C++ C CMake Matlab Python Java Other
Latest commit 51f991d Mar 22, 2017 @chrisdembia chrisdembia committed on GitHub Merge pull request #1574 from opensim-org/python_standalone
Allow making a standalone Python package

README.md

OpenSim Core

Travis Appveyor ZenHub

NOTE: This repository cannot be used to build OpenSim 3.x or earlier. For OpenSim 3.x, see here.

OpenSim is software that lets users develop models of musculoskeletal structures and create dynamic simulations of movement, such as this one:

Simulation of human running by Sam Hamner (doi: 10.1016/j.jbiomech.2010.06.025)

More information can be found at our websites:

This repository contains the source code for OpenSim's C++ libraries, C++ examples, command-line applications (inverse kinematics, computed muscle control, etc.), and Java and Python wrapping. This repository does not include source code for the OpenSim GUI.

Simple example

Let's simulate a simple arm whose elbow is actuated by a muscle, using the C++ interface (You can find a Python version of this example at Bindings/Python/examples/build_simple_arm_model.py):

#include <OpenSim/OpenSim.h>
using namespace SimTK;
using namespace OpenSim;
int main() {
    Model model;
    model.setUseVisualizer(true);

    // Create two links, each with a mass of 1 kg, center of mass at the body's
    // origin, and moments and products of inertia of zero.
    OpenSim::Body* humerus = new OpenSim::Body("humerus", 1, Vec3(0), Inertia(0));
    OpenSim::Body* radius  = new OpenSim::Body("radius",  1, Vec3(0), Inertia(0));

    // Connect the bodies with pin joints. Assume each body is 1 m long.
    PinJoint* shoulder = new PinJoint("shoulder",
            // Parent body, location in parent, orientation in parent.
            model.getGround(), Vec3(0), Vec3(0),
            // Child body, location in child, orientation in child.
            *humerus, Vec3(0, 1, 0), Vec3(0));
    PinJoint* elbow = new PinJoint("elbow",
            *humerus, Vec3(0), Vec3(0), *radius, Vec3(0, 1, 0), Vec3(0));

    // Add a muscle that flexes the elbow.
    Millard2012EquilibriumMuscle* biceps = new
        Millard2012EquilibriumMuscle("biceps", 200, 0.6, 0.55, 0);
    biceps->addNewPathPoint("origin",    *humerus, Vec3(0, 0.8, 0));
    biceps->addNewPathPoint("insertion", *radius,  Vec3(0, 0.7, 0));

    // Add a controller that specifies the excitation of the muscle.
    PrescribedController* brain = new PrescribedController();
    brain->addActuator(*biceps);
    // Muscle excitation is 0.3 for the first 0.5 seconds, then increases to 1.
    brain->prescribeControlForActuator("biceps",
            new StepFunction(0.5, 3, 0.3, 1));

    // Add components to the model.
    model.addBody(humerus);    model.addBody(radius);
    model.addJoint(shoulder);  model.addJoint(elbow);
    model.addForce(biceps);
    model.addController(brain);

    // Add a console reporter to print the muscle fiber force and elbow angle.
    ConsoleReporter* reporter = new ConsoleReporter();
    reporter->set_report_time_interval(1.0);
    reporter->addToReport(biceps->getOutput("fiber_force"));
    reporter->addToReport(
        elbow->getCoordinate(PinJoint::Coord::RotationZ).getOutput("value"),
        "elbow_angle");
    model.addComponent(reporter);

    // Add display geometry.
    Ellipsoid bodyGeometry(0.1, 0.5, 0.1);
    bodyGeometry.setColor(Gray);
    // Attach an ellipsoid to a frame located at the center of each body.
    PhysicalOffsetFrame* humerusCenter = new PhysicalOffsetFrame(
        "humerusCenter", "humerus", Transform(Vec3(0, 0.5, 0)));
    humerus->addComponent(humerusCenter);
    humerusCenter->attachGeometry(bodyGeometry.clone());
    PhysicalOffsetFrame* radiusCenter = new PhysicalOffsetFrame(
        "radiusCenter", "radius", Transform(Vec3(0, 0.5, 0)));
    radius->addComponent(radiusCenter);
    radiusCenter->attachGeometry(bodyGeometry.clone());

    // Configure the model.
    State& state = model.initSystem();
    // Fix the shoulder at its default angle and begin with the elbow flexed.
    shoulder->getCoordinate().setLocked(state, true);
    elbow->getCoordinate().setValue(state, 0.5 * Pi);
    model.equilibrateMuscles(state);

    // Configure the visualizer.
    model.updMatterSubsystem().setShowDefaultGeometry(true);
    Visualizer& viz = model.updVisualizer().updSimbodyVisualizer();
    viz.setBackgroundColor(White);

