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Message #11001
[Bug 1333699] Re: libyade.so: undefined symbol: openblas_set_num_threads
Fixed by installing openblas locally.
For the record (I think it has been mentionned before, but not so sure): installing openblas on 12.04 breaks numpy.
The solution is to type "sudo update-alternatives" and to unselect openblas as the default for libblas.so and libblas.so.3gf.
Both standard blas or "atlas" blas are valid replacements.
Openblas will be used only if explicitely linked, which is the case in yade code.
** Changed in: yade
Status: New => Invalid
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https://bugs.launchpad.net/bugs/1333699
Title:
libyade.so: undefined symbol: openblas_set_num_threads
Status in Yet Another Dynamic Engine:
Invalid
Bug description:
Hi，
I can compile yade from trunk, but when I launch it, that complains:
Welcome to Yade 2014-06-23.git-6d9f9b3
Traceback (most recent call last):
File "./yade-chao", line 127, in <module>
import yade
File "/home/3S-LAB/cyuan/yade/lib/x86_64-linux-gnu/yade-chao/py/yade/__init__.py", line 65, in <module>
import boot
ImportError: /home/3S-LAB/cyuan/yade/lib/x86_64-linux-gnu/yade-chao/libyade.so: undefined symbol: openblas_set_num_threads
CMake configure:
cmake -DINSTALL_PREFIX=/home/3S-LAB/cyuan/yade/ /home/3S-LAB/cyuan/trunk -DSUFFIX="-chao"
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - 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
-- Found PythonLibs: /usr/lib/libpython2.7.so
-- Found PythonInterp: /usr/bin/python (found version "2.7.3")
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- 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 (found version "4.8.1")
-- Version is set to 2014-06-24.git-c38c4a6
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /usr/lib/x86_64-linux-gnu/libX11.so
-- 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/CGAL, /usr/lib/libCGAL.so
-- Found NumPy: version "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include
-- Found Loki: /usr/include
-- Boost version: 1.46.1
-- Found the following Boost libraries:
-- python
-- thread
-- filesystem
-- iostreams
-- regex
-- serialization
-- system
-- date_time
-- Boost_VERSION: 104601
-- Boost_LIB_VERSION: 1_46_1
-- Boost_INCLUDE_DIRS: /usr/include
-- Boost_LIBRARIES: /usr/lib/libboost_python.so/usr/lib/libboost_thread-mt.sopthread/usr/lib/libboost_filesystem-mt.so/usr/lib/libboost_iostreams-mt.so/usr/lib/libboost_regex-mt.so/usr/lib/libboost_serialization-mt.so/usr/lib/libboost_system-mt.so/usr/lib/libboost_date_time-mt.so
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0")
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so - found
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.3.4")
-- Found Eigen3, version: 3.2.0
CMake Warning at CMakeLists.txt:139 (MESSAGE):
Minimal recommended Eigen3 version is 3.2.1
-- Disable vectorization
-- Boost Odeint can be enabled, only if Boost>=1.53 is used
-- 1
-- 46
-- Found VTK
-- 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 files HAVE_GLIB_GREGEX_H
-- Looking for include files HAVE_GLIB_GREGEX_H - found
-- Found GTS
-- Found Qt4: /usr/bin/qmake (found version "4.8.1")
-- Found QGLViewer: /usr/lib/x86_64-linux-gnu/libqglviewer-qt4.so
-- Found GUI-LIBS
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found GMP: /usr/include
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found CGAL
-- Found Cholmod: /usr/lib/libcholmod.so
-- Found OpenBlas: /usr/lib/libblas.so
-- Found Metis: /usr/include/metis
-- Found Cholmod
-- Found OpenBlas
-- Found Metis
-- Found GL2PS
-- Boost version is less than 1.47, using embedded version of floating_point_utilities_v3
-- Consider updating boost or system, as this embedded library will be removed soon
Yade will be installed to /home/3S-LAB/cyuan/yade
-- Suffix is set to -chao
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/3S-LAB/cyuan/yade
-- Could NOT find gts (missing: PY_gts)
-- Use embedded version of gts. Please, consider installing the corresponding package
-- Could NOT find minieigen (missing: PY_minieigen)
-- Use embedded version of minieigen. Please, consider installing the corresponding package
-- Found Tkinter: /usr/lib/python2.7/lib-tk/Tkinter.pyc
-- ===========================================================
-- Yade configured with following features: Eigen3 VTK OpenMP GTS GUI CGAL PFVflow LinSolv GL2PS
-- Disabled features: Odeint SPH LIQMIGRATION LBMFLOW MASK_ARBITRARY
-- Optimized build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/3S-LAB/cyuan/build
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