRARY_DEBUG to empty strings to avoid errors, as recommended in a previous post (https://lists.phys.ethz.ch/pipermail/comp-phys-alps-users/2013/002300.html)
I get errors telling me that variables like MPI_C_LIBRARIES or SZIP_LIBRARIES are missing, even if I tried to define them in the command above. The full output of cmake is copied at the end of the message.
I would really appreciate some help ! Regards.
CMAKE OUTPUT
CMake Error: Could not open file for write in copy operation /CMakeSystem.cmake.tmp CMake Error: : System Error: Permission denied CMake Error at /usr/share/cmake/Modules/CMakeDetermineSystem.cmake:182 (configure_file): configure_file Problem configuring file Call Stack (most recent call first): CMakeLists.txt:110 (include)
-- The C compiler identification is Intel 15.0.0.20140723 -- The CXX compiler identification is Intel 15.0.0.20140723 -- Check for working C compiler: /opt/software/intel/composer_xe_2015.0.090/bin/intel64/icc -- Check for working C compiler: /opt/software/intel/composer_xe_2015.0.090/bin/intel64/icc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /opt/software/intel/composer_xe_2015.0.090/bin/intel64/icpc -- Check for working CXX compiler: /opt/software/intel/composer_xe_2015.0.090/bin/intel64/icpc -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Build type: Release -- Python interpreter /opt/software/tools/python/2.7.8/bin/python -- Python interpreter ok : version 2.7.8 -- PYTHON_INCLUDE_DIRS = /opt/software/tools/python/2.7.8/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/software/tools/python/2.7.8/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- ALPS version: 2.1.1 -- 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 -- Looking for Boost Source -- Found Boost Source: /home/boeris/lib/boost-1.49.0 -- Boost Version: 1_49_0 -- Could NOT find MPI_C (missing: MPI_C_LIBRARIES) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIBRARIES) -- MPI compiler was -- The Fortran compiler identification is Intel -- Check for working Fortran compiler: /opt/software/intel/composer_xe_2015.0.090/bin/intel64/ifort -- Check for working Fortran compiler: /opt/software/intel/composer_xe_2015.0.090/bin/intel64/ifort -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /opt/software/intel/composer_xe_2015.0.090/bin/intel64/ifort supports Fortran 90 -- Checking whether /opt/software/intel/composer_xe_2015.0.090/bin/intel64/ifort supports Fortran 90 -- yes Falling back to CMake provied LAPACK/BLAS detection. -- 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 -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- A library with BLAS API found. -- A library with BLAS API found. -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- A library with LAPACK API found. -- SQLite Library: not found -- Found FFTW: /opt/software/libraries/fftw3/3.3.4/lib/libfftw3.a -- LPSolve Library: not found -- Found ZLIB: /usr/lib64/libz.so -- Could NOT find SZIP (missing: SZIP_LIBRARIES SZIP_INCLUDE_DIRS) -- Found HDF5: debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so -- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND -- Python interpreter /opt/software/tools/python/2.7.8/bin/python -- Python interpreter ok : version 2.7.8 -- PYTHON_INCLUDE_DIRS = /opt/software/tools/python/2.7.8/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/software/tools/python/2.7.8/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- Numpy include in /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- ALPS XML dir is /home/boeris/lib/alps-2.1.1/lib/xml -- Adding Boost dir: /home/boeris/lib/boost-1.49.0 -- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND;HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND CMake Warning (dev) at src/alps/CMakeLists.txt:85 (target_link_libraries): Link library type specifier "debug" is followed by specifier "optimized" instead of a library name. The first specifier will be ignored. This warning is for project developers. Use -Wno-dev to suppress it.
-- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND;HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND -- tebd will not be built -- Configuring incomplete, errors occurred! See also "/home/boeris/lib/build-alps/CMakeFiles/CMakeOutput.log". See also "/home/boeris/lib/build-alps/CMakeFiles/CMakeError.log".
Hi,
How about setting C and CXX to mpi-aware compilers? For example, C=mpiicc and CXX=mpiicpc (or, MPI wrapper of icc/icpc).
This may fix this issue, since quite often the command line setting is override by running CMake command.
And, also, setting C=icpc (using C++ compiler) might help some of the compilation issue.
