Skip to content

Latest commit

 

History

History
481 lines (340 loc) · 25.4 KB

README.md

File metadata and controls

481 lines (340 loc) · 25.4 KB
Raw

Simbody Travis Appveyor

Simbody is a high-performance, open-source toolkit for science- and engineering-quality simulation of articulated mechanisms, including biomechanical structures such as human and animal skeletons, mechanical systems like robots, vehicles, and machines, and anything else that can be described as a set of rigid bodies interconnected by joints, influenced by forces and motions, and restricted by constraints. Simbody includes a multibody dynamics library for modeling motion in generalized/internal coordinates in O(n) time. This is sometimes called a Featherstone-style physics engine.

Simbody provides a C++ API that is used to build domain-specific applications; it is not a standalone application itself. For example, it is used by biomechanists in OpenSim, by roboticists in Gazebo, and for biomolecular research in MacroMoleculeBuilder (MMB). Here's an artful simulation of several RNA molecules containing thousands of bodies, performed with MMB by Samuel Flores:

Sam Flores' Simbody RNA simulation

Read more about Simbody at the Simbody homepage.

Simple example: a double pendulum

Here's some code to simulate and visualize a 2-link chain:

#include "Simbody.h"
using namespace SimTK;
int main() {
    // Define the system.
    MultibodySystem system;
    SimbodyMatterSubsystem matter(system);
    GeneralForceSubsystem forces(system);
    Force::Gravity gravity(forces, matter, -YAxis, 9.8);

    // Describe mass and visualization properties for a generic body.
    Body::Rigid bodyInfo(MassProperties(1.0, Vec3(0), UnitInertia(1)));
    bodyInfo.addDecoration(Transform(), DecorativeSphere(0.1));

    // Create the moving (mobilized) bodies of the pendulum.
    MobilizedBody::Pin pendulum1(matter.Ground(), Transform(Vec3(0)),
            bodyInfo, Transform(Vec3(0, 1, 0)));
    MobilizedBody::Pin pendulum2(pendulum1, Transform(Vec3(0)),
            bodyInfo, Transform(Vec3(0, 1, 0)));

    // Set up visualization.
    Visualizer viz(system);
    system.addEventReporter(new Visualizer::Reporter(viz, 0.01));

    // Initialize the system and state.
    State state = system.realizeTopology();
    pendulum2.setRate(state, 5.0);

    // Simulate for 20 seconds.
    RungeKuttaMersonIntegrator integ(system);
    TimeStepper ts(system, integ);
    ts.initialize(state);
    ts.stepTo(20.0);
}

Double-pendulum simulation in Simