Chaste on Mountain Lion
Warning this currently experimental with OSX Mavericks let us know if you have issues.
Xcode
Install Xcode from app store.
- In Xcode select preferences->downloads and install "Command Line Tools"
- Xcode command line tools comes with Subversion version 1.6. Alternatively, Homebrew has version 1.8 of Subversion.
- Xcode command line tools provides the "g++" compiler
Home Brew
see http://mxcl.github.com/homebrew/
ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)" # Later libraries (PETSc, METIS, VTK and parMETIS) need a "science" repository brew tap homebrew/science
You can roll the next few installs together if you wish. However, some of these (PETSc and Sundials) need some configuration to build in the correct way (see below). It will take a while.
brew install wget scons boost gfortran openmpi valgrind xerces-c petsc parmetis metis vtk sundials brew install hdf5 --enable-parallel
SCons
Homebrew has version 2.3.0 of Scons:
brew install scons
Boost
Homebrew has version 1.53.0 of boost:
brew install boost
OpenMPI
Homebrew has version 1.6.5 of OpenMPI: needs fortran compiler
brew install gfortran brew install openmpi
Xerces-c
Xerces-c 3.1.1 is available on homebrew:
brew install xerces-c
wget
To simplify later downloads install wget (v1.14):
brew install wget
PETSc (from home-brew/science)
Homebrew has version 3.3.p5 of PETSc.
Important: Some parts of Chaste require shared libraries so you should edit the configuration of PETSc to build shared libraries for you.
brew edit petsc
Add the --with-shared-libraries flag at line 13:
- system "./configure", "--with-debugging=0", "--prefix=#{prefix}"
+ system "./configure", "--with-debugging=0", "--with-shared-libraries", "--prefix=#{prefix}"
Now install:
brew install petsc
ParMETIS and METIS
Building ParMETIS also builds METIS so, if the installer worked better, you ought to be able to install both in a single line. However here we take the dangerous approach of install both separately. This is only dangerous if the versions go out of sync. Calls into METIS are soon to be deprecated...
Important: Some parts of Chaste require shared libraries so you should edit the configuration of ParMETIS and METIS to build shared libraries for you.
ParMETIS 4.0.2
brew edit parmetis
Add the shared=1 flag at line 12:
- system "make", "config", "prefix=#{prefix}"
+ system "make", "config", "shared=1", "prefix=#{prefix}"
METIS 5.0.2
brew install parmetis
brew edit parmetis
Add the shared=1 flag at line 14:
- system "make", "config", "prefix=#{prefix}"
+ system "make", "config", "shared=1", "prefix=#{prefix}"
brew install metis
VTK
VTK 5.10.1
brew install vtk
NOTE if you are using Mavericks then you should install VTK5 as the default version (6.0) has some incompatibilities
brew install vtk5
You will also need to edit the local.py file to replace the line
ldflags='-framework vecLib'
with
ldflags='-framework Accelerate'
and to remove vtkFiltering and vtkzlib from the other_libraries.
CVODE (Sundials)
Sundials 2.5.0
Important: Some parts of Chaste require shared libraries so you should edit the configuration of Sundials to build shared libraries for you.
brew edit sundials
Add the -enable-shared flag at line 10:
system "./configure", "--disable-debug", "--disable-dependency-tracking",
- "--prefix=#{prefix}"
+ "-enable-shared", "--prefix=#{prefix}"
brew install sundials
HDF5
Homebrew has version 1.8.11 of HDF5:
brew install hdf5 --enable-parallel
Codesynthesis XSD
Codesynthesis XSD is not available in Macports and must be installed directly:
wget http://www.codesynthesis.com/download/xsd/3.3/macosx/i686/xsd-3.3.0-i686-macosx.tar.bz2 tar xvfz xsd-3.3.0-i686-macosx.tar.bz2 #These instructions assume that homebrew has created /usr/local/ and that the current user has permission to write to it. cp xsd-3.3.0-i686-macosx/bin/xsd /usr/local/bin/ cp -r xsd-3.3.0-i686-macosx/libxsd /usr/local/opt/
You also need to change the call setg (b, b, e) on line 35 of xsd/cxx/zc-istream.txx like this:
bash-3.2$ diff -u /usr/local/opt/libxsd/xsd/cxx/zc-istream.txx.orig /usr/local/opt/libxsd/xsd/cxx/zc-istream.txx
--- /usr/local/lib/libxsd/xsd/cxx/zc-istream.txx.orig 2013-07-10 11:00:23.000000000 +0100
+++ /usr/local/lib/libxsd/xsd/cxx/zc-istream.txx 2013-07-10 11:00:59.000000000 +0100
@@ -32,7 +32,7 @@
C* b (const_cast<C*> (str_.data ()));
C* e (b + str_.size ());
- setg (b, b, e);
+ std::streambuf::setg (b, b, e);
}
Python XML tool support
Libraries needed by PyCml, the heart component and the Functional Curation bolt-on project.
# Note that Amara at version 2 is not suitable, so version 1.2 is forced. sudo easy_install https://pypi.python.org/packages/2.5/A/Amara/Amara-1.2.0.2-py2.5.egg sudo easy_install rdflib sudo easy_install lxml
Host Config
Use attachment:local.py (experimental) for your host config. Save it as python/hostconfig/local.py.
More for the developer
Eclipse
- Download the Eclipse IDE for C++ developers (or a more appropriate file) from http://www.eclipse.org/downloads/
- Open the resulting tar file to produce a folder named "eclipse"
- Drag and drop the "eclipse" folder to "Applications" in FileFinder
- Open from Applications -> eclipse -> Eclipse
- (You might be prompted to install a Java runtime when you first run Eclipse)
- If you want to alias or add the path, the location is /Applications/eclipse/eclipse
Valgrind
Valgrind version 3.8.1 (not necessary, but useful to the serious developer)
brew install valgrind
Handy things
To be able to see the tmp folder in finder use
sudo chflags nohidden /tmp
Useful aliases to add to ~/.bashrc
alias eclipse=/Applications/eclipse/eclipse alias cdchaste='cd /Users/chaste/eclipse/workspace/Chaste' #Or similar