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compucell3d_installation [2016/12/16 10:15] (Version actuelle)
Ligne 1: Ligne 1:
 +Modifié par Calvat, le 27 May 2015\\
 +\\
 +
 +====== Compucell3D installation ======
 +
 +\\
 +\\
 +
 +=====  Compucell3D compliation on redhat ​ =====
 +
 +
 +====  Prérequis ​ ====
 +
 +Les compilations seront effectuées pour l'​environnement SL6 64 bits.
 +  * Se connecter sur ccagesl6.in2p3.fr
 +  * Créer un répertoire /​scratch/​compil
 +  * Répertoire d'​installation : /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64
 +
 +{{:​compucell3d3.1installguidelinux.pdf|compucell3d3 installation guide}} ​
 +====  CMake 2.8.2 installation ​ ====
 +
 +<​code>​
 +cd /​scratch/​compil
 +wget http://​www.cmake.org/​files/​v2.8/​cmake-2.8.12.tar.gz
 +tar vxfz cmake-2.8.12.tar.gz
 +./configure --prefix=/​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​cmake-2.8.12
 +make
 +make install
 +</​code>​
 +Modifier $HOME/​.cshrc
 +<​code>​
 +setenv PATH /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​cmake-2.8.12/​bin:​${PATH}:​.
 +</​code>​
 +
 +====  Qt 4.8 installation ​ ====
 +
 +<​code>​
 +cd /​scratch/​compil
 +wget http://​download.qt-project.org/​official_releases/​qt/​4.8/​4.8.5/​qt-everywhere-opensource-src-4.8.5.tar.gz
 +tar xvfz qt-everywhere-opensource-src-4.8.5.tar.gz
 +./configure -no-xkb -no-phonon -no-phonon-backend -no-dbus -nomake demos -nomake examples --prefix=/​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​qt-4.8.5
 +  ->o
 +  ->yes
 +gmake
 +gmake install
 +</​code>​
 +
 +====  Python-2.7.5 installation ​ ====
 +
 +<​code>​
 +cd /​scratch/​compil
 +wget http://​www.python.org/​ftp/​python/​2.7.5/​Python-2.7.5.tar.bz2
 +tar -xvjpf Python-2.7.5.tar.bz2
 +cd Python-2.7.5
 +./configure --prefix=/​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​python-2.7.5 --enable-shared --enable-unicode=ucs4
 +make
 +make install
 +</​code>​
 +From "​make"​ : Missing module
 +<​code>​
 +Python build finished, but the necessary bits to build these modules were not found:
 +bsddb185 ​          ​dl ​                ​imageop
 +sunaudiodev
 +To find the necessary bits, look in setup.py in detect_modules() for the module'​s name.
 +</​code>​
 +Modifier $HOME/​.cshrc
 +<​code>​
 +setenv PATH /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​python-2.7.5/​bin:​${PATH}:​.
 +</​code>​
 +
 +====  vtk-5.8.0 installation ​ ====
 +
 +<​code>​
 +cd /​scratch/​compil
 +wget http://​www.vtk.org/​files/​release/​5.8/​vtk-5.8.0.tar.gz
 +tar xvfz vtk-5.8.0.tar.gz
 +cd VTK
 +</​code>​
 +<​code>​
 +ccmake .
 +  -> c
 +  -> CMAKE_INSTALL_PREFIX=/​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​vtk-5.8.0
 +  -> PYTHON_EXECUTABLE=/​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​python-2.7.5
 +  -> VTK_PYTHON_WRAP to ON 
 +  -> BUILD_SHARED_LIBS to ON
 +  -> c
 +  -> c
 +  -> g
 +make 
 +make install
 +</​code>​
 +
 +====  QScintilla-2.7.2 installation ​ ====
 +
 +{{:​qscintilla.pdf|qscintilla installation guide}}
 +<​code>​
 +cd /​scratch/​compil
 +wget http://​sourceforge.net/​projects/​pyqt/​files/​QScintilla2/​QScintilla-2.7.2/​QScintilla-gpl-2.7.2.tar.gz
 +tar xvfz QScintilla-gpl-2.7.2.tar.gz
 +cd QScintilla-gpl-2.7.2
 +cd Qt4Qt5
 +/​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​qt-5.1.1/​bin/​qmake
 +make
