Building CompuCell3D on Mac OS X

Compiling CompuCell3D from source code requires several 3rd-party software libraries. Once all software dependencies have been satisfied, building CompuCell3D from source on Mac OS X systems is fairly straightforward.

Prerequisites

Software

gcc

Default compilers on Mac OS X are Clang and LLVM. Recent Xcode dev tools don't include standard gcc compilers.

To rely on a single C/C++ compiler, CC3D is compiled using standard gcc on Mac OS X as well. Various precompiled gcc packages for Mac OS X are available at http://hpc.sourceforge.net.

CC3D 3.6.2 source code is currently compiled with gcc 4.6. To compile CC3D with gcc 4.7 or newer (on any platform), there are porting issues caused by name lookup changes in gcc. Adding the "-fpermissive" flag when invoking gcc allows gcc 4.7 to compile CC3D.

cmake

CC3D is built using cmake. Binary distributions can be obtained from the Kitware cmake website .

Software Dependencies

Both the gcc binary distribution for OS X, as well as other required 3rd-party software libraries, can be placed in any directory. A subdirectory of /Users/Shared/ can be used for system-wide access from any username.

A known working set of required software libraries and versions for compiling CompuCell3D on OS X 10.8:

Qt - 4.8.3
sip - 4.13.3
PyQt - 4.9.4
PyQwt - 5.2.0
QScintilla - 2.6.2
VTK - 5.8.0

For more details about building all the required 3rd-party software libraries from source code on Mac OS X, the Building CompuCell3D from source code on Mac OS X document is available on the CompuCell 3D Developer Site on github.iu.edu .

Hardware

CompuCell3D builds and runs on any Mac hardware capable of running OS X 10.8 "Mountain Lion".

Source Code

Once all 3rd-party software dependencies have been satisfied, obtain the source code from our SVN repository using the following command:

mkdir CC3D_GIT
cd CC3D_GIT
git clone -b 3.7.0 https://github.com/CompuCell3D/CompuCell3D.git .

This will download the source code into CC3D_GIT.

Compiling CC3D

A complete CompuCell3D distribution can be built with the following Python script. Set the PATH strings in the Python script to where gcc and other 3rd-party libraries have been installed. Running the following script will produce a complete CC3D 3.6.2 binary distribution on Mac OS X 10.8.x :

{{{#!/usr/bin/env python # <--- the above line asks the 'env' system command to find the python executable, and then executes it. # everything below is in python

# # # this script builds CompuCell3D 3.6.2 on Mac OS X 10.8.x # # #

# # # assuming that you already have installed Qt on your system, and # # downloaded and built VTK, SIP, PyQt, QScintilla, etc... # # # # this script also assumes that you have downloaded and built # # gcc 4.7.1 (or newer) including its OpenMP support libraries # # #

# # # 2010-2013 compucell3d.org # # edited by Mitja Hmeljak, # # based on 2009 script by Benjamin Zaitlen # # #

# # *** Please note *** # # this file will start working *only* after you manually set: # the PATH_TO_WORK_DIR string to your OWN path where you want to build CC3D, # as for example "/Users/Shared/CC3Ddev/CC3D362build" # the QT_LIB_DIR to your OWN path where you have installed Qt libraries, # as for example "/Users/Shared/CC3Ddev/Qt-4.8.3/lib" # the PYQT_SITE_PACKAGES_DIR to your OWN path where you have installed PyQt, # as for example "/Library/Python/2.6/site-packages" # the QWT_LIB_DIR to your OWN path where you have installed qwt, # as for example "/Users/Shared/CC3Ddev/PyQwt-5.2.0/PyQwt-5.2.0/qwt-5.2/lib" # the VTK_BIN_AND_BUILD_DIR to your OWN path where you have installed VTK, # as for example "/Users/Shared/CC3Ddev/VTK_5.8.0_bin_and_build" # the GCC_DIR string to your OWN path where you have the GCC 4.7.1 distribution: # as for example "/Users/Shared/CC3Ddev/gcc_4.7.1" # the CC3D_LOCAL_GIT string to your OWN path where you keep the local CC3D 3.6.2 git repository: # as for example "/Users/Shared/CC3Ddev/git_CC3D/CompuCell3D/CompuCell3D" # the BIONET_LOCAL_GIT string to your OWN path where you keep the BIONET 0.0.6 git repository: # as for example "/Users/Shared/CC3Ddev/git_CC3D/CompuCell3D/BionetSolver/0.0.6" # the CELLDRAW_LOCAL_GIT string to your OWN path where you keep the CELLDRAW git repository: # as for example "/Users/Shared/CC3Ddev/git_CC3D/CompuCell3D/CellDraw/1.5.1/src"

PATH_TO_WORK_DIR = "/Users/Shared/CC3Ddev/CC3D362build" QT_LIB_DIR = "/Users/Shared/CC3Ddev/Qt-4.8.3/lib" PYQT_SITE_PACKAGES_DIR = "/Library/Python/2.6/site-packages" QWT_LIB_DIR = "/usr/local/qwt-5.2.1-svn/lib" VTK_BIN_AND_BUILD_DIR = "/Users/Shared/CC3Ddev/VTK_5.8.0_bin_and_build" GCC_DIR = "/Users/Shared/CC3Ddev/gcc_4.7.1" CC3D_LOCAL_GIT = "/Users/Shared/CC3Ddev/git_CC3D/CompuCell3D/CompuCell3D" BIONET_LOCAL_GIT = "/Users/Shared/CC3Ddev/git_CC3D/CompuCell3D/BionetSolver/0.0.6" CELLDRAW_LOCAL_GIT = "/Users/Shared/CC3Ddev/git_CC3D/CompuCell3D/CellDraw/1.5.1/src"

# # after you've set the above PATH strings with your own setting, run this script in Terminal.app #

import sys, shutil, os from subprocess import call

print "###########################################" print "building CompuCell3D 3.6.2 on Mac OS X 10.8" print "###########################################"

if (PATH_TO_WORK_DIR == "") or (QT_LIB_DIR == "") or (PYQT_SITE_PACKAGES_DIR == "") or (VTK_BIN_AND_BUILD_DIR == "") or (GCC_DIR == "") or (CC3D_LOCAL_GIT == "") or (BIONET_LOCAL_GIT == "") or (CELLDRAW_LOCAL_GIT == ""):

print "This file will start working *only* after you manually..." print "... set the PATH_TO_WORK_DIR string to your OWN path where you want to build CC3D," print "... set the QT_LIB_DIR string to your OWN path where you have installed Qt libraries,"
print "... set the PYQT_SITE_PACKAGES_DIR string to your OWN path where you have installed PyQt," print "... set the QWT_LIB_DIR string to your OWN path where you have installed Qwt," print "... set the VTK_BIN_AND_BUILD_DIR to your OWN path where you have installed VTK," print "... set the GCC_DIR string to your OWN path where you have installed GCC 4.7.1," print "... set the CC3D_LOCAL_GIT string to your OWN path to your local CC3D 3.6.2 git copy." print "... set the BIONET_LOCAL_GIT string to your OWN path to your local BIONET 0.0.6 git copy." print "... and the CELLDRAW_LOCAL_GIT string to your OWN path to your local CellDraw git copy." print "" print "Please open this script in a text editor and read code comments for more information." print "" sys.exit(1)

else:

print "=====>=====> PATH_TO_WORK_DIR = " + PATH_TO_WORK_DIR print "=====>=====> QT_LIB_DIR = " + QT_LIB_DIR print "=====>=====> PYQT_SITE_PACKAGES_DIR " + PYQT_SITE_PACKAGES_DIR print "=====>=====> QWT_LIB_DIR " + QWT_LIB_DIR print "=====>=====> VTK_BIN_AND_BUILD_DIR = " + VTK_BIN_AND_BUILD_DIR print "=====>=====> GCC_DIR = " + GCC_DIR print "=====>=====> CC3D_LOCAL_GIT = " + CC3D_LOCAL_GIT print "=====>=====> BIONET_LOCAL_GIT = " + BIONET_LOCAL_GIT print "=====>=====> CELLDRAW_LOCAL_GIT = " + CELLDRAW_LOCAL_GIT print "... CC3D build starting ..."

# # # set, clear and create directories # # for building CC3D using CMAKE, # # 3rd party supporting libraries, # # distribution binaries # # #

print "=====>=====> the previous umask was =", os.umask(022) print "=====>=====> now the umask is =", os.umask(022)

CC3D_ENDUSER_DIR_NAME = 'CC3D_3.6.2_MacOSX_10.8' CC3D_ENDUSER_DIR_NAME_TMP = 'CC3D_3.6.2_MacOSX_10.8_tmp' CC3D_ARCHIVE = 'CC3D_3.6.2_MacOSX_10.8.zip'

# # WHY are in some "os.path.join()" calls passed *two* arguments to join directory paths, when the 2nd argument is an absolute path anyway? #

# # # BUILD_DIR_FOR_CMAKE # # #

# BUILD_DIR_FOR_CMAKE is the directory into which CMAKE will conduct the entire build: # # (this directory is NOT the place where we run the scripts to prepare a CC3D distribution) # BUILD_DIR_FOR_CMAKE=os.path.join(PATH_TO_WORK_DIR, 'build_dir_aka_cmake_install_dir') print "=====>=====> BUILD_DIR_FOR_CMAKE = " + BUILD_DIR_FOR_CMAKE

# first clean, then create the directory - if os.path.isdir(BUILD_DIR_FOR_CMAKE):

print "=====>=====> Build directory (for CMAKE doing CC3D) exists... Removing ", BUILD_DIR_FOR_CMAKE, " and creating new directory." shutil.rmtree(BUILD_DIR_FOR_CMAKE)

# create the directory used during CMAKE's build and its own installation procedure: os.mkdir(BUILD_DIR_FOR_CMAKE)

# # # DEP_DIR creation # # #

# # DEP_DIR is the directory into which we place ALL 3rd party dependency libraries, for building # DEP_DIR=os.path.join(PATH_TO_WORK_DIR, 'third_party_support_libs_dependencies') print "=====>=====> DEP_DIR = " + DEP_DIR

# For CC3D 3.6.2, it is necessary to manually include two libraries to support OpenMP: OPENMP_LIBS_DEP_DIR=os.path.join(DEP_DIR,'OpenMPlib') print "=====>=====> OPENMP_LIBS_DEP_DIR = " + OPENMP_LIBS_DEP_DIR

# For CC3D 3.6.2, it is necessary to manually include QScintilla libraries for twedit++: QSCINTILLA_LIBS_DEP_DIR=os.path.join(DEP_DIR,'QScintillalib') print "=====>=====> QSCINTILLA_LIBS_DEP_DIR = " + QSCINTILLA_LIBS_DEP_DIR

# For CC3D 3.6.2, only Qt libraries go in the DEP_DIR directory. # (in CC3D 3.4.1 and previous, versions of VTK, Qt, etc. were placed in other subdirectories) # The Qt binaries copied from within the Qt installation frameworks go in here: QT_DEPS_DEP_DIR=os.path.join(DEP_DIR,'Deps') print "=====>=====> QT_DEPS_DEP_DIR = " + QT_DEPS_DEP_DIR

# For CC3D 3.6.2, almost all dependencies are placed temporarily in this directory: FOR_PLAYER_DEP_DIR=os.path.join(DEP_DIR,'ForPlayerDir') print "=====>=====> FOR_PLAYER_DEP_DIR = " + FOR_PLAYER_DEP_DIR # # Subdirectories have to be created (inside what will become "player/" in the final distribution) into which various libraries will be copied: # VTKLibs/ <--- all .dylib library files from the VTK distribution's "lib/vtk-5.8/" directory # vtk/ <--- all files from the VTK distribution's "Wrapping/Python/vtk/" for Python AND ALSO all files ending in .so from VTK's build/bin directory # PyQt4/ <--- the "PyQt4" directory from the system-wide "site-packages/" PyQt distribution # no subdirectory for sip* files from the system-wide "site-packages/" PyQt distribution # so the above directory for 3rd party support libraries has to contain the following: DEP_LIBVTK_DIR=os.path.join(FOR_PLAYER_DEP_DIR,'VTKLibs') print "=====>=====> DEP_LIBVTK_DIR = " + DEP_LIBVTK_DIR DEP_VTK_DIR=os.path.join(FOR_PLAYER_DEP_DIR,'vtk') print "=====>=====> DEP_VTK_DIR = " + DEP_VTK_DIR DEP_PYQT_DIR=os.path.join(FOR_PLAYER_DEP_DIR,'PyQt4') print "=====>=====> DEP_PYQT_DIR = " + DEP_PYQT_DIR DEP_PYQWT_DIR=os.path.join(DEP_PYQT_DIR,'Qwt5')

if os.path.isdir(DEP_DIR):

print "=====>=====> 3rd party dependency libraries directory exists... Removing ", DEP_DIR, " and creating new 3rd party directory." shutil.rmtree(DEP_DIR)

print "=====>=====> Creating 3rd party dependency libraries directories, DEP_DIR = ", DEP_DIR os.mkdir(DEP_DIR) print "=====>=====> Creating 3rd party dependency libraries directories, OPENMP_LIBS_DEP_DIR = ", OPENMP_LIBS_DEP_DIR os.mkdir(OPENMP_LIBS_DEP_DIR) print "=====>=====> Creating 3rd party dependency libraries directories, QSCINTILLA_LIBS_DEP_DIR = ", QSCINTILLA_LIBS_DEP_DIR os.mkdir(QSCINTILLA_LIBS_DEP_DIR) print "=====>=====> Creating 3rd party dependency libraries directories, QT_DEPS_DEP_DIR = ", QT_DEPS_DEP_DIR os.mkdir(QT_DEPS_DEP_DIR) print "=====>=====> Creating 3rd party dependency libraries directories, FOR_PLAYER_DEP_DIR = ", FOR_PLAYER_DEP_DIR os.mkdir(FOR_PLAYER_DEP_DIR) print "=====>=====> Creating 3rd party dependency libraries directories, DEP_LIBVTK_DIR = ", DEP_LIBVTK_DIR os.mkdir(DEP_LIBVTK_DIR) print "=====>=====> Creating 3rd party dependency libraries directories, DEP_VTK_DIR = ", DEP_VTK_DIR os.mkdir(DEP_VTK_DIR) print "=====>=====> Creating 3rd party dependency libraries directories, DEP_PYQT_DIR = ", DEP_PYQT_DIR os.mkdir(DEP_PYQT_DIR)

# # # DEP_DIR file copy # # #

print "=====>=====> now getting all 3rd party (previously compiled) dependency libraries into one place <=====<====="

os.chdir(OPENMP_LIBS_DEP_DIR) call('pwd') # in here we copy: three library files grabbed from the GCC 4.7.1 distribution we have on our system: # (if you download or build GCC 4.7.1 separately, modify the GCC_DIR path at the top of this script) call('rsync -rlPpa '+GCC_DIR+'/lib/libgomp.1.dylib . ',shell=True) call('rsync -rlPpa '+GCC_DIR+'/lib/libgcc_s.1.dylib . ',shell=True) call('rsync -rlPpa '+GCC_DIR+'/lib/libstdc++.6.dylib . ',shell=True)

os.chdir(QSCINTILLA_LIBS_DEP_DIR) call('pwd') # in here we copy: a library file grabbed from the QScintilla distribution, and create the necessary symlinks: call('rsync -rlPpa '+QT_LIB_DIR+'/libqscintilla2.8.0.2.dylib . ',shell=True) call('ln -f -s ./libqscintilla2.8.0.2.dylib ./libqscintilla2.dylib',shell=True) call('ln -f -s ./libqscintilla2.8.0.2.dylib ./libqscintilla2.8.dylib',shell=True) call('ln -f -s ./libqscintilla2.8.0.2.dylib ./libqscintilla2.8.0.dylib',shell=True)

os.chdir(QT_DEPS_DEP_DIR) call('pwd') # in here we copy: four binary files grabbed from WITHIN the frameworks that are part of the main Qt distribution: # (this could be done cleaner on Mac OS X - read developer.apple.com about it) call('rsync -rlPpa '+QT_LIB_DIR+'/QtGui.framework/Versions/Current/QtGui . ',shell=True) call('rsync -rlPpa '+QT_LIB_DIR+'/QtCore.framework/Versions/Current/QtCore . ',shell=True) call('rsync -rlPpa '+QT_LIB_DIR+'/QtNetwork.framework/Versions/Current/QtNetwork . ',shell=True) call('rsync -rlPpa '+QT_LIB_DIR+'/QtOpenGL.framework/Versions/Current/QtOpenGL . ',shell=True) call('rsync -rlPpa '+QT_LIB_DIR+'/QtXml.framework/Versions/Current/QtXml . ',shell=True) # in here also copy: the QtSvg library, even if it isn't used by any CC3D code, but qwt links to it: call('rsync -rlPpa '+QT_LIB_DIR+'/QtSvg.framework/Versions/Current/QtSvg . ',shell=True) # in here we copy: ALSO a .nib directory (although it might be cleaner to provide the entire framework) call('rsync -rlPpa '+QT_LIB_DIR+'/QtGui.framework/Versions/Current/Resources/qt_menu.nib . ',shell=True)

# 2011: include QScintilla libraries in the install: # 2012: unnecessary, because they're already included in the QSCINTILLA_LIBS_DEP_DIR and subsequently moved into the lib/ directory. # call('rsync -rlPpa '+QT_LIB_DIR+'/libqscintilla2.8.0.2.dylib . ',shell=True) # call('ln -f -s ./libqscintilla2.8.0.2.dylib ./libqscintilla2.dylib',shell=True) # call('ln -f -s ./libqscintilla2.8.0.2.dylib ./libqscintilla2.8.dylib',shell=True) # call('ln -f -s ./libqscintilla2.8.0.2.dylib ./libqscintilla2.8.0.dylib',shell=True)

os.chdir(DEP_LIBVTK_DIR) call('pwd') # in here we copy: all .dylib files (including all the symbolic links to them in the same dir) call('rsync -rlPpa '+VTK_BIN_AND_BUILD_DIR+'/lib/vtk-5.8/*dylib . ',shell=True)

# # a useful note from rsync's man page: # # A trailing slash on the source changes this behavior to avoid creating an additional directory level at the destination. # You can think of a trailing / on a source as meaning "copy the contents of this directory" as opposed to "copy the directory by name", # but in both cases the attributes of the containing directory are transferred to the containing directory on the destination. # In other words, each of the following commands copies the files in the same way, # including their setting of the attributes of /dest/foo: # # rsync -av /src/foo /dest # rsync -av /src/foo/ /dest/foo # os.chdir(DEP_VTK_DIR) call('pwd') # in here we copy: all files from VTK's Wrapping directory for Python: call('rsync -rlPpa '+VTK_BIN_AND_BUILD_DIR+'/Wrapping/Python/vtk/ . ',shell=True) # in here we ALSO copy: all files ending in .so from VTK's build/bin directory: call('rsync -rlPpa '+VTK_BIN_AND_BUILD_DIR+'/bin/*.so . ',shell=True)

os.chdir(DEP_PYQT_DIR) call('pwd') # in here we copy: the PyQt4 directory as created by the original (system-wide) PyQt install procedure) call('rsync -rlPpa '+PYQT_SITE_PACKAGES_DIR+'/PyQt4/ . ',shell=True)

os.chdir(DEP_PYQWT_DIR) call('pwd') # in here we copy: a library file grabbed from the qwt build, and create the necessary symlinks: call('rsync -rlPpa '+QWT_LIB_DIR+'/libqwt.5.2.1.dylib . ',shell=True) call('ln -f -s ./libqwt.5.2.1.dylib ./libqwt.dylib',shell=True) call('ln -f -s ./libqwt.5.2.1.dylib ./libqwt.5.dylib',shell=True) call('ln -f -s ./libqwt.5.2.1.dylib ./libqwt.5.2.dylib',shell=True)

# PyQwt and qwt fix - change the id and the paths so that the loader can find libqwt: call('install_name_tool -id @loader_path/libqwt.5.dylib libqwt.5.2.1.dylib',shell=True) call('otool -L libqwt.5.2.1.dylib',shell=True) call('install_name_tool -change /usr/local/qwt-5.2.1-svn/lib/libqwt.5.dylib @loader_path/libqwt.5.dylib Qwt.so',shell=True) call('otool -L Qwt.so',shell=True) call('install_name_tool -change /usr/local/qwt-5.2.1-svn/lib/libqwt.5.dylib @loader_path/libqwt.5.dylib _iqt.so',shell=True) call('otool -L _iqt.so',shell=True)

os.chdir(FOR_PLAYER_DEP_DIR) call('pwd') # in here we copy: some files from Python's directory into FOR_PLAYER_DEP_DIR: call('rsync -rlPpa '+PYQT_SITE_PACKAGES_DIR+'/sip.so . ',shell=True) call('rsync -rlPpa '+PYQT_SITE_PACKAGES_DIR+'/sipconfig.py . ',shell=True) call('rsync -rlPpa '+PYQT_SITE_PACKAGES_DIR+'/sipdistutils.py . ',shell=True)

# # # CUR_DIR # # #

# other references: CUR_DIR=os.path.join(os.getcwd(), PATH_TO_WORK_DIR) print "=====>=====> CUR_DIR = " + CUR_DIR

# # # BIN_DIR # # #

# here will go the resulting complete distribution archive: BIN_DIR=os.path.join(CUR_DIR, CC3D_ENDUSER_DIR_NAME) print "=====>=====> BIN_DIR = " + BIN_DIR

# first clean, then create - if os.path.isdir(BIN_DIR):

print "=====>=====> Binary distribution directory exists... Removing", BIN_DIR, " and creating new binary directory." shutil.rmtree(BIN_DIR)

# create a directory where the complete cc3d binary+supporting libraries will be placed for distribution os.mkdir(BIN_DIR)

# # # SRC_DIR # # #

# this MUST be a directory called "CompuCell3D" because we grab the "CompuCell3D" directory from the git repository, it's hardcoded in this script: SRC_DIR=os.path.join(PATH_TO_WORK_DIR, 'CompuCell3D') print "=====>=====> SRC_DIR = " + SRC_DIR

# assure that the source directory is cleared, we're going to build cc3d from it. # the following has to be removed but NOT recreated right away, because it'll be downloaded below using git: if os.path.isdir(SRC_DIR):

print "=====>=====> Source directory exists... Removing", SRC_DIR, " <=====<=====" shutil.rmtree(SRC_DIR)

# # # build CC3D # # #

print "=====>=====> now finally BUILD CompuCell 3D <=====<====="

print "=====>=====> obtaining the latest CC3D source code from our OWN local copy of the CC3D 3.6.2 git repository:" # cd to the directory we're using to hold it all, and grab the latest source code from our OWN local copy of the CC3D 3.6.2 git repository: os.chdir(CUR_DIR) call('pwd') # call('git ...something... http://code.compucell3d.org/svn/cc3d/branch/3.6.2',shell=True) call('rsync -rlPpa '+CC3D_LOCAL_GIT+' . ', shell=True)

print "=====>=====> building CC3D:" # cd to the directory holding all the cc3d source code, and compile it: os.chdir(SRC_DIR) call('pwd')

print "=====>=====> prepare all make files using cmake with a few command-line settings/options:"

# this setting would build "fat" 32bit+64bit code, but the OpenMP libraries we use are 64 bit only anyway: # call('cmake -DCMAKE_INSTALL_PREFIX:PATH='+BUILD_DIR_FOR_CMAKE+ " -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.6 -DVTK_DIR:PATH="+VTK_BIN_AND_BUILD_DIR+"/lib/vtk-5.8 -DCMAKE_OSX_ARCHITECTURES:STRING=i386\;x86_64" ,shell=True)

# this setting would build CC3D 3.6.2 (64bit code only) using gcc 4.2.0 as included with the Xcode distribution : #call('cmake -DCMAKE_INSTALL_PREFIX:PATH='+BUILD_DIR_FOR_CMAKE+ " -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.6 -DVTK_DIR:PATH="+VTK_BIN_AND_BUILD_DIR+"/lib/vtk-5.8 -DCMAKE_OSX_ARCHITECTURES:STRING=x86_64" ,shell=True)

# this setting builds CC3D 3.6.2 (64bit code only) using gcc 4.7.1 from its own separate compiler distribution directory: # add the -ftree-vectorizer-verbose=1 (or other levels) flag, to see what functions the vectorizer addresses # add the -Q flag, to list print out each function name as it is compiled, and print some statistics about each pass when it finishes # add the -ftime-report -fmem-report, to list detailed reports about time and memory used by gcc # add the -O3 flag, to add maximum GCC optimization levels # add the -fpermissive (required!) to compile CC3D using gcc 4.7.1, because of name lookup changes. See http://gcc.gnu.org/gcc-4.7/porting_to.html

# call('cmake -DCMAKE_C_COMPILER='+GCC_DIR+'/bin/gcc -DCMAKE_CXX_COMPILER='+GCC_DIR+'/bin/g++ -DCMAKE_CXX_FLAGS="-O3 -g -ftree-vectorizer-verbose=1 -time -m64" -DCMAKE_C_FLAGS="-O3 -g -ftree-vectorizer-verbose=1 -time -m64" -DCMAKE_INSTALL_PREFIX:PATH='+BUILD_DIR_FOR_CMAKE+ " -DVTK_DIR:PATH="+VTK_BIN_AND_BUILD_DIR+"/lib/vtk-5.8" , shell=True)

# Randy's cmake call, to which we add the VTK_DIR definition: # call('cmake -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.6 -DCMAKE_INSTALL_PREFIX:PATH='+BUILD_DIR_FOR_CMAKE+' -DCMAKE_CXX_COMPILER:FILEPATH='+GCC_DIR+'/bin/g++ -DCMAKE_C_COMPILER:FILEPATH='+GCC_DIR+'/bin/gcc -DVTK_DIR:PATH='+VTK_BIN_AND_BUILD_DIR+'/lib/vtk-5.8 -DCMAKE_CXX_FLAGS="-mmacosx-version-min=10.6 -O3 -g -ftree-vectorizer-verbose=1 -time -m64" -DCMAKE_C_FLAGS="-mmacosx-version-min=10.6 -O3 -g -ftree-vectorizer-verbose=1 -time -m64"', shell=True)

# cmake call for 10.6 backwards-compatible compile: # call('cmake -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.6 -DCMAKE_C_COMPILER:FILEPATH='+GCC_DIR+'/bin/gcc -DCMAKE_CXX_COMPILER:FILEPATH='+GCC_DIR+'/bin/g++ -DCMAKE_INSTALL_PREFIX:PATH='+BUILD_DIR_FOR_CMAKE+ ' -DVTK_DIR:PATH='+VTK_BIN_AND_BUILD_DIR+'/lib/vtk-5.8'+ ' -DCMAKE_CXX_FLAGS="-mmacosx-version-min=10.6 -O3 -g -ftree-vectorizer-verbose=1 -time -m64" -DCMAKE_C_FLAGS="-mmacosx-version-min=10.6 -O3 -g -ftree-vectorizer-verbose=1 -time -m64"' , shell=True)

# cmake call without 10.6 backwards-compatible compile flags: # -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.6 call('cmake -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2.6 -DPYTHON_INCLUDE_DIR:PATH=/System/Library/Frameworks/Python.framework/Versions/2.6/Headers -DPYTHON_LIBRARY:FILEPATH=/usr/lib/libpython2.6.dylib ' + ' -DCMAKE_C_COMPILER:FILEPATH='+GCC_DIR+'/bin/gcc -DCMAKE_CXX_COMPILER:FILEPATH='+GCC_DIR+'/bin/g++ -DCMAKE_INSTALL_PREFIX:PATH='+BUILD_DIR_FOR_CMAKE+ ' -DVTK_DIR:PATH='+VTK_BIN_AND_BUILD_DIR+'/lib/vtk-5.8'+ ' -DCMAKE_CXX_FLAGS="-O3 -g -fpermissive -m64" -DCMAKE_C_FLAGS="-O3 -g -fpermissive -m64"' , shell=True)

print "=====>=====> make CC3D:" # avoid parallel make until all works" # call('make install',shell=True) call('make install -j16',shell=True) os.chdir(CUR_DIR) call('pwd')

# # # copy files into CC3D distribution directory # # #

print "=====>=====> copy all the 3rd party supporting libraries into one directory for distribution" # now copy all the supporting libraries that are necessary for the cc3d player into the directory for distribution:

call('rsync -rlPp '+OPENMP_LIBS_DEP_DIR+'/ '+BIN_DIR+'/lib',shell=True)

call('rsync -rlPpa '+QSCINTILLA_LIBS_DEP_DIR+'/ '+BIN_DIR+'/lib',shell=True)

call('rsync -rlPp '+FOR_PLAYER_DEP_DIR+'/ '+BIN_DIR+'/player',shell=True)

call('rsync -rlPp '+QT_DEPS_DEP_DIR+' ' + BIN_DIR,shell=True)

print "=====>=====> copy the compiled CC3D from the install directory used by cmake, and various shell files"

# new 2010 style: call('chmod ugo+rx compucell3d.command compucell3d.sh runScript.command runScript.sh twedit++.command twedit++.sh celldraw.command celldraw.sh ', shell=True) call('rsync -rPlp '+BUILD_DIR_FOR_CMAKE+'/ compucell3d.command runScript.command twedit++.command celldraw.command '+BIN_DIR,shell=True)

# remove twedit++.sh from the distribution directory and replace it with our newer version, this could be fixed in CMake files <

TODO if os.path.isfile(BIN_DIR+'/twedit++.sh'):

os.remove(BIN_DIR+'/twedit++.sh')

call('rsync -rPlp twedit++.sh '+BIN_DIR,shell=True)

# remove compucell3d.sh from the distribution directory and replace it with our newer version, this could be fixed in CMake files <

TODO if os.path.isfile(BIN_DIR+'/compucell3d.sh'):

os.remove(BIN_DIR+'/compucell3d.sh')

call('rsync -rPlp compucell3d.sh '+BIN_DIR,shell=True)

# remove celldraw.sh from the distribution directory and replace it with our newer version, this could be fixed in CMake files <

TODO if os.path.isfile(BIN_DIR+'/celldraw.sh'):

os.remove(BIN_DIR+'/celldraw.sh')

call('rsync -rPlp celldraw.sh '+BIN_DIR,shell=True)

# rename old runScript.sh file in the distribution directory: if os.path.isfile(BIN_DIR+'/runScript.sh'):

os.rename(BIN_DIR+'/runScript.sh', BIN_DIR+'/runScript_older.sh')

# # # new 2011.07 include BionetSolver in the binary build: # # #

# this MUST be a directory called "0.0.6" because we grab the "0.0.6" version from the git repository, it's hardcoded in this script: BIONET_SRC_DIR=os.path.join(PATH_TO_WORK_DIR, '0.0.6') print "=====>=====> BIONET_SRC_DIR = " + BIONET_SRC_DIR

