OUT OF DATE

Building OpenSim in Linux

See section on BioX Cluster below for additional things necessary to get it running in that environment
CMake: download and install the binary one
Xerces:
- Just download and install a xerces binaries and headers (most linux distributions will have xerces-c and xerces-c-devel packages for this)
- In the location of the xerces libraries (e.g. /usr/lib or /usr/lib64 for 64bit), make symlinks:libxerces-c_2.so -> libxerces-c.so
  libxerces-c_2D.so -> libxerces-c.so
  because OpenSim looks for libraries named xerces-c_2 and xerces-c_2D
set LD_LIBRARY_PATH to where the libraries are
To build:
- Go to the directory containing the top-level CMakeLists.txt file and run cmake -i . for interactive mode (it'll prompt you for settings) orcmake . for non-interactive mode (uses previous settings; use this if you've made some changes to the code structure requiring a regeneration of make files).
- Make sure the ARCH64 cmake option is set to the right ON/OFF value for your machine (64 bit linux distributions put libraries in a directory called lib64 instead of lib).
- Then simply run make
Libraries and executables will be built in that same directory as the top-level CMakeLists.txt (where you ran cmake from).

Since I didn't have root access here, I installed things to /home/erang/local instead of /usr/local.
- For CMake, this is specified by user when the setup script is run
- For Xerces, I still downloaded the rpms (both the xerces-c and xerces-c-devel) but I wasn't sure how to install them in a manual location so I extracted the contents into a temporary directory using rpm2cpio <rpmfile> | cpio -idmv and moved the contents that were supposed to go into /usr to /home/erang/local.
- Also all of the SimTK things that needed to be "installed" in the system I installed into /home/erang/local. This required carefully setting cmake values to install the SimTK core stuff there and to look for the SimTK core stuff there.
They recommend compiling with intel compiler, but I haven't tried that yet.
Creating an interactive job (e.g. opening a shell in one of the compute nodes): bsub -Is bash
If compile takes less than 5 minutes, okay to run interactive job on a node... else submit it as a job (you'll get emailed warnings if you don't)
svn is available on the root node but not on the compute nodes apparently

Can't use (or even refer to) vtkAVTIWriter in OpenSimBaseCanvas
Sometimes there are issues with 64 bit machines where things look for libraries in /lib but they're in /lib64 or vice versa.

To see verbose output from make when building OpenSim, add SET(CMAKE_VERBOSE_MAKEFILE ON) to CMakeLists.txt file
Some issues with gcov, gcov_init, not sure what that's all about yet, so I turned off the gcov flags from CMakeLists.txt. The error messages were
hidden symbol `__gcov_init' in /usr/lib/gcc-lib/i586-suse-linux/3.3.5/libgcc.a(_gcov.oS) is referenced by DSO
/usr/lib/gcc-lib/i586-suse-linux/3.3.5/../../../../i586-suse-linux/bin/ld: final link failed: Nonrepresentable section on output