Undefined symbol : zpotrf_

Hi Hicham,
zpotrf is a Lapack function. So for some reason lapack is wrongly linked.
But I am not able to tell you how to fix it..
cheers
Jan

2016-05-09 17:13 GMT+02:00 Hicham BENNIOU <
<email address hidden>>:

> New question #293500 on Yade:
> https://answers.launchpad.net/yade/+question/293500
>
> Hello everyone,
>
> So In order to prepare for a pull request, I merged the changes in the
> Yade trunk with my fork then updated the local files and compiled from
> scratch (clean build) to check for issues.
>
> cmake : gives no errors or warnings.
>
> make install : runs smoothly
>
> but when I run yade I get this :
>
> Welcome to Yade 2016-05-09.git-145e975
> Traceback (most recent call last):
> File "./yade-2016-05-09.git-145e975", line 129, in <module>
> import yade
> File
> "/home/3S-LAB/hbenniou/Yade/install/lib/x86_64-linux-gnu/yade-2016-05-09.git-145e975/py/yade/__init__.py",
> line 65, in <module>
> import boot
> ImportError:
> /home/3S-LAB/hbenniou/Yade/install/lib/x86_64-linux-gnu/yade-2016-05-09.git-145e975/libyade.so:
> undefined symbol: zpotrf_
>
> Any ideas where this comes from ?
>
>
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Thanks Jan for the answer.

However, after multiple verification, everything seems installed and up to date.

other versions run with no problem. I think I'll stick with an older version for now.

I'll post here if I find the problem.

Please specify an operating system, which you use.

Hi Anton,

I'm on Ubuntu 14.04

By the way, here is the cmake "produce"

-- The C compiler identification is GNU 4.8.4
-- The CXX compiler identification is GNU 4.8.4
-- 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
-- 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 PythonInterp: /usr/bin/python (found version "2.7.6")
-- 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 "4.8.6")
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.26")
-- Version is set to 2016-05-09.git-145e975
-- 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 "1.8.2" /usr/lib/python2.7/dist-packages/numpy/core/include
-- Found Loki: /usr/include
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0 and -save-temps
-- Boost version: 1.54.0
-- Found the following Boost libraries:
-- python
-- thread
-- filesystem
-- iostreams
-- regex
-- serialization
-- system
-- date_time
-- Boost_VERSION: 105400
-- Boost_LIB_VERSION: 1_54
-- Boost_INCLUDE_DIRS: /usr/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/libpthread.so
-- Found Eigen3: /usr/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 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 "1.2.8")
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found version "2.7.6")
-- Found Eigen3, version: 3.2.1
-- Disable vectorization
-- 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 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: /usr/include/QGLViewer
-- Found Qt4: /usr/bin/qmake (found version "4.8.6")
-- 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/x86_64-linux-gnu
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found CGAL
-- Found Cholmod: /usr/local/lib/libcholmod.a
-- Found OpenBlas: /usr/lib/libopenblas.so
-- Found Metis: /usr/include/metis
-- Found Cholmod
-- Found OpenBlas
-- Found Metis
-- Found GL2PS
LBMFLOW is still experimental, building and running LBM engine are at your own risk!
Yade will be installed to /home/3S-LAB/hbenniou/Yade/install
-- Suffix is set to -2016-05-09.git-145e975
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/3S-LAB/hbenniou/Yade/install
-- Found gts: /usr/lib/python2.7/dist-packages/gts
-- Use system gts version
-- Found minieigen: /usr/lib/python2.7/dist-packages/minieigen.so
-- Found Tkinter: /usr/lib/python2.7/lib-tk/Tkinter.pyc
-- ===========================================================
-- Yade configured with following features: Odeint VTK OpenMP GTS GUI CGAL PFVFLOW LINSOLV GL2PS LBMFLOW
-- Disabled features: SPH LIQMIGRATION MASK_ARBITRARY PROFILING PotentialParticles
-- Optimized build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/3S-LAB/hbenniou/Yade/build

Thanks Anton Gladky, that solved my question.

Thanks Anton,

By deleting /usr/local/lib/libcholmod.a and recompiling a fresh build, it worked perfectly !