 +make install
 +</​code>​
 +
 +====  swig-2.0.11 installation ​ ====
 +
 +<​code>​
 +cd /​scratch/​compil
 +wget http://​downloads.sourceforge.net/​project/​swig/​swig/​swig-2.0.11/​swig-2.0.11.tar.gz
 +tar xvfz swig-2.0.11.tar.gz
 +cd swig-2.0.11
 +configure --without-pcre --prefix=/​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​swig-2.0.11
 +make
 +make install
 +</​code>​
 +
 +====  sip-4.15.3 installation ​ ====
 +
 +<​code>​
 +cd /​scratch/​compil
 +wget http://​sourceforge.net/​projects/​pyqt/​files/​sip/​sip-4.15.3/​sip-4.15.3.tar.gz
 +tar xvfz sip-4.15.3.tar.gz
 +cd sip-4.15.3
 +python configure.py
 +make
 +make install
 +</​code>​
 +
 +====  PyQt4 installation ​ ====
 +
 +<​code>​
 +cd /​scratch/​compil
 +wget http://​sourceforge.net/​projects/​pyqt/​files/​PyQt4/​PyQt-4.10.3/​PyQt-x11-gpl-4.10.3.tar.gz
 +tar xvfz PyQt-x11-gpl-4.10.3.tar.gz
 +cd PyQt-x11-gpl-4.10.3
 +python configure.py -q /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​qt-4.8.5/​bin/​qmake
 +make 
 +make install
 +</​code>​
 +
 +====  Qwt 6.0.2 installation ​ ====
 +
 +<​code>​
 +cd /​scratch/​compil
 +wget http://​ftp5.gwdg.de/​pub/​linux/​archlinux/​extra/​os/​x86_64/​qwt-6.0.2-2-x86_64.pkg.tar.xz
 +tar xvfJ qwt-6.0.2-2-x86_64.pkg.tar.xz
 +cp -r usr/ /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​qwt-6.0.2
 +</​code>​
 +
 +====  BionetSolver first method ​ ====
 +
 +
 +===  SBML installation ​ ===
 +
 +<​code>​
 +cd /​scratch/​compil
 +./configure --prefix=/​afs/​in2p3.fr/​throng/​cgmc/​sl6_64/​libsbml-3.4.1
 +unzip libsbml-3.4.1-src.zip
 +cd libsbml-3.4.1
 +make
 +make install
 +</​code>​
 +
 +===  Sundials installation ​ ===
 +
 +<​code>​
 +cd /​scratch/​compil
 +tar xvfz sundials-2.3.0.tar.gz
 + cd sundials-2.3.0
 +./configure --prefix=/​afs/​in2p3.fr/​throng/​cgmc/​sl6_64/​sundials-2.3.0
 +make 
 +make install
 +</​code>​
 +
 +===  BionetSolver installation ​ ===
 +
 +<​code>​
 +cd /​scratch/​compil
 +git clone -b 3.6.2 https://​github.com/​CompuCell3D/​CompuCell3D.git
 +cd BionetSolver/​0.0.6
 +ccmake .
 +</​code>​
 +<​code>​
 +BUILD_PYTHON_BINDINGS -> ON
 +BUILD_SHARED_LIB -> OFF
 +BUILD_STATIC_LIB -> OFF
 +CMAKE_AR -> /usr/bin/ar
 +CMAKE_BACKWARDS_COMPATIBILITY -> 2.4
 +CMAKE_BUILD_TYPE
 +CMAKE_COLOR_MAKEFILE -> ON
 +CMAKE_CXX_COMPILER -> /​usr/​bin/​c++
 +CMAKE_CXX_FLAGS
 +CMAKE_CXX_FLAGS_DEBUG -> -g
 +CMAKE_CXX_FLAGS_MINSIZEREL -> -Os -DNDEBUG
 +CMAKE_CXX_FLAGS_RELEASE -> -O3 -DNDEBUG
 +CMAKE_CXX_FLAGS_RELWITHDEBINFO -> -O2 -g
 +CMAKE_C_COMPILER -> /​usr/​bin/​gcc
 +CMAKE_C_FLAGS
 +CMAKE_C_FLAGS_DEBUG -> -g
 +CMAKE_C_FLAGS_MINSIZEREL -> -Os -DNDEBUG
 +CMAKE_C_FLAGS_RELEASE -> -O3 -DNDEBUG
 +CMAKE_C_FLAGS_RELWITHDEBINFO -> -O2 -g
 +CMAKE_EXE_LINKER_FLAGS
 +CMAKE_EXE_LINKER_FLAGS_DEBUG
 +CMAKE_EXE_LINKER_FLAGS_MINSIZE
 +CMAKE_EXE_LINKER_FLAGS_RELEASE
 +CMAKE_EXE_LINKER_FLAGS_RELWITH
 +CMAKE_INSTALL_PREFIX -> /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​compucell3d-3.6.2
 +CMAKE_LINKER -> /usr/bin/ld
 +CMAKE_MAKE_PROGRAM -> /​usr/​bin/​gmake
 +CMAKE_MODULE_LINKER_FLAGS
 +CMAKE_MODULE_LINKER_FLAGS_DEBU
 +CMAKE_MODULE_LINKER_FLAGS_MINS
 +CMAKE_MODULE_LINKER_FLAGS_RELE
 +CMAKE_MODULE_LINKER_FLAGS_RELW
 +CMAKE_NM -> /usr/bin/nm
 +CMAKE_OBJCOPY -> /​usr/​bin/​objcopy
 +CMAKE_OBJDUMP -> /​usr/​bin/​objdump
 +CMAKE_RANLIB -> /​usr/​bin/​ranlib
 +CMAKE_SHARED_LINKER_FLAGS