    // Simulate.
    RungeKuttaMersonIntegrator integrator(model.getSystem());
    Manager manager(model, integrator);
    manager.setInitialTime(0); manager.setFinalTime(10.0);
    manager.integrate(state);
    
    return 0;
};

This code produces the following animation:

Simulation of an arm actuated by a muscle

and prints the following information to the console:

    [reporter]
                |           /m|             |
                | odel_/biceps|             |
            time| |fiber_force|  elbow_angle|
    ------------| ------------| ------------|
               0|     1.180969|    1.5707963|
               1|     57.27509|   0.77066412|
               2|    19.728411|    1.5680456|
               3|    56.090431|    1.4419861|
               4|     34.54835|     1.508348|
               5|    32.603721|    1.5180237|
               6|    37.136052|    1.5021235|
               7|    35.698502|    1.5071888|
               8|     34.18601|    1.5079186|
               9|    34.341649|     1.506727|
              10|    35.784713|     1.507164|

Building from the source code

NOTE -- In all platforms (Windows, OSX, Linux), it is advised to build all OpenSim Dependencies (Simbody, BTK etc) with same CMAKE_BUILD_TYPE (Linux) / CONFIGURATION (MSVC/Xcode) as OpenSim. For example, if OpenSim is to be built with CMAKE_BUILD_TYPE/CONFIGURATION as Debug, Simbody, BTK and all other OpenSim dependencies also should be built with CMAKE_BUILD_TYPE/CONFIGURATION as Debug. Failing to do so may result in mysterious runtime errors like 'segfault' in standard c++ library implementation.

We support a few ways of building OpenSim:

  1. On Windows using Microsoft Visual Studio. In a rush? Use these instructions.
  2. On Mac OSX using Xcode. Need extended instructions? Use these instructions.
  3. On Ubuntu using Unix Makefiles. In a rush? Use these instructions.

On Windows using Visual Studio

Get the dependencies

  • operating system: Windows 7 or 8.
  • cross-platform build system: CMake >= 3.2
  • compiler / IDE: Visual Studio 2015.
    • Visual Studio Community 2015 is sufficient and is free for everyone. If you want to use Visual Studio Enterprise 2015, you may be able to get it for free at Dreamspark if you are at an academic institution.

    • Visual Studio 2015 does not install C++ support by default. During the installation you must select Custom, and check Programming Languages > Visual C++ > Common Tools for Visual C++ 2015. You can uncheck all other boxes. If Visual Studio is installed without C++ support, CMake will report the following errors:

      The C compiler identification is unknown
      The CXX compiler identification is unknown
      

      If you have already installed Visual Studio without C++ support, simply re-run the installer and select Modify. Alternatively, go to File > New > Project... in Visual Studio, select Visual C++, and click Install Visual C++ 2015 Tools for Windows Desktop.

  • physics engine: Simbody >= 3.6. Two options:
  • C3D file support: Biomechanical-ToolKit Core. Two options:
  • command-line argument parsing: docopt.cpp. Two options:
    • Let OpenSim get this for you using superbuild (see below); much easier!
    • Build on your own (no instructions).
  • API documentation (optional): Doxygen >= 1.8.6
  • version control (optional): git. There are many options:
  • Bindings (optional): SWIG 3.0.6
    • MATLAB scripting (optional): Java development kit >= 1.7.
      • Note: Older versions of MATLAB may use an older version of JVM. Run 'ver' in MATLAB to check MATLAB's JVM version (must be >= 1.7).
    • Python scripting (optional):
    • The choice between 32-bit/64-bit must be the same between Java, Python, and OpenSim.

Download the OpenSim-Core source code

  • Method 1: If you want to get going quickly, download the source code from https://github.com/opensim-org/opensim-core/releases, for the version of OpenSim you want. We'll assume you unzipped the source code into C:/opensim-core-source.

  • Method 2: If you plan on updating your OpenSim installation or you want to contribute back to the project, clone the opensim-core git repository into C:/opensim-core-source. If using TortoiseGit, open Windows Explorer, right-click in the window, select Git Clone..., and provide the following:

    • URL: https://github.com/opensim-org/opensim-core.git.
    • Directory: C:/opensim-core-source.

    If using a Git Bash or Git Shell, run the following:

      $ git clone https://github.com/opensim-org/opensim-core.git C:/opensim-core-source
    

    This will give you a bleeding-edge version of OpenSim-Core.

[Optional] Superbuild: download and build OpenSim dependencies

  1. Open the CMake GUI.

  2. In the field Where is the source code, specify C:/opensim-core-source/dependencies.

  3. In the field Where to build the binaries, specify a directory under which to build dependencies. Let's say this is C:/opensim-core-dependencies-build.

