Install on Ubuntu 16.04 from source

Asked by WANG Chao

I have typed the following commands and installed the minieigen package

gcf@gcf-OptiPlex-9020:/media/gcf/3TB-FOUR/YadeWC/build$ sudo apt-get install python3-minieigen
Reading package lists... Done
Building dependency tree
Reading state information... Done
python3-minieigen is already the newest version (0.50.3+dfsg1-4build1).
0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.

BUT when i excute 'cmake' , it turns out that i have not installed the minieigen:

gcf@gcf-OptiPlex-9020:/media/gcf/3TB-FOUR/YadeWC/build$ cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk-2018.02b/
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- 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: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PythonInterp: /home/gcf/anaconda3/bin/python (found version "3.6.3")
CMake Warning (dev) at /home/gcf/anaconda3/share/cmake-3.9/Modules/FindOpenMP.cmake:200 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted. Run "cmake --help-policy CMP0054" for policy
  details. Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "c" will no longer be dereferenced when the policy is
  set to NEW. Since the policy is not set the OLD behavior will be used.
Call Stack (most recent call first):
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindOpenMP.cmake:324 (_OPENMP_GET_FLAGS)
  CMakeLists.txt:37 (INCLUDE)
This warning is for project developers. Use -Wno-dev to suppress it.

-- Found OpenMP_C: -fopenmp (found version "4.0")
-- Found OpenMP_CXX: -fopenmp (found version "4.0")
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake-qt4 (found version "4.8.7")
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Version is set to 2018.02b
-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libGL.so
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Found GL2PS: /usr/lib/libgl2ps.so
-- Found CGAL: /usr/include, /usr/lib/x86_64-linux-gnu/libCGAL.so
-- Found NumPy: version "1.13.3" /home/gcf/anaconda3/lib/python3.6/site-packages/numpy/core/include
-- Found Loki: /usr/include
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0 and -save-temps
-- GCC Version >= 4.9. Adding -fstack-protector-strong
CMake Warning at /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:786 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:892 (_Boost_COMPONENT_DEPENDENCIES)
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:1523 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:95 (FIND_PACKAGE)

CMake Warning at /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:786 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:892 (_Boost_COMPONENT_DEPENDENCIES)
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:1523 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:95 (FIND_PACKAGE)

CMake Warning at /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:786 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:892 (_Boost_COMPONENT_DEPENDENCIES)
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:1523 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:95 (FIND_PACKAGE)

CMake Warning at /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:786 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:892 (_Boost_COMPONENT_DEPENDENCIES)
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:1523 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:95 (FIND_PACKAGE)

CMake Warning at /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:786 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:892 (_Boost_COMPONENT_DEPENDENCIES)
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:1523 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:95 (FIND_PACKAGE)

CMake Warning at /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:786 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:892 (_Boost_COMPONENT_DEPENDENCIES)
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:1523 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:95 (FIND_PACKAGE)

CMake Warning at /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:786 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:892 (_Boost_COMPONENT_DEPENDENCIES)
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:1523 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:95 (FIND_PACKAGE)

CMake Warning at /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:786 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:892 (_Boost_COMPONENT_DEPENDENCIES)
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:1523 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:95 (FIND_PACKAGE)

CMake Warning at /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:786 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:892 (_Boost_COMPONENT_DEPENDENCIES)
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:1523 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:95 (FIND_PACKAGE)

CMake Warning at /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:786 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:892 (_Boost_COMPONENT_DEPENDENCIES)
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindBoost.cmake:1523 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:95 (FIND_PACKAGE)

-- Looking for pthread.h
-- Looking for 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
-- Boost version: 1.67.0
-- Found the following Boost libraries:
-- python
-- thread
-- filesystem
-- iostreams
-- regex
-- serialization
-- system
-- date_time
-- chrono
-- atomic
-- Boost_VERSION: 106700
-- Boost_LIB_VERSION: 1_67
-- Boost_INCLUDE_DIRS: /usr/local/include
-- Boost_LIBRARIES: /usr/lib/x86_64-linux-gnu/libboost_python.so/usr/lib/x86_64-linux-gnu/libboost_thread.so/usr/lib/x86_64-linux-gnu/libboost_filesystem.so/usr/lib/x86_64-linux-gnu/libboost_iostreams.so/usr/lib/x86_64-linux-gnu/libboost_regex.so/usr/lib/x86_64-linux-gnu/libboost_serialization.so/usr/lib/x86_64-linux-gnu/libboost_system.so/usr/lib/x86_64-linux-gnu/libboost_date_time.so/usr/lib/x86_64-linux-gnu/libboost_chrono.so/usr/lib/x86_64-linux-gnu/libboost_atomic.so
-- Found Eigen3: /usr/local/include/eigen3 (Required is at least version "2.91.0")
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Found ZLIB: /usr/local/lib/libz.so (found version "1.2.9")
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found version "2.7.12")
-- Found Eigen3, version: 3.3.90
-- Disable vectorization
-- Found VTK
-- Found OpenMP_C: -fopenmp (found version "4.0")
-- Found OpenMP_CXX: -fopenmp (found version "4.0")
-- Found OpenMP
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Checking for one of the modules 'glib-2.0'
-- Found GLib2: glib-2.0 /usr/include/glib-2.0;/usr/lib/x86_64-linux-gnu/glib-2.0/include
-- Looking for include file glib/gregex.h
-- Looking for include file glib/gregex.h - not found
-- Found GTS
-- Found GLUT: /usr/lib/x86_64-linux-gnu/libglut.so
-- Found QGLVIEWER-qt5: /usr/include/QGLViewer
-- Found GUI-Qt5-LIBS
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found GMP: /usr/include/x86_64-linux-gnu
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found CGAL
-- SuiteSparse version 4.4.6 found, CHOLMOD direct solver for CPU activated.
-- Found Cholmod: /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas: /usr/lib/libopenblas.so
-- Found Metis: /usr/local/include
-- Found Cholmod in /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas in /usr/lib/libopenblas.so
-- Found Metis in /usr/local/lib/libmetis.a
-- Found GL2PS
LBMFLOW is still experimental, building and running LBM engine are at your own risk!
Yade will be installed to /media/gcf/3TB-FOUR/YadeWC/install
-- Suffix is set to -2018.02b
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /media/gcf/3TB-FOUR/YadeWC/install
-- Could NOT find gts (missing: PY_gts)
-- Use embedded version of gts. Please, consider installing the corresponding package
CMake Error at /home/gcf/anaconda3/share/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find minieigen (missing: PY_minieigen)
Call Stack (most recent call first):
  /home/gcf/anaconda3/share/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:377 (_FPHSA_FAILURE_MESSAGE)
  cMake/FindPythonModule.cmake:22 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
  CMakeLists.txt:559 (find_python_module)

Question information

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Revision history for this message
Robert Caulk (rcaulk) said :
#1

Hello,

You seem to be missing other libraries in addition to python-minieigen. I would recommend following this document closely [1] and installing all libraries.

Based on your cmake outout you at the very least need:

sudo apt-get install python-minieigen python-gts libboost-all-dev

Cheers,

Robert

[1]https://yade-dem.org/doc/installation.html#prerequisites

Revision history for this message
WANG Chao (cwangbh) said :
#2

Dear Robert,

Thank you for your kind reply, I just tried your suggestions and find that i have installed all the libraries.
I followed the whole procedure and updated my boost_python libraries, but it still not works.

gcf@gcf-OptiPlex-9020:/media/gcf/3TB-FOUR/YadeWC/build$ sudo apt-get install python-minieigen python-gts libboost-all-dev
[sudo] password for gcf:
Reading package lists... Done
Building dependency tree
Reading state information... Done
libboost-all-dev is already the newest version (1.58.0.1ubuntu1).
python-gts is already the newest version (0.3.1-6).
python-minieigen is already the newest version (0.50.3+dfsg1-4build1).
0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.

Revision history for this message
Robert Caulk (rcaulk) said :
#3

Hello Wang,

Very strange, will you try preceding your cmake command with "sudo"?

Let me know,

rc

Revision history for this message
JIPEIQI (jpq-learning) said :
#4

try
python -c "import minieigen"

Revision history for this message
WANG Chao (cwangbh) said :
#5

Dear JIPEIQI,

I tried and it gives me the following message:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0: undefined symbol: PyClass_Type

Revision history for this message
Jérôme Duriez (jduriez) said :
#6

Hi,

According to your initial question, you have installed both "python3-minieigen" (for Python 3) and "python-minieigen" (for Python 2, e.g. 2.7).

I'm fearing this can confuse your computer and prevent YADE/Python to access the right version of this package (the python-minieigen one, for 2.7, I think).

At the very least, I would try uninstall python3-minieigen package ?

Can you help with this problem?

Provide an answer of your own, or ask WANG Chao for more information if necessary.

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