 +CMAKE_SHARED_LINKER_FLAGS_DEBU
 +CMAKE_SHARED_LINKER_FLAGS_MINS
 +CMAKE_SHARED_LINKER_FLAGS_RELE
 +CMAKE_SHARED_LINKER_FLAGS_RELW
 +CMAKE_SKIP_RPATH -> OFF
 +CMAKE_STRIP -> /​usr/​bin/​strip
 +CMAKE_USE_RELATIVE_PATHS OFF
 +CMAKE_VERBOSE_MAKEFILE OFF
 +EXECUTABLE_OUTPUT_PATH
 +LIBRARY_OUTPUT_PATH
 +LIBSBML_INSTALL_DIR -> /​afs/​in2p3.fr/​throng/​cgmc/​sl6_64/​libsbml-3.4.1
 +PYTHON_EXECUTABLE -> /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​python-2.7.5/​bin/​python
 +PYTHON_INCLUDE_PATH -> /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​python-2.7.5/​include/​python2.7
 +PYTHON_LIBRARY -> /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​python-2.7.5/​lib/​libpython2.7.so
 +SUNDIALS_INSTALL_DIR -> /​afs/​in2p3.fr/​throng/​cgmc/​sl6_64/​sundials-2.3.0
 +SWIG_DIR -> /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​swig-2.0.11/​share/​swig/​2.0.11
 +SWIG_EXECUTABLE -> /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​swig-2.0.11/​bin/​swig
 +SWIG_VERSION -> 2.0.11
 +</​code>​
 +<​code>​
 +make
 +make install
 +</​code>​
 +It doesn'​t work during the runtime:\\
 +**\\
 +runScript.sh -i $THRONG_DIR/​sl6_64/​compucell3d-3.6.2/​Demos/​BionetSolverExamples/​DeltaNotchWithMitosis/​DeltaNotchWithMitosis.cc3d\\
 +->\\
 +“import Error/​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​compucell3d-3.6.2/​lib/​python/​_BionetSolverPy.so:​ undefined symbol: _ZNK25BionetworkTemplateLibrary18getSBMLModelByNameESs”\\
 +** 
 +====  BionetSolver second method ​ ====
 +
 +<​code>​
 +tar xvfz 3.7.0.tar.gz
 +cd 3.7.0
 +cp lib/​python/​BionetSolverPy.py
 +cp lib/​python/​BionetSolverPy.py $THRONG_DIR/​sl6_64/​compucell3d-3.6.2/​lib/​python/​
 +cp lib/​python/​_BionetSolverPy.so $THRONG_DIR/​sl6_64/​compucell3d-3.6.2/​lib/​python/​
 +cp pythonSetupScripts/​bionetAPI.py $THRONG_DIR/​sl6_64/​compucell3d-3.6.2/​pythonSetupScripts/​
 +cp lib/​libbionetsolver.so $THRONG_DIR/​sl6_64/​compucell3d-3.6.2/​lib/​
 +cp lib/​libsbmlsolver.so $THRONG_DIR/​sl6_64/​compucell3d-3.6.2/​lib/​
 +</​code>​
 +
 +====  Compucell3D installation ​ ====
 +
 +<​code>​
 +cd /​scratch/​compil
 +git clone -b 3.6.2 https://​github.com/​CompuCell3D/​CompuCell3D.git
 +cd CompuCell3D/​
 +ccmake CompuCell3D/​
 +  -> c
 +  -> CMAKE_INSTALL_PREFIX = /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​compucell3d-3.6.2
 +  -> VTK_DIR = /​afs/​in2p3.fr/​home/​throng/​cgmc/​sl6_64/​vtk-5.8.0/​lib/​vtk-5.8
 +  -> c
 +  -> g
 +make 
 +make install
 +</​code>​
 +=====  Compucell3D installation on ubuntu 64 bits Ubuntu_12.04_amd64 ​ =====
 +
 +<​code>​
 +>uname -a
 +Linux cmdbuild-vm 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
 +</​code>​
 +Install dependencies
 +<​code>​
 +apt-get install libvtk5-qt4-dev g++ swig libqwt5-qt4-dev python-qt4 python-qscintilla2 cmake-gui python-qt4-gl python-vtk python-qwt5-qt4 python-dev libxml2-dev build-essential git
 +</​code>​
 +Intall compucell3d deb package
 +<​code>​
 +wget http://​sourceforge.net/​projects/​cc3d/​files/​3.7.0/​linux/​compucell3d-3.7.0-12.04-x86_64-20130920.deb
 +
 +dpkg  --force-all -i compucell3d-3.7.0-12.04-x86_64-20130920.deb
 +</​code>​
 +Run compucell3D
 +<​code>​
 +/​usr/​lib/​compucell3d/​compucell3d.sh ​
 +</​code>​
 +
  
  • compucell3d_installation.txt
  • Dernière modification: 2016/12/16 10:15
  • (modification externe)