Best regards,
Hi,
Thank you very much for your answers ! Here is what I did following your advice :
- setting C=mpiicc and CXX=mpiicpc : yes, this worked and removed the errors like "Could NOT find MPI_C (missing: MPI_C_LIBRARIES)" - I changed somes values in CMakeCache.txt - I still have the error : CMake Error: Could not open file for write in copy operation /CMakeSystem.cmake.tmp CMake Error: : System Error: Permission denied
I checked that I was running cmake in a directory like $HOME/build with full write permissions. Moreover, this error does not show when I try to install ALPS 2.2.0b3 instead.
Do you have any idea ? Thanks you.
-------------------------------------- CMake output :
CMake Error: Could not open file for write in copy operation /CMakeSystem.cmake.tmp CMake Error: : System Error: Permission denied CMake Error at /usr/share/cmake/Modules/CMakeDetermineSystem.cmake:182 (configure_file): configure_file Problem configuring file Call Stack (most recent call first): CMakeLists.txt:110 (include)
-- Build type: Release -- Python interpreter /opt/software/tools/python/2.7.8/bin/python -- Python interpreter ok : version 2.7.8 -- PYTHON_INCLUDE_DIRS = /opt/software/tools/python/2.7.8/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/software/tools/python/2.7.8/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- ALPS version: 2.1.1 -- Looking for Boost Source -- Found Boost Source: /home/boeris/lib/boost/1.49.0 -- Boost Version: 1_49_0 -- MPI compiler was /opt/software/intel/impi/5.0.1.035/bin64/mpiicpc Falling back to CMake provied LAPACK/BLAS detection. -- A library with BLAS API found. -- A library with BLAS API found. -- A library with LAPACK API found. -- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND -- Python interpreter /opt/software/tools/python/2.7.8/bin/python -- Python interpreter ok : version 2.7.8 -- PYTHON_INCLUDE_DIRS = /opt/software/tools/python/2.7.8/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/software/tools/python/2.7.8/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- Numpy include in /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- ALPS XML dir is /home/boeris/lib/alps-2.1.1/lib/xml -- Adding Boost dir: /home/boeris/lib/boost/1.49.0 -- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND;HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND CMake Warning (dev) at src/alps/CMakeLists.txt:85 (target_link_libraries): Link library type specifier "debug" is followed by specifier "optimized" instead of a library name. The first specifier will be ignored. This warning is for project developers. Use -Wno-dev to suppress it.
-- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND;HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND -- tebd will not be built -- Configuring incomplete, errors occurred!
As Synge Todo suggested, you need to run it from a directory where you have write permission, like somewhere in your home directory.
On Feb 3, 2015, at 17:32, Guilhem Boeris guilhemboeris@yahoo.fr wrote:
Hi,
Thank you very much for your answers ! Here is what I did following your advice :
setting C=mpiicc and CXX=mpiicpc : yes, this worked and removed the errors like "Could NOT find MPI_C (missing: MPI_C_LIBRARIES)"
I changed somes values in CMakeCache.txt
I still have the error : CMake Error: Could not open file for write in copy operation /CMakeSystem.cmake.tmp CMake Error: : System Error: Permission denied
I checked that I was running cmake in a directory like $HOME/build with full write permissions. Moreover, this error does not show when I try to install ALPS 2.2.0b3 instead.Do you have any idea ? Thanks you.
CMake output :
CMake Error: Could not open file for write in copy operation /CMakeSystem.cmake.tmp CMake Error: : System Error: Permission denied CMake Error at /usr/share/cmake/Modules/CMakeDetermineSystem.cmake:182 (configure_file): configure_file Problem configuring file Call Stack (most recent call first): CMakeLists.txt:110 (include)
-- Build type: Release -- Python interpreter /opt/software/tools/python/2.7.8/bin/python -- Python interpreter ok : version 2.7.8 -- PYTHON_INCLUDE_DIRS = /opt/software/tools/python/2.7.8/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/software/tools/python/2.7.8/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- ALPS version: 2.1.1 -- Looking for Boost Source -- Found Boost Source: /home/boeris/lib/boost/1.49.0 -- Boost Version: 1_49_0 -- MPI compiler was /opt/software/intel/impi/5.0.1.035/bin64/mpiicpc Falling back to CMake provied LAPACK/BLAS detection. -- A library with BLAS API found. -- A library with BLAS API found. -- A library with LAPACK API found. -- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND -- Python interpreter /opt/software/tools/python/2.7.8/bin/python -- Python interpreter ok : version 2.7.8 -- PYTHON_INCLUDE_DIRS = /opt/software/tools/python/2.7.8/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/software/tools/python/2.7.8/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- Numpy include in /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- ALPS XML dir is /home/boeris/lib/alps-2.1.1/lib/xml -- Adding Boost dir: /home/boeris/lib/boost/1.49.0 -- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND;HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND CMake Warning (dev) at src/alps/CMakeLists.txt:85 (target_link_libraries): Link library type specifier "debug" is followed by specifier "optimized" instead of a library name. The first specifier will be ignored. This warning is for project developers. Use -Wno-dev to suppress it.
-- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND;HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND -- tebd will not be built -- Configuring incomplete, errors occurred!
Hi,
- I changed somes values in CMakeCache.txt
Before running cmake again, you may need to remove all the cache files like CMakeCache.txt.
Haruhiko
On Wed, Feb 4, 2015 at 5:47 AM, Matthias Troyer troyer@phys.ethz.ch wrote:
As Synge Todo suggested, you need to run it from a directory where you have write permission, like somewhere in your home directory.
On Feb 3, 2015, at 17:32, Guilhem Boeris guilhemboeris@yahoo.fr wrote:
Hi,
Thank you very much for your answers ! Here is what I did following your advice :
- setting C=mpiicc and CXX=mpiicpc : yes, this worked and removed the errors
like "Could NOT find MPI_C (missing: MPI_C_LIBRARIES)"
- I changed somes values in CMakeCache.txt
- I still have the error : CMake Error: Could not open file for write in
copy operation /CMakeSystem.cmake.tmp CMake Error: : System Error: Permission denied
I checked that I was running cmake in a directorylike $HOME/build with full write permissions. Moreover, this error does not show when I try to install ALPS 2.2.0b3 instead.
Do you have any idea ? Thanks you.
CMake output :
CMake Error: Could not open file for write in copy operation /CMakeSystem.cmake.tmp CMake Error: : System Error: Permission denied CMake Error at /usr/share/cmake/Modules/CMakeDetermineSystem.cmake:182 (configure_file): configure_file Problem configuring file Call Stack (most recent call first): CMakeLists.txt:110 (include)
-- Build type: Release -- Python interpreter /opt/software/tools/python/2.7.8/bin/python -- Python interpreter ok : version 2.7.8 -- PYTHON_INCLUDE_DIRS = /opt/software/tools/python/2.7.8/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/software/tools/python/2.7.8/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- ALPS version: 2.1.1 -- Looking for Boost Source -- Found Boost Source: /home/boeris/lib/boost/1.49.0 -- Boost Version: 1_49_0 -- MPI compiler was /opt/software/intel/impi/5.0.1.035/bin64/mpiicpc Falling back to CMake provied LAPACK/BLAS detection. -- A library with BLAS API found. -- A library with BLAS API found. -- A library with LAPACK API found. -- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND -- Python interpreter /opt/software/tools/python/2.7.8/bin/python -- Python interpreter ok : version 2.7.8 -- PYTHON_INCLUDE_DIRS = /opt/software/tools/python/2.7.8/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/software/tools/python/2.7.8/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- Numpy include in /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- ALPS XML dir is /home/boeris/lib/alps-2.1.1/lib/xml -- Adding Boost dir: /home/boeris/lib/boost/1.49.0 -- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND;HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND CMake Warning (dev) at src/alps/CMakeLists.txt:85 (target_link_libraries): Link library type specifier "debug" is followed by specifier "optimized" instead of a library name. The first specifier will be ignored. This warning is for project developers. Use -Wno-dev to suppress it.
-- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND;HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND -- tebd will not be built -- Configuring incomplete, errors occurred!
Hi,
- the problem was not a lack of permissions for the build directory, but just cmake trying to write at the root of the filesystem. I commented out line 110 of CMakeLists.txt. I saw that this is also done in ALPS 2.2.0b3, but maybe this should be fixed in 2.1.1 version as well. Now CMake runs without errors.
