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Re: [Question #703349]: ImportError: /lustre/rcghead1/users/c3358697/myYade/install/lib64/yadeCloud/libpost_vtk.so: undefined symbol: cholmod_defaults

 

Question #703349 on Yade changed:
https://answers.launchpad.net/yade/+question/703349

Xin Li posted a new comment:
This is the cmake output:
-- Version is set to 2022-09-26.git-b31bb2d
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- GCC Version >= 4.8. Adding -save-temps
-- Log filtering: enabled
-- Enabling boost::log library and DEBUG=OFF. Logging will work nicely, backtraces will not have debug info, files will be small.
-- Architecture: unknown
Loop on the following python versions and check available dependencies:3.10;3.9;3.8;3.7;3.6;3.5;3.4;3.3;3.2;3.1;3.0
Using user defined PYTHON_EXECUTABLE: /cm/software/apps/python/3.6.3/bin/python
Trying python version: 3.10 parsed as 3 10
Using user defined PYTHON_EXECUTABLE: /cm/software/apps/python/3.6.3/bin/python
Trying python version: 3.9 parsed as 3 9
Using user defined PYTHON_EXECUTABLE: /cm/software/apps/python/3.6.3/bin/python
Trying python version: 3.8 parsed as 3 8
Using user defined PYTHON_EXECUTABLE: /cm/software/apps/python/3.6.3/bin/python
Trying python version: 3.7 parsed as 3 7
-- Found PythonInterp: /cm/software/apps/python/3.6.3/bin/python3.6 (found version "3.6.3")
Using user defined PYTHON_EXECUTABLE: /cm/software/apps/python/3.6.3/bin/python
Trying python version: 3.6 parsed as 3 6
Python version 3.6.3 found, try to import dependencies...
Boost_VERSION=107200, adding boost_python36 lib
-- Found PythonInterp: /cm/software/apps/python/3.6.3/bin/python (found version "3.6.3")
--   Boost_VERSION: 107200
--   Boost_LIB_VERSION: 1_72
--   Boost_INCLUDE_DIRS: /cm/software/apps/boost/gcc8/1.72-python3.6/include
--   Boost_LIBRARIES: /cm/software/apps/boost/gcc8/1.72-python3.6/lib/libboost_python36.so/cm/software/apps/boost/gcc8/1.72-python3.6/lib/libboost_thread.so-lpthread/cm/software/apps/boost/gcc8/1.72-python3.6/lib/libboost_filesystem.so/cm/software/apps/boost/gcc8/1.72-python3.6/lib/libboost_iostreams.so/cm/software/apps/boost/gcc8/1.72-python3.6/lib/libboost_regex.so/cm/software/apps/boost/gcc8/1.72-python3.6/lib/libboost_serialization.so/cm/software/apps/boost/gcc8/1.72-python3.6/lib/libboost_system.so/cm/software/apps/boost/gcc8/1.72-python3.6/lib/libboost_date_time.so/cm/software/apps/boost/gcc8/1.72-python3.6/lib/libboost_log.so/cm/software/apps/boost/gcc8/1.72-python3.6/lib/libboost_chrono.so/cm/software/apps/boost/gcc8/1.72-python3.6/lib/libboost_atomic.so/cm/software/apps/boost/gcc8/1.72-python3.6/lib/libboost_log_setup.solibboost_python36.so
Found all python dependencies with version 3.6.3, will compile yade with that.
-- Almost all useful errors are enabled and it is g++ version 8.3.1
-- Except for this one g++ bug https://gcc.gnu.org/bugzilla/show_bug.cgi?id=53431#c34 , so we add -Wno-comment
-- Determining preferred precision of Real numbers
-- Will now try to find python-mpmath using /cm/software/apps/python/3.6.3/bin/python
-- Disabling RealHP<N>, this compiler is too old to make this work.
-- MPFR MPC disabled
-- Will use PrecisionDouble as Real type with 15 decimal places precision and use 64 bits of storage.
CMake Warning (dev) at CMakeLists.txt:770 (FIND_PACKAGE):
  Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
  Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  Environment variable ZLIB_ROOT is set to:

    /cm/software/apps/zlib/gcc8/1.2.11

  For compatibility, CMake is ignoring the variable.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found Eigen3, version: 3.3.7
-- Disable vectorization
-- Checking supported libvtk versions: 9;8.2;8.1;6
-- Found VTK, version: 6.3.0
-- Found OpenMP
-- GTS using gts-config /cm/software/apps/gts/gcc8/0.7.6/bin/gts-config
-- Using GTS from /cm/software/apps/gts/gcc8/0.7.6
-- Checking for one of the modules 'glib-2.0'
-- GTS NOT found
-- GMP libs: /cm/software/apps/gmp/gcc8/6.1.2/lib/libgmp.so /cm/software/apps/gmp/gcc8/6.1.2/lib/libgmp.so
-- GMP libs: /cm/software/apps/gmp/gcc8/6.1.2/lib/libgmp.so /cm/software/apps/gmp/gcc8/6.1.2/lib/libgmp.so
-- Found CGAL
-- Using typical suitesparse path /usr
-- SuiteSparse version 4.4.4 found, CHOLMOD direct solver for CPU activated.
-- BLAS_INCLUDE_DIR=/cm/software/apps/openblas/gcc8/0.3.7/include
-- Found Cholmod in /cm/software/apps/suitesparse/gcc8/4.4.4/lib/libcholmod.a
-- Found OpenBlas in /cm/software/apps/openblas/gcc8/0.3.7/lib/libopenblas.a
-- Found Metis in /cm/software/apps/metis/gcc8/5.1.0/lib/libmetis.a
-- MPI found
-- Found GL2PS
LBMFLOW is still experimental, building and running LBM engine are at your own risk!
ENABLE_THERMAL is currently supported only on amd64 architecture, disabling.
-- BLAS_INCLUDE_DIR=/cm/software/apps/openblas/gcc8/0.3.7/include
-- A library with LAPACK API found.
-- Found OpenBlas
-- Found Lapack
-- CLP not found.
-- BLAS_INCLUDE_DIR=/cm/software/apps/openblas/gcc8/0.3.7/include
-- A library with LAPACK API found.
-- CLP NOT found
-- WARNING: coinutils version older than 2.11.3. Falling back to C++14.
Yade will be installed to /lustre/rcghead1/users/c3358697/myYade/install
-- Suffix is set to Cloud
-- LIBRARY_OUTPUT_PATH is set to lib64
-- runtimePREFIX is set to /lustre/rcghead1/users/c3358697/myYade/install
-- pkg:
 + common
 + dem
 + fem
 + lbm
 + levelSet
 + openfoam
 + pfv
 + polyhedra
 + potential
-- preprocessing:
 + dem
 + potential
-- postprocessing:
 + image
 + vtk
-- ===========================================================
-- Yade configured with following features: LOGGER USEFUL_ERRORS COMPLEX_MP VTK OPENMP CGAL PFVFLOW PFVFLOW LINSOLV MPI TWOPHASEFLOW LS_DEM FEMLIKE GL2PS LBMFLOW PARTIALSAT POTENTIAL_PARTICLES
-- Disabled features: ASAN FAST_NATIVE MPFR MPC GTS GUI CHOLMOD_GPU SPH DEFORM LIQMIGRATION MASK_ARBITRARY THERMAL PROFILING POTENTIAL_BLOCKS
-- Using MAX_LOG_LEVEL=5, ENABLE_LOGGER=ON
-- Optimized build
-- C++ standard version: 14
-- ===========================================================
-- CMAKE_CXX_FLAGS =  -march=native -mtune=native -fPIC  -Werror -Wformat -Wformat-security -Wformat-nonliteral -Wall -Wextra -Wnarrowing -Wreturn-type -Wuninitialized -Wfloat-conversion -Wcast-align -Wdisabled-optimization -Wtrampolines -Wpointer-arith -Wswitch-bool -Wwrite-strings -Wnon-virtual-dtor -Wreturn-local-addr -Wsuggest-override -Wshadow -Wswitch-default  -Wno-error=maybe-uninitialized -Wno-comment -Wno-error=cpp -fdce -fstack-protector-strong -DYADE_VTK -DYADE_OPENMP -fopenmp  -DYADE_CGAL -DFLOW_ENGINE -DFLOW_ENGINE  -DLINSOLV -pthread -DYADE_MPI -DTWOPHASEFLOW -DYADE_GL2PS -DLBM_ENGINE -DPARTIALSAT
-- CMAKE_CXX_FLAGS_RELEASE =  -O3 -DNDEBUG
-- CMAKE_CXX_FLAGS_DEBUG =  -g
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /lustre/rcghead1/users/c3358697/myYade/build

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