ye-luo
commented
1 year ago Make a fresh build and provide all cmake printout.
Closed YanyongW91 closed 1 year ago
ye-luo
commented
1 year ago Make a fresh build and provide all cmake printout.
ye-luo
commented
1 year ago Also ls /home/ywang/code/hdf5-1.14.0/hdf5 what is the output
YanyongW91
commented
1 year ago here is the cmake output:
-- The C compiler identification is GNU 9.5.0
-- The CXX compiler identification is GNU 9.5.0
-- Check for working C compiler: /home/ywang/code/openmpi-4.1.5ing/bin/mpicc
-- Check for working C compiler: /home/ywang/code/openmpi-4.1.5ing/bin/mpicc - works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /home/ywang/code/openmpi-4.1.5ing/bin/mpicxx
-- Check for working CXX compiler: /home/ywang/code/openmpi-4.1.5ing/bin/mpicxx - works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Defining the float point precision
Base precision = double
Full precision = double
-- CMAKE_BUILD_TYPE is RELEASE
-- Enable sanitizer ENABLE_SANITIZER=none
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Trying to figure out compiler options ....
-- C++ Compiler is identified by QMCPACK as : GNU
-- Looking for C++ include cstdio
-- Looking for C++ include cstdio - found
-- libstdc++/C++ compiler version compatibility check pass
-- C++17 standard library supported
-- QMC_SIMD_ALIGNMENT is set to 32
-- OpenMP taskloop functionality check pass
-- ENABLE_OMP_TASKLOOP is set to ON
-- Found MPI_CXX: /home/ywang/code/openmpi-4.1.5ing/bin/mpicxx (found version "3.1")
-- Found MPI: TRUE (found version "3.1") found components: CXX
-- Detected Open MPI. Setting bind-to options for thread affinity in MPIEXEC_PREFLAGS.
-- MPI runner MPIEXEC_EXECUTABLE : /opt/intel/oneapi/intelpython/latest/bin/mpiexec
-- MPIEXEC_NUMPROC_FLAG : -n
-- MPIEXEC_PREFLAGS : --bind-to;none
-- Tests run as : /opt/intel/oneapi/intelpython/latest/bin/mpiexec -n NUM_PROCS --bind-to none EXECUTABLE
-- MPI is enabled
-- Performing Test TEST_CXX_COMPILE_MAIN
-- Performing Test TEST_CXX_COMPILE_MAIN - Success
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Trying to find LAPACK from Intel MKL
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_intel_lp64.so;/opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_sequential.so;/opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.so;-lm;-ldl
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- LAPACK linker flags:
-- LAPACK libraries: /opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_intel_lp64.so;/opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_sequential.so;/opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.so;-lm;-ldl;-lm;-ldl
-- Looking for Intel MKL library header files
-- MKL_INCLUDE: /opt/intel/oneapi/mkl/latest/include
-- MKL found: HAVE_MKL=TRUE, HAVE_MKL_FFTW3=TRUE
-- Selected vendor math library INTEL_VML
-- Setting up Intel MKL Vector Math Library (VML)
-- Looking for C++ include mkl_vml_functions.h
-- Looking for C++ include mkl_vml_functions.h - found
-- MKL VML found
-- SINCOS_INCLUDE : cmath
-- Performing Test HAVE_SINCOS
-- Performing Test HAVE_SINCOS - Success
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.7")
-- Linking dynamic HDF5 library
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /opt/intel/oneapi/intelpython/latest/lib/libhdf5.so;/usr/lib64/librt.so;/usr/lib64/libpthread.so;/opt/intel/oneapi/intelpython/latest/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found suitable version "1.10.2", minimum required is "1.10") found components: C
-- Serial HDF5 library found
-- Using HDF5 non-scalable serial I/O code paths
CMake Warning at CMakeLists.txt:701 (message):
MPI builds may have performance loss by not using parallel HDF5! (Safe to
ignore for workstation builds).