  4. Click the Configure button.

    1. Choose the Visual Studio 14 generator (for Visual Studio 2015). To build as 64-bit, select Visual Studio 14 Win64.
    2. Click Finish.
  5. Where do you want to install OpenSim dependencies on your computer? Set this by changing the CMAKE_INSTALL_PREFIX variable. Let's say this is C:/opensim-core-dependencies-install.

  6. Variables named SUPERBUILD_<dependency-name> allow you to selectively download dependencies. By default, all dependencies are downloaded, configured and built.

  7. Click the Configure button again. Then, click Generate to make Visual Studio project files in the build directory.

  8. Go to the build directory you specified in step 3 using the command:

     cd C:/opensim-core-dependencies-build
    
  9. Use CMake to download, compile and install the dependencies:

    cmake --build . --config RelWithDebInfo
    

Alternative values for --config in this command are: * Debug: debugger symbols; no optimizations (more than 10x slower). Library names end with _d. * Release: no debugger symbols; optimized. * RelWithDebInfo: debugger symbols; optimized. Bigger but not slower than Release; choose this if unsure. * MinSizeRel: minimum size; optimized.

  You must run this command for each of the configurations you plan to use
  with OpenSim (see below). You should run this command for the release
  configuration *last* to ensure that you use the release version of the
  command-line applications instead of the slow debug versions.
  1. If you like, you can now remove the directory used for building dependencies (c:/opensim-core-dependencies-build).

Configure and generate project files

  1. Open the CMake GUI.
  2. In the field Where is the source code, specify C:/opensim-core-source.
  3. In the field Where to build the binaries, specify something like C:/opensim-core-build, or some other path that is not inside your source directory. This is not where we are installing OpenSim-Core; see below.
  4. Click the Configure button.
    1. Choose the Visual Studio 14 generator (for Visual Studio 2015). To build as 64-bit, select Visual Studio 14 Win64. The choice between 32-bit/64-bit must be the same across all dependencies.
    2. Click Finish.
  5. Where do you want to install OpenSim-Core on your computer? Set this by changing the CMAKE_INSTALL_PREFIX variable. We'll assume you set it to C:/opensim-core. If you choose a different installation location, make sure to use yours where we use C:/opensim-core below.
  6. Tell CMake where to find dependencies. This depends on how you got them.
    • Superbuild: Set the variable OPENSIM_DEPENDENCIES_DIR to the root directory you specified with superbuild for installation of dependencies. In our example, it would be c:/opensim-core-dependencies-install.
    • Obtained on your own:
      1. Simbody: Set the SIMBODY_HOME variable to where you installed Simbody (e.g., C:/Simbody).
      2. BTK: Set the variable BTK_DIR to the directory containing BTKConfig.cmake. If the root directory of your BTK installation is C:/BTKCore-install, then set this variable to C:/BTKCore-install/share/btk-0.4dev.
      3. docopt.cpp. Set the variable docopt_DIR to the directory containing docopt-config.cmake. If the root directory of your docopt.cpp installation is C:/docopt.cpp-install, then set this variable to C:/docopt.cpp-install/lib/cmake.
  7. Set the remaining configuration options.
    • BUILD_API_EXAMPLES to compile C++ API examples.
    • BUILD_TESTING to ensure that OpenSim works correctly. The tests take a while to build; if you want to build OpenSim quickly, you can turn this off.
    • BUILD_JAVA_WRAPPING if you want to access OpenSim through MATLAB or Java; see dependencies above.
    • BUILD_PYTHON_WRAPPING if you want to access OpenSim through Python; see dependencies above. CMake sets PYTHON_* variables to tell you the Python it will use for building the wrappers.
    • BUILD_API_ONLY if you don't want to build the command-line applications.
  8. Click the Configure button again. Then, click Generate to make Visual Studio project files in the build directory.

Build and install

  1. Open C:/opensim-core-build/OpenSim.sln in Visual Studio.

  2. Select your desired Solution configuration from the drop-down at the top.

    • Debug: debugger symbols; no optimizations (more than 10x slower). Library names end with _d.
    • Release: no debugger symbols; optimized.
    • RelWithDebInfo: debugger symbols; optimized. Bigger but not slower than Release; choose this if unsure.
    • MinSizeRel: minimum size; optimized.

    You at least want release libraries (the last 3 count as release), but you can have debug libraries coexist with them. To do this, go through the installation process twice, once for each of the two configurations. You should install the release configuration last to ensure that you use the release version of the command-line applications instead of the slow debug versions.

  3. Build the API documentation. This is optional, and you can only do this if you have Doxygen. Build the documentation by right-clicking doxygen and selecting Build.

  4. Build the libraries, etc. by right-clicking ALL_BUILD and selecting Build.

  5. Run the tests by right-clicking RUN_TESTS_PARALLEL and selecting Build.

  6. Install OpenSim-Core by right-clicking INSTALL and selecting Build.

Set environment variables

In order to use the OpenSim-Core command-line applications or use OpenSim-Core libraries in your own application, you must add the OpenSim-Core bin/ directory to your PATH environment variable.

  1. In the Windows toolbar (Windows 10), Start screen (Windows 8) or Start menu (Windows 7), search environment.
  2. Select Edit the system environment variables.
  3. Click Environment Variables....
  4. Under System variables, click Path, then click Edit.
  5. Add C:/opensim-core/bin; to the front of of the text field. Don't forget the semicolon!

For the impatient (Windows)

  • Get Visual Studio Community from here.
  • Choose Custom' installation.
  • Choose Programming Languages -> Visual C++.
  • Get git from here.
  • Choose Use Git from the Windows Command Prompt.
  • Get CMake from here.
  • Choose Add CMake to the system PATH for all users.
  • Get Chocolatey from here.
  • In PowerShell, run as Administrator --
choco install python2 jdk8 swig
  • In PowerShell --
git clone https://github.com/opensim-org/opensim-core.git
mkdir opensim_dependencies_build
cd .\opensim_dependencies_build
cmake ..\opensim-core\dependencies                             `
     -G"Visual Studio 14 2015 Win64"                          `
     -DCMAKE_INSTALL_PREFIX="..\opensim_dependencies_install"
cmake --build . --config RelWithDebInfo -- /maxcpucount:8
cd ..
mkdir opensim_build
cd .\opensim_build
cmake ..\opensim-core                                              `
     -G"Visual Studio 14 2015 Win64"                              `
     -DCMAKE_INSTALL_PREFIX="..\opensim_install"                  `
     -DOPENSIM_DEPENDENCIES_DIR="..\opensim_dependencies_install" `
     -DBUILD_JAVA_WRAPPING=ON                                     `
     -DBUILD_PYTHON_WRAPPING=ON                                   `
     -DWITH_BTK=ON
cmake --build . --config RelWithDebInfo -- /maxcpucount:8
ctest -C RelWithDebInfo --parallel 8

On Mac OSX using Xcode

For Mac OSX 10.11 El Capitan

Get Xcode from the App store. Open Xcode and Agree to license agreement. To Agree to to the license agreement, you may need to type in Terminal:

sudo xcodebuild -license

If you already have Xcode, update it to 7.3, or the latest version.

Then, in Terminal, copy and paste commands below, line by line, one at a time. Be sure the output doesn't contain errors.

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install cmake swig
brew cask install java
git clone https://github.com/opensim-org/opensim-core.git
mkdir opensim_dependencies_build
cd opensim_dependencies_build
cmake ../opensim-core/dependencies \
      -DCMAKE_INSTALL_PREFIX="~/opensim_dependencies_install" \
      -DCMAKE_BUILD_TYPE=RelWithDebInfo
make -j8
cd ..
mkdir opensim_build
cd opensim_build
cmake ../opensim-core \
      -DCMAKE_INSTALL_PREFIX="~/opensim_install" \
      -DCMAKE_BUILD_TYPE=RelWithDebInfo \
      -DBUILD_PYTHON_WRAPPING=ON \
      -DBUILD_JAVA_WRAPPING=ON \
      -DOPENSIM_DEPENDENCIES_DIR="~/opensim_dependencies_install" \
      -DWITH_BTK=ON
make -j8
ctest -j8

Extended Instructions for OSX

Get the dependencies

  • operating system: Mac OSX 10.11 El Capitan.
  • cross-platform build system: CMake >= 3.2
  • compiler / IDE: Xcode >= 7.3 (the latest version), through the Mac App Store.
  • physics engine: Simbody >= 3.6. Two options:
  • C3D file support: Biomechanical-ToolKit Core. Two options:
  • command-line argument parsing: docopt.cpp. Two options:
    • Let OpenSim get this for you using superbuild (see below); much easier!
    • Build on your own (no instructions).
  • API documentation (optional): Doxygen >= 1.8.6
  • version control (optional): git.
    • Xcode Command Line Tools gives you git on the command line.
    • GitHub for Mac, for a simple-to-use GUI.
  • Bindings (optional): SWIG 3.0.6
    • MATLAB scripting (optional): Java development kit >= 1.7.
      • Note: Older versions of MATLAB may use an older version of JVM. Run 'ver' in MATLAB to check MATLAB's JVM version (must be >= 1.7).
    • Python scripting (optional):

You can get most of these dependencies using Homebrew:

$ brew install cmake doxygen swig

Download the OpenSim-Core source code

  • Method 1; If you want to get going quickly, download the source code from https://github.com/opensim-org/opensim-core/releases, for the version of OpenSim you want. We'll assume you unzipped the source code into ~/opensim-core-source.

  • Method 2: If you plan on updating your OpenSim installation or you want to contribute back to the project, clone the opensim-core git repository into ~/opensim-core-source. Run the following in a terminal, or find a way to run the equivalent commands in a GUI client:

      $ git clone https://github.com/opensim-org/opensim-core.git ~/opensim-core-source
    

    This will give you a bleeding-edge version of OpenSim-Core.

[Optional] Superbuild: download and build OpenSim dependencies

  1. Open the CMake GUI.

  2. In the field Where is the source code, specify ~/opensim-core-source/dependencies.

  3. In the field Where to build the binaries, specify a directory under which to build dependencies. Let's say this is ~/opensim-core-dependencies-build.

  4. Click the Configure button. Choose Xcode. Click Finish.

  5. Where do you want to install OpenSim dependencies on your computer? Set this by changing the CMAKE_INSTALL_PREFIX variable. Let's say this is ~/opensim-core-dependencies-install.

  6. Variables named SUPERBUILD_<dependency-name> allow you to selectively download dependencies. By default, all dependencies are downloaded, configured and built.

  7. Click the Configure button again. Then, click Generate to make Xcode files in the build directory.

  8. Open ~/opensim-core-dependencies/build/OpenSimDependencies.xcodeproj in Xcode.

  9. Choose your Build Configuration for the ALL_BUILD Scheme by pressing Command-Shift , (or, Command-LessThan), or navigating to Product -> Scheme -> Edit Scheme...; and changing the Build Configuration field.

    • Debug: debugger symbols; no optimizations (more than 10x slower). Library names end with _d.
    • Release: no debugger symbols; optimized.
    • RelWithDebInfo: debugger symbols; optimized. Bigger but not slower than Release; choose this if unsure.
    • MinSizeRel: minimum size; optimized.

    You must build each of the configurations you plan to use with OpenSim (see below). You should install the release configuration last to ensure that you use the release version of the command-line applications instead of the slow debug versions.

  10. Compile. Run the Scheme ALL_BUILD by clicking the play button in the upper left. If necessary, change the build configuration (previous step) and run ALL_BUILD again.

Configure and generate project files

  1. Open the CMake GUI.
  2. In the field Where is the source code, specify ~/opensim-core-source.
  3. In the field Where to build the binaries, specify something like ~/opensim-core-build, or some other path that is not inside your source directory. This is not where we are installing OpenSim-Core; see below.
  4. Click the Configure button. Choose Xcode. Click Finish.
  5. Where do you want to install OpenSim-Core on your computer? Set this by changing the CMAKE_INSTALL_PREFIX variable. We'll assume you set it to ~/opensim-core. If you choose a different installation location, make sure to use yours where we use ~/opensim-core below. You should not use /usr/, /usr/local/, etc. (because our installation does not yet conform to the FHS).
  6. Tell CMake where to find dependencies. This depends on how you got them.
    • Superbuild: Set the variable OPENSIM_DEPENDENCIES_DIR to the root directory you specified with superbuild for installation of dependencies. In our example, it would be ~/opensim-core-dependencies-install.
    • Obtained on your own:
      1. Simbody: Set the SIMBODY_HOME variable to where you installed Simbody (e.g., ~/simbody). If you installed Simbody using brew, then CMake will find Simbody automatically.
      2. BTK: Set the BTK_DIR variable to the directory containing BTKConfig.cmake. If you installed BTK in ~/BTKCore-install, then set BTK_DIR to ~/BTKCore-install/share/btk-0.4dev
      3. docopt.cpp. Set the variable docopt_DIR to the directory containing docopt-config.cmake. If the root directory of your docopt.cpp installation is ~/docopt.cpp-install, then set this variable to ~/docopt.cpp-install/lib/cmake.
  7. Set the remaining configuration options.
    • BUILD_API_EXAMPLES to compile C++ API examples.
    • BUILD_TESTING to ensure that OpenSim works correctly. The tests take a while to build; if you want to build OpenSim quickly, you can turn this off.
    • BUILD_JAVA_WRAPPING if you want to access OpenSim through MATLAB or Java; see dependencies above.
    • BUILD_PYTHON_WRAPPING if you want to access OpenSim through Python; see dependencies above. CMake sets PYTHON_* variables to tell you the Python it will use for building the wrappers. (If you installed Python with Homebrew, CMake will not find the Homebrew Python libraries on its own; you must set the CMake variable PYTHON_LIBRARIES manually. Use '$(python-config --prefix)/lib/libpython2.7.dylib' in bash to get the correct value.)
    • BUILD_API_ONLY if you don't want to build the command-line applications.
  8. Click the Configure button again. Then, click Generate to create Xcode project files in the build directory.

Build and install

  1. Open ~/opensim-core-build/OpenSim.xcodeproj in Xcode.

  2. Choose your Build Configuration for the ALL_BUILD Scheme by pressing Command-Shift , (or, Command-LessThan), or navigating to Product -> Scheme -> Edit Scheme...; and changing the Build Configuration field.

    • Debug: debugger symbols; no optimizations (more than 10x slower). Library names end with _d.
    • Release: no debugger symbols; optimized.
    • RelWithDebInfo: debugger symbols; optimized. Bigger but not slower than Release; choose this if unsure.
    • MinSizeRel: minimum size; optimized.

    You at least want release libraries (the last 3 count as release), but you can have debug libraries coexist with them. To do this, go through the installation process twice, once for each of the two configurations. You should install the release configuration last to ensure that you use the release version of the command-line applications instead of the slow debug versions.

  3. Compile. Run the Scheme ALL_BUILD by clicking the play button in the upper left.

  4. Test. Click on ALL_BUILD in the upper left, and select RUN_TESTS_PARALLEL. Change the Build Configuration of this Scheme to the same as you used for ALL_BUILD (using the same instructions as above). Click the play button.

  5. Build the API documentation. This is optional, and you can only do this if you have Doxygen. Click on the current Scheme (RUN_TESTS_PARALLEL) and select doxygen. Click the play button.

  6. Install. Click on the current Scheme (RUN_TESTS_PARALLEL or doxygen), and select install. Click the play button.

Set environment variables

  1. Executables. If you want to run OpenSim-Core's executables from anywhere on your computer, you must update your PATH. Note some of the names of OpenSim-Core executables conflict with some UNIX commands (e.g., id). To give preference to OpenSim-Core's executables, we must prepend OpenSim-Core's bin/ directory to the path. Open a terminal and type:

     $ echo 'export PATH=~/opensim-core/bin:$PATH' >> ~/.bash_profile
    
  2. Libraries. Hopefully you can skip this step. This step is required if:

  3. You are using CMake version 2.8.11 or older.

  4. You plan on building C++ executables or libraries on top of OpenSim, and you plan to "install" them in the CMake sense of the word (that is, you're not going to simply use them from your project's build directory).

  5. You plan to use the Java or MATLAB scripting.

If any of these are true, then you must add OpenSim-Core libraries to your linker path. Open a terminal and type:

      $ echo 'export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:~/opensim-core/lib' >> ~/.bash_profile

Your changes will only take effect in new terminal windows.

On Ubuntu using Unix Makefiles

Get the dependencies

Most dependencies can be obtained via the Ubuntu software repositories; especially if you are using Ubuntu 15.10 or later. On each line below, we show the Ubuntu package names for the dependencies. You can find instructions for specific Ubuntu versions under 'For the impatient' below.

  • cross-platform build system: CMake >= 3.2; cmake-gui.
  • compiler: gcc >= 4.9; g++-4.9, or Clang >= 3.4; clang-3.4.
  • physics engine: Simbody >= 3.6. Two options:
  • C3D file support: Biomechanical-ToolKit Core. Two options:
  • command-line argument parsing: docopt.cpp. Two options:
    • Let OpenSim get this for you using superbuild (see below); much easier!
    • Build on your own (no instructions).
  • API documentation (optional): Doxygen >= 1.8.6; doxygen.
  • version control (optional): git; git.
  • Bindings (optional): SWIG 3.0.6; must get from SWIG website.
    • MATLAB scripting (optional): Java development kit >= 1.7; openjdk-6-jdk or openjdk-7-jdk.
      • Note: Older versions of MATLAB may use an older version of JVM. Run 'ver' in MATLAB to check MATLAB's JVM version (must be >= 1.7).
    • Python scripting (optional): python-dev.

For example, you could get the required dependencies (except Simbody) via:

$ sudo apt-get install cmake-gui g++-4.9

And you could get all the optional dependencies via:

$ sudo apt-get install doxygen git swig openjdk-7-jdk python-dev

Download the OpenSim-Core source code

  • Method 1; If you want to get going quickly, download the source code from https://github.com/opensim-org/opensim-core/releases, for the version of OpenSim you want. We'll assume you unzipped the source code into ~/opensim-core-source.

  • Method 2: If you plan on updating your OpenSim installation or you want to contribute back to the project, clone the opensim-core git repository into C:/opensim-core-source. Run the following in a terminal:

      $ git clone https://github.com/opensim-org/opensim-core.git ~/opensim-core-source
    

    This will give you a bleeding-edge version of OpenSim-Core.

[Optional] Superbuild: download and build OpenSim dependencies

  1. Open the CMake GUI.

  2. In the field Where is the source code, specify ~/opensim-core-source/dependencies.

  3. In the field Where to build the binaries, specify a directory under which to build dependencies. Let's say this is ~/opensim-core-dependencies-build.

  4. Click the Configure button. Choose Unix Makefiles. Click Finish.

  5. Where do you want to install OpenSim dependencies on your computer? Set this by changing the CMAKE_INSTALL_PREFIX variable. Let's say this is ~/opensim-core-dependencies-install.

  6. Variables named SUPERBUILD_<dependency-name> allow you to selectively download dependencies. By default, all dependencies are downloaded, configured and built.

  7. Choose your build type by setting CMAKE_BUILD_TYPE to one of the following:

    • Debug: debugger symbols; no optimizations (more than 10x slower). Library names end with _d.
    • Release: no debugger symbols; optimized.
    • RelWithDebInfo: debugger symbols; optimized. Bigger but not slower than Release; choose this if unsure.
    • MinSizeRel: minimum size; optimized.

    You must perform the superbuild procedure for each of the build types you plan to use with OpenSim (see below). You might want to use different build directories for each build type, though you can use the same install directory for all build types. You should install the release build type last to ensure that you use the release version of the command-line applications instead of the slow debug versions.

  8. Click the Configure button again. Then, click Generate to make Unix Makefiles in the build directory.

  9. Open a terminal and navigate to the build directory.

     $ cd ~/opensim-core-dependencies-build
    
  10. Compile. Use the -jn flag to build using n concurrent jobs (potentially in parallel); this will greatly speed up your build. For example:

     $ make -j8
    
  11. If necessary, repeat this whole procedure for other build types.

Configure and generate project files

  1. Open the CMake GUI.

  2. In the field Where is the source code, specify ~/opensim-core-source.

  3. In the field Where to build the binaries, specify something like ~/opensim-core-build, or some other path that is not inside your source directory. This is not where we are installing OpenSim-Core; see below.

  4. Click the Configure button. Choose Unix Makefiles. Click Finish.

  5. Where do you want to install OpenSim-Core on your computer? Set this by changing the CMAKE_INSTALL_PREFIX variable. We'll assume you set it to ~/opensim-core. If you choose a different installation location, make sure to use yours where we use ~/opensim-core below. You should not use /usr/, /usr/local/, etc. (because our installation does not yet conform to the FHS), but /opt/ is okay.

  6. Tell CMake where to find dependencies. This depends on how you got them.

    • Superbuild: Set the variable OPENSIM_DEPENDENCIES_DIR to the root directory you specified with superbuild for installation of dependencies. In our example, it would be ~/opensim-core-dependencies-install.
    • Obatained on your own:
      1. Simbody: Set the SIMBODY_HOME variable to where you installed Simbody (e.g., ~/simbody).
      2. BTK: Set the BTK_DIR variable to the directory containing BTKConfig.cmake. If you installed BTK in ~/BTK-install, then set BTK-DIR to ~/BTK-install/share/btk-0.4dev.
      3. docopt.cpp. Set the variable docopt_DIR to the directory containing docopt-config.cmake. If the root directory of your docopt.cpp installation is ~/docopt.cpp-install, then set this variable to ~/docopt.cpp-install/lib/cmake.
  7. Choose your build type by setting CMAKE_BUILD_TYPE to one of the following:

    • Debug: debugger symbols; no optimizations (more than 10x slower). Library names end with _d.
    • Release: no debugger symbols; optimized.
    • RelWithDebInfo: debugger symbols; optimized. Bigger but not slower than Release; choose this if unsure.
    • MinSizeRel: minimum size; optimized.

    You at least want release libraries (the last 3 count as release), but you can have debug libraries coexist with them. To do this, go through the installation process twice, once for each of the two build types. It is typical to use a different build directory for each build type (e.g., ~/opensim-core-build-debug and ~/opensim-core-build-release). You should install the release build type last to ensure that you use the release version of the command-line applications instead of the slow debug versions.

  8. Set the remaining configuration options.

    • BUILD_API_EXAMPLES to compile C++ API examples.
    • BUILD_TESTING to ensure that OpenSim works correctly. The tests take a while to build; if you want to build OpenSim quickly, you can turn this off.
    • BUILD_JAVA_WRAPPING if you want to access OpenSim through MATLAB or Java; see dependencies above.
    • BUILD_PYTHON_WRAPPING if you want to access OpenSim through Python; see dependencies above.
    • BUILD_API_ONLY if you don't want to build the command-line applications.
    • OPENSIM_COPY_SIMBODY to decide if Simbody headers and libraries should be installed inside OpenSim; you want this off if you're installing Simbody and OpenSim into /usr/ or /usr/local/.
  9. Click the Configure button again. Then, click Generate to create Makefiles in the build directory.

Build and install

  1. Open a terminal and navigate to the build directory.

     $ cd ~/opensim-core-build
    
  2. Build the API documentation. This is optional, and you can only do this if you have Doxygen.

     $ make doxygen
    
  3. Compile. Use the -jn flag to build using n concurrent jobs (potentially in parallel); this will greatly speed up your build. For example:

     $ make -j8
    
  4. Run the tests.

     $ ctest -j8
    
  5. Install (to ~/opensim-core).

     $ make -j8 install
    

Set environment variables

  1. Executables. Add OpenSim-Core's executables to the path so you can access them from any directory on your computer. NOTE that some of the names of OpenSim-Core executables conflict with some UNIX commands (e.g., id). To give preference to OpenSim-Core's executables, we must prepend OpenSim-Core's bin/ directory to the path.