- I now get the following error during the compilation :
[ 63%] Built target jacobi [ 63%] Built target jacobidavidson1 [ 63%] Building CXX object example/ietl/CMakeFiles/jacobidavidson2.dir/jacobidavidson2.cpp.o /home/boeris/build/alps-2.1.1-r6176-src/alps/src/boost/numeric/bindings/lapack/computational/getrf.hpp(197): error: no instance of overloaded function "boost::numeric::bindings::lapack::detail::getrf" matches the argument list argument types are: (order, ptrdiff_t, ptrdiff_t, double *, ptrdiff_t, int *) return detail::getrf( order(), bindings::size_row(a).
I don't know if it's due to the fact that I use Intel MKL. Do you know how to fix this ?
Thank you for your help.
Le Mercredi 4 février 2015 1h58, Haruhiko Matsuo halm.matsuo@gmail.com a écrit :
Hi,
- I changed somes values in CMakeCache.txt
Before running cmake again, you may need to remove all the cache files like CMakeCache.txt.
Haruhiko
On Wed, Feb 4, 2015 at 5:47 AM, Matthias Troyer troyer@phys.ethz.ch wrote:
As Synge Todo suggested, you need to run it from a directory where you have write permission, like somewhere in your home directory.
On Feb 3, 2015, at 17:32, Guilhem Boeris guilhemboeris@yahoo.fr wrote:
Hi,
Thank you very much for your answers ! Here is what I did following your advice :
- setting C=mpiicc and CXX=mpiicpc : yes, this worked and removed the errors
like "Could NOT find MPI_C (missing: MPI_C_LIBRARIES)"
- I changed somes values in CMakeCache.txt
- I still have the error : CMake Error: Could not open file for write in
copy operation /CMakeSystem.cmake.tmp CMake Error: : System Error: Permission denied
I checked that I was running cmake in a directory like $HOME/build with full write permissions. Moreover, this error does not show when I try to install ALPS 2.2.0b3 instead.
Do you have any idea ? Thanks you.
CMake output :
CMake Error: Could not open file for write in copy operation /CMakeSystem.cmake.tmp CMake Error: : System Error: Permission denied CMake Error at /usr/share/cmake/Modules/CMakeDetermineSystem.cmake:182 (configure_file): configure_file Problem configuring file Call Stack (most recent call first): CMakeLists.txt:110 (include)
-- Build type: Release -- Python interpreter /opt/software/tools/python/2.7.8/bin/python -- Python interpreter ok : version 2.7.8 -- PYTHON_INCLUDE_DIRS = /opt/software/tools/python/2.7.8/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/software/tools/python/2.7.8/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- ALPS version: 2.1.1 -- Looking for Boost Source -- Found Boost Source: /home/boeris/lib/boost/1.49.0 -- Boost Version: 1_49_0 -- MPI compiler was /opt/software/intel/impi/5.0.1.035/bin64/mpiicpc Falling back to CMake provied LAPACK/BLAS detection. -- A library with BLAS API found. -- A library with BLAS API found. -- A library with LAPACK API found. -- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND -- Python interpreter /opt/software/tools/python/2.7.8/bin/python -- Python interpreter ok : version 2.7.8 -- PYTHON_INCLUDE_DIRS = /opt/software/tools/python/2.7.8/include/python2.7 -- PYTHON_NUMPY_INCLUDE_DIR = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- PYTHON_SITE_PKG = /opt/software/tools/python/2.7.8/lib/python2.7/site-packages -- PYTHON_LIBRARY = /opt/software/tools/python/2.7.8/lib/python2.7/config/libpython2.7.a -- PYTHON_EXTRA_LIBS =-lpthread -ldl -lutil -- PYTHON_LINK_FOR_SHARED = -Xlinker -export-dynamic -- Numpy include in /opt/software/tools/python/2.7.8/lib/python2.7/site-packages/numpy/core/include -- ALPS XML dir is /home/boeris/lib/alps-2.1.1/lib/xml -- Adding Boost dir: /home/boeris/lib/boost/1.49.0 -- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND;HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND CMake Warning (dev) at src/alps/CMakeLists.txt:85 (target_link_libraries): Link library type specifier "debug" is followed by specifier "optimized" instead of a library name. The first specifier will be ignored. This warning is for project developers. Use -Wno-dev to suppress it.
-- HDF5: /usr/include debug;optimized;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND;HDF5_DLL-NOTFOUND;HDF5_HL_DLL-NOTFOUND -- tebd will not be built -- Configuring incomplete, errors occurred!
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