-- Found Boost: /usr/include (found suitable version "1.66.0", minimum required is "1.61.0")
-- Setting Boost_INCLUDE_DIRS=/usr/include
-- CUDA disabled
-- CUDA NVTX APIs disabled
-- VTune ittnotify APIs disabled
Project C_FLAGS: -fopenmp -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -Wno-deprecated -Werror=vla -ffast-math -march=native -O3 -DNDEBUG
Project CXX_FLAGS: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -Wno-deprecated -Wvla -Wcomment -Wmisleading-indentation -Wmaybe-uninitialized -Wuninitialized -Wreorder -Wno-unknown-pragmas -Wno-sign-compare -Wsuggest-override -ffast-math -march=native -O3 -DNDEBUG
Project INCLUDE_DIRECTORIES: /home/ywang/code/testing/new/qmcpack-3.16.0/build_gnu/src;/home/ywang/code/testing/new/qmcpack-3.16.0/src
Project EXE_LINKER_FLAGS:
Project SHARED_LINKER_FLAGS:
-- Found Git: /usr/bin/git (found version "2.27.0")
-- QMC_SYMLINK_TEST_FILES = ON. Using symbolic links for large test files may cause test failures if the build is installed on a separate filesystem from the source.
-- Found Python3: /opt/intel/oneapi/intelpython/latest/bin/python3.7 (found version "3.7.10") found components: Interpreter
-- Unable to import PySCF python module. PySCF tests will not be run.
-- Unable to import GPAW python module. GPAW converter tests will not be run.
-- Did not find a patched Quantum ESPRESSO (QE) distribution with pw2qmcpack.x. QE tests will not be run.
-- Did not find RMG (rmg-cpu). RMG tests will not be run.
-- Ready to parse QMCPACK source tree
-- Adding integration tests for QMCPACK
Use --log-level=VERBOSE CMake option for details of which tests will be enabled.
Adding estimator tests for QMCPACK
Adding I/O tests for QMCPACK
QMC_DATA is not set. Performance tests will be skipped.
Adding system tests for QMCPACK
Traceback (most recent call last):
File "/home/ywang/code/testing/new/qmcpack-3.16.0/tests/molecules/He_param/convert_vp_format.py", line 211, in <module>
convert_from_text_to_hdf(fname_in, fname_out, args.complex)
File "/home/ywang/code/testing/new/qmcpack-3.16.0/tests/molecules/He_param/convert_vp_format.py", line 179, in convert_from_text_to_hdf
write_to_hdf(vp, fname_out, output_complex)
File "/home/ywang/code/testing/new/qmcpack-3.16.0/tests/molecules/He_param/convert_vp_format.py", line 163, in write_to_hdf
f.create_dataset("timestamp",data=np.array([vp.timestamp],dtype=object),dtype=h5py.string_dtype('ascii'))
AttributeError: module 'h5py' has no attribute 'string_dtype'
Adding example tests for QMCPACK
Adding Nexus tests
-- Configuring done
CMake Warning at src/io/hdf/tests/CMakeLists.txt:21 (add_executable):
Cannot generate a safe runtime search path for target test_io_hdf5 because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/io/OhmmsData/tests/CMakeLists.txt:19 (add_executable):
Cannot generate a safe runtime search path for target test_io_ohmmsdata
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/einspline/tests/CMakeLists.txt:25 (add_executable):
Cannot generate a safe runtime search path for target test_einspline
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/Particle/tests/CMakeLists.txt:34 (add_executable):
Cannot generate a safe runtime search path for target test_distance_table
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/Particle/tests/CMakeLists.txt:16 (add_executable):
Cannot generate a safe runtime search path for target test_particle because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/Particle/Lattice/tests/CMakeLists.txt:16 (add_executable):
Cannot generate a safe runtime search path for target test_lattice because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/Particle/LongRange/tests/CMakeLists.txt:16 (add_executable):
Cannot generate a safe runtime search path for target test_longrange
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/Particle/ParticleIO/tests/CMakeLists.txt:16 (add_executable):
Cannot generate a safe runtime search path for target test_particleio
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/Particle/ParticleBase/tests/CMakeLists.txt:16 (add_executable):
Cannot generate a safe runtime search path for target test_particle_base
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/Utilities/tests/CMakeLists.txt:37 (add_executable):
Cannot generate a safe runtime search path for target
test_utilities_output_manager because files in some directories may
conflict with libraries in implicit directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/Utilities/tests/CMakeLists.txt:16 (add_executable):
Cannot generate a safe runtime search path for target test_utilities
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/Numerics/tests/CMakeLists.txt:34 (add_executable):
Cannot generate a safe runtime search path for target test_numerics because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/spline2/tests/CMakeLists.txt:18 (add_executable):
Cannot generate a safe runtime search path for target test_spline2 because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCWaveFunctions/tests/CMakeLists.txt:169 (add_executable):
Cannot generate a safe runtime search path for target
test_wavefunction_trialwf because files in some directories may conflict
with libraries in implicit directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCWaveFunctions/tests/CMakeLists.txt:169 (add_executable):
Cannot generate a safe runtime search path for target