     $ echo 'export PATH=~/opensim-core/bin:$PATH' >> ~/.bashrc
    
  2. Libraries. Allow executables to find OpenSim-Core libraries by adding the OpenSim-Core lib/ directory to your linker path.

     $ echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/opensim-core/lib' >> ~/.bashrc
    

Your changes will only take effect in new terminal windows.

For the impatient (Ubuntu)

Ubuntu 14.04 Trusty Tahr

In Terminal --

sudo add-apt-repository --yes ppa:george-edison55/cmake-3.x
sudo apt-add-repository --yes ppa:fenics-packages/fenics-exp
sudo apt-get update
sudo apt-get --yes install git cmake cmake-curses-gui clang-3.6 \
                           freeglut3-dev libxi-dev libxmu-dev \
                           liblapack-dev swig3.0 python-dev \
                           openjdk-7-jdk
sudo rm -f /usr/bin/cc /usr/bin/c++
sudo ln -s /usr/bin/clang-3.6 /usr/bin/cc
sudo ln -s /usr/bin/clang++-3.6 /usr/bin/c++
export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64
git clone https://github.com/opensim-org/opensim-core.git
mkdir opensim_dependencies_build
cd opensim_dependencies_build
cmake ../opensim-core/dependencies/ \
      -DCMAKE_INSTALL_PREFIX='~/opensim_dependencies_install' \
      -DCMAKE_BUILD_TYPE=RelWithDebInfo
make -j8
cd ..
mkdir opensim_build
cd opensim_build
cmake ../opensim-core \
      -DCMAKE_INSTALL_PREFIX="~/opensim_install" \
      -DCMAKE_BUILD_TYPE=RelWithDebInfo \
      -DOPENSIM_DEPENDENCIES_DIR="~/opensim_dependencies_install" \
      -DBUILD_PYTHON_WRAPPING=ON \
      -DBUILD_JAVA_WRAPPING=ON \
      -DWITH_BTK=ON
make -j8
ctest -j8
Ubuntu 15.10 Wily Werewolf

In Terminal --

sudo apt-add-repository --yes ppa:fenics-packages/fenics
sudo apt-get update
sudo apt-get --yes install git cmake cmake-curses-gui \
                           freeglut3-dev libxi-dev libxmu-dev \
                           liblapack-dev swig3.0 python-dev \
                           openjdk-8-jdk
export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64
git clone https://github.com/opensim-org/opensim-core.git
mkdir opensim_dependencies_build
cd opensim_dependencies_build
cmake ../opensim-core/dependencies/ \
      -DCMAKE_INSTALL_PREFIX='~/opensim_dependencies_install' \
      -DCMAKE_BUILD_TYPE=RelWithDebInfo
make -j8
cd ..
mkdir opensim_build
cd opensim_build
cmake ../opensim-core \
      -DCMAKE_INSTALL_PREFIX="~/opensim_install" \
      -DCMAKE_BUILD_TYPE=RelWithDebInfo \
      -DOPENSIM_DEPENDENCIES_DIR="~/opensim_dependencies_install" \
      -DBUILD_PYTHON_WRAPPING=ON \
      -DBUILD_JAVA_WRAPPING=ON \
      -DWITH_BTK=ON
make -j8
ctest -j8
Ubuntu 16.04 Xenial Xerus AND Ubuntu 16.10 Yakkety Yak

In Terminal --

sudo apt-get update
sudo apt-get --yes install git cmake cmake-curses-gui \
                           freeglut3-dev libxi-dev libxmu-dev \
                           liblapack-dev swig python-dev \
                           openjdk-8-jdk
export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64
git clone https://github.com/opensim-org/opensim-core.git
mkdir opensim_dependencies_build
cd opensim_dependencies_build
cmake ../opensim-core/dependencies/ \
      -DCMAKE_INSTALL_PREFIX='~/opensim_dependencies_install' \
      -DCMAKE_BUILD_TYPE=RelWithDebInfo
make -j8
cd ..
mkdir opensim_build
cd opensim_build
cmake ../opensim-core \
      -DCMAKE_INSTALL_PREFIX="~/opensim_install" \
      -DCMAKE_BUILD_TYPE=RelWithDebInfo \
      -DOPENSIM_DEPENDENCIES_DIR="~/opensim_dependencies_install" \
      -DBUILD_PYTHON_WRAPPING=ON \
      -DBUILD_JAVA_WRAPPING=ON \
      -DWITH_BTK=ON
make -j8
ctest -j8