# assure that the source directory is cleared, we're going to build BionetSolver from it. # the diretory has to be removed but NOT recreated right away, because it'll be downloaded using git: if os.path.isdir(BIONET_SRC_DIR):

print "=====>=====> BionetSolver directory exists... Removing", BIONET_SRC_DIR, " <=====<=====" shutil.rmtree(BIONET_SRC_DIR)

# BIONET_BUILD_DIR_FOR_CMAKE is the directory into which CMAKE will conduct the entire build: BIONET_BUILD_DIR_FOR_CMAKE=os.path.join(PATH_TO_WORK_DIR, 'bionet_build_dir') print "=====>=====> BIONET_BUILD_DIR_FOR_CMAKE = " + BIONET_BUILD_DIR_FOR_CMAKE

# first clean, then create the directory - if os.path.isdir(BIONET_BUILD_DIR_FOR_CMAKE):

print "=====>=====> Build directory (for CMAKE doing BionetSolver) exists... Removing ", BIONET_BUILD_DIR_FOR_CMAKE, " and creating new directory." shutil.rmtree(BIONET_BUILD_DIR_FOR_CMAKE)

# create the directory used during CMAKE's build and its own installation procedure: os.mkdir(BIONET_BUILD_DIR_FOR_CMAKE)

print "=====>=====> now BUILD BionetSolver <=====<====="

print "=====>=====> obtaining the latest BionetSolver source code from our OWN local copy of the BIONET 0.0.6 git repository:" # cd to the directory we're using to hold it all, and grab the latest source code from our OWN local copy of the BIONET 0.0.6 git repository: os.chdir(CUR_DIR) call('pwd') #call('git ...something... export http://code.compucell3d.org/svn/cc3d/branch/BionetSolver/0.0.6',shell=True) call('rsync -rlPpa '+BIONET_LOCAL_GIT+' . ', shell=True)

print "=====>=====> building BionetSolver:" # cd to the directory holding all the cc3d source code, and compile it: os.chdir(BIONET_SRC_DIR) call('pwd')

print "=====>=====> prepare all make files using cmake with a few command-line settings/options:" # this setting builds bionetsolver (64bit code only) using gcc 4.7.1 from its own separate compiler distribution directory: # add the -ftree-vectorizer-verbose=1 (or other levels) flag, to see what functions the vectorizer addresses # add the -Q flag, to list print out each function name as it is compiled, and print some statistics about each pass when it finishes # add the -ftime-report -fmem-report, to list detailed reports about time and memory used by gcc # add the -O3 flag, to add maximum GCC optimization levels # add the -fpermissive (required!) to compile CC3D using gcc 4.7.1, because of name lookup changes. See http://gcc.gnu.org/gcc-4.7/porting_to.html

# cmake call for 10.6 backwards-compatible compile: # call('cmake -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.6 -DCMAKE_C_COMPILER='+GCC_DIR+'/bin/gcc -DCMAKE_CXX_COMPILER='+GCC_DIR+'/bin/g++ -DCMAKE_CXX_FLAGS="-mmacosx-version-min=10.6 -O3 -g -ftree-vectorizer-verbose=1 -time -m64" -DCMAKE_C_FLAGS="-mmacosx-version-min=10.6 -O3 -g -ftree-vectorizer-verbose=1 -time -m64" -DCMAKE_INSTALL_PREFIX:PATH='+BIONET_BUILD_DIR_FOR_CMAKE , shell=True)

# cmake call without 10.6 backwards-compatible compile flags: # -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.6 call('cmake -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2.6 -DPYTHON_INCLUDE_DIR:PATH=/System/Library/Frameworks/Python.framework/Versions/2.6/Headers -DPYTHON_LIBRARY:FILEPATH=/usr/lib/libpython2.6.dylib ' + ' -DCMAKE_C_COMPILER='+GCC_DIR+'/bin/gcc -DCMAKE_CXX_COMPILER='+GCC_DIR+'/bin/g++ -DCMAKE_CXX_FLAGS="-O3 -g -fpermissive -m64" -DCMAKE_C_FLAGS="-O3 -g -fpermissive -m64" -DCMAKE_INSTALL_PREFIX:PATH='+BIONET_BUILD_DIR_FOR_CMAKE , shell=True)

# the following would build bionetsolver with the gcc compiler provided with Mac OS X 10.8: # cmake -DCMAKE_INSTALL_PREFIX:PATH=//Users/Shared/CC3Ddev/BionetworkSolver/fsht/BionetSolver/build_test_20110718 -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.6 -DCMAKE_OSX_ARCHITECTURES:STRING=x86_64

print "=====>=====> make BionetSolver:" # avoid parallel make until all works" # call('make install',shell=True) call('make install -j16',shell=True) os.chdir(BIONET_BUILD_DIR_FOR_CMAKE) call('pwd') call('find . -exec setlabel -s Orange {} \;',shell=True)

# copy BionetSolver files into CC3D distribution directory

call('rsync -rlPp '+BIONET_BUILD_DIR_FOR_CMAKE+'/Demos/BionetSolverExamples '+BIN_DIR+'/Demos',shell=True)

# reminder from rsync's man page: # a trailing / on a source as meaning "copy the contents of this directory" as opposed to "copy the directory by name" : call('rsync -rlPp '+BIONET_BUILD_DIR_FOR_CMAKE+'/include/ '+BIN_DIR+'/include ',shell=True)

call('rsync -rlPp '+BIONET_BUILD_DIR_FOR_CMAKE+'/lib/python/ '+BIN_DIR+'/lib/python',shell=True)

call('rsync -rlPp '+BIONET_BUILD_DIR_FOR_CMAKE+'/lib/pkgconfig '+BIN_DIR+'/lib',shell=True)

call('rsync -rlPp '+BIONET_BUILD_DIR_FOR_CMAKE+'/lib/*.a '+BIN_DIR+'/lib',shell=True)

call('rsync -rlPp '+BIONET_BUILD_DIR_FOR_CMAKE+'/lib/*.dylib '+BIN_DIR+'/lib',shell=True)

call('rsync -rlPp '+BIONET_BUILD_DIR_FOR_CMAKE+'/pythonSetupScripts/ '+BIN_DIR+'/pythonSetupScripts ',shell=True)

os.chdir(BIN_DIR)

# BionetSolver build and packaging completed #

# # # new 2012.02 include CellDraw in the binary build script: # # #

print "=====>=====> include CellDraw:" os.chdir(CUR_DIR) call('pwd')

CELLDRAW_SRC_DIR=os.path.join(PATH_TO_WORK_DIR, 'build_CellDraw_src_dir') print "=====>=====> CELLDRAW_SRC_DIR = " + CELLDRAW_SRC_DIR

# assure that the source directory is cleared, we're going to build CellDraw from it. # the diretory has to be removed and recreated right away, because we'll place CellDraw's source code dir into it from git: if os.path.isdir(CELLDRAW_SRC_DIR):

print "=====>=====> CellDraw directory exists... Removing", CELLDRAW_SRC_DIR, " and creating new directory." shutil.rmtree(CELLDRAW_SRC_DIR)

# create the directory used during CellDraw installation procedure: os.mkdir(CELLDRAW_SRC_DIR)

print "=====>=====> now BUILD CellDraw <=====<====="

print "=====>=====> obtaining the latest CellDraw source code from our OWN local copy of the CellDraw git repository:" # cd to the directory we're using to hold it all, and grab the latest source code from our OWN local copy of the CellDraw git repository: os.chdir(CELLDRAW_SRC_DIR) call('pwd') #call('git ...something... http://code.compucell3d.org/svn/cc3d/branch/CellDraw/1.5.1/src',shell=True) call('rsync -rlPpa '+CELLDRAW_LOCAL_GIT+' . ', shell=True) call('\mv -f ./src '+BIN_DIR+'/CellDraw', shell=True)

os.chdir(CUR_DIR) call('pwd')

# CellDraw build and packaging completed #

print "=====>=====> clearing all the *.pyc, .DS_Store, .git/ and .svn/ from the CC3D directory:"

call("pwd", shell=True) # remove any precompiled python code, and any Mac OS X Finder-specific files: # call("find . -type f -iname \'*.pyc\' -exec ls -lad {} \;", shell=True) call("find . -type f -iname \'*.pyc\' -exec rm -f {} \;", shell=True) # call("find . -type f -iname \'*.pyc\' -exec ls -lad {} \;", shell=True)

# call("find . -type f -iname \'.DS_Store\' -exec ls -lad {} \;", shell=True) call("find . -type f -iname \'.DS_Store\' -exec rm -f {} \;", shell=True) # call("find . -type f -iname \'.DS_Store\' -exec ls -lad {} \;", shell=True)

# also remove any .svn directories from the distributed archive: # call("find . -type d -iname \'.svn\' -exec ls -lad {} \;", shell=True) call("find . -type d -iname \'.svn\' -exec rm -rf {} \;", shell=True) # call("find . -type d -iname \'.svn\' -exec ls -lad {} \;", shell=True)

# also remove any .git directories from the distributed archive: # call("find . -type d -iname \'.git\' -exec ls -lad {} \;", shell=True) call("find . -type d -iname \'.git\' -exec rm -rf {} \;", shell=True) # call("find . -type d -iname \'.git\' -exec ls -lad {} \;", shell=True)

# create the .zip archive for distribution: print "=====>=====> zipping the CC3D directory using \'ditto\':" os.chdir(CUR_DIR) call("rm -f " + CC3D_ARCHIVE, shell=True) call('ditto -rsrcFork -arch x86_64 ' + CC3D_ENDUSER_DIR_NAME + ' ' + CC3D_ENDUSER_DIR_NAME_TMP, shell=True) call("rm -rf " + CC3D_ENDUSER_DIR_NAME, shell=True) call('mv ' + CC3D_ENDUSER_DIR_NAME_TMP + ' ' + CC3D_ENDUSER_DIR_NAME, shell=True) call('ditto -c -k --keepParent -rsrcFork ' + CC3D_ENDUSER_DIR_NAME + ' ' + CC3D_ARCHIVE, shell=True) call("ls -lad " + CC3D_ARCHIVE, shell=True)

print "=====>=====>=================<=====<=====" print "===> CC3D 3.6.2 distribution ready!! <===" print "=====>=====>=================<=====<=====" }}}

CompuCell3D: SrcBin/MacOSXCompile (last edited 2013-08-21 16:36:28 by 129-79-59-98)

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