test_wavefunction_common because files in some directories may conflict
with libraries in implicit directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCWaveFunctions/tests/CMakeLists.txt:169 (add_executable):
Cannot generate a safe runtime search path for target
test_wavefunction_determinant because files in some directories may
conflict with libraries in implicit directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCWaveFunctions/tests/CMakeLists.txt:169 (add_executable):
Cannot generate a safe runtime search path for target
test_wavefunction_sposet because files in some directories may conflict
with libraries in implicit directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCWaveFunctions/tests/CMakeLists.txt:169 (add_executable):
Cannot generate a safe runtime search path for target
test_wavefunction_jastrow because files in some directories may conflict
with libraries in implicit directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCHamiltonians/tests/CMakeLists.txt:68 (add_executable):
Cannot generate a safe runtime search path for target
test_hamiltonian_force because files in some directories may conflict with
libraries in implicit directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCHamiltonians/tests/CMakeLists.txt:68 (add_executable):
Cannot generate a safe runtime search path for target test_hamiltonian_ham
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCHamiltonians/tests/CMakeLists.txt:68 (add_executable):
Cannot generate a safe runtime search path for target
test_hamiltonian_coulomb because files in some directories may conflict
with libraries in implicit directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCHamiltonians/tests/CMakeLists.txt:68 (add_executable):
Cannot generate a safe runtime search path for target
test_hamiltonian_ewald2d because files in some directories may conflict
with libraries in implicit directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/Estimators/tests/CMakeLists.txt:70 (add_executable):
Cannot generate a safe runtime search path for target test_estimators_mpi
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/Estimators/tests/CMakeLists.txt:44 (add_executable):
Cannot generate a safe runtime search path for target test_estimators
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCDrivers/tests/CMakeLists.txt:94 (add_executable):
Cannot generate a safe runtime search path for target test_new_drivers
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCDrivers/tests/CMakeLists.txt:118 (add_executable):
Cannot generate a safe runtime search path for target test_drivers_mpi
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCDrivers/tests/CMakeLists.txt:43 (add_executable):
Cannot generate a safe runtime search path for target test_drivers because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCApp/CMakeLists.txt:35 (add_executable):
Cannot generate a safe runtime search path for target qmcpack because files
in some directories may conflict with libraries in implicit directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCTools/CMakeLists.txt:55 (add_executable):
Cannot generate a safe runtime search path for target qmcfinitesize because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCTools/CMakeLists.txt:36 (add_executable):
Cannot generate a safe runtime search path for target
qmc-extract-eshdf-kvectors because files in some directories may conflict
with libraries in implicit directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCTools/CMakeLists.txt:21 (add_executable):
Cannot generate a safe runtime search path for target convert4qmc because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCTools/CMakeLists.txt:46 (add_executable):
Cannot generate a safe runtime search path for target convertpw4qmc because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
CMake Warning at src/QMCTools/tests/CMakeLists.txt:23 (add_executable):
Cannot generate a safe runtime search path for target test_tools because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libxml2.so.2] in /usr/lib64 may be hidden by files in:
/opt/intel/oneapi/intelpython/latest/lib
Some of these libraries may not be found correctly.
-- Generating done
-- Build files have been written to: /home/ywang/code/testing/new/qmcpack-3.16.0/build_gnuAlso
ls /home/ywang/code/hdf5-1.14.0/hdf5what is the output
ywang@panghu:~/code/hdf5-1.14.0/hdf5$ ls
bin include lib shareYou are using MKL and thus, we prefer the fftw3 provided by MKL instead of standalone fftw3. CMake insisted finding
-- Found HDF5: /opt/intel/oneapi/intelpython/latest/lib/libhdf5.so;/usr/lib64/librt.so;/usr/lib64/libpthread.so;/opt/intel/oneapi/intelpython/latest/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found suitable version "1.10.2", minimum required is "1.10") found components: C It is unclear to me why this happened. There is an issue with hdf5 1.14.0 and 1.12.2. https://github.com/spack/spack/issues/35893 1.12.0 or 1.12.1 should work.
YanyongW91
commented
1 year ago so I better use 1.12.0 or 1.12.1 for hdf5, and others needn't to change, right? Also the issue you mentioned also occur for me when I try to install qmcpack on my laptop
hi, developers, here is my cmake script:
here is the resulting qmcpack.settings
My question is: Why dependencies like HDF5, Libxml2 and boot are not the ones that specified in the cmake script, and fftw is empty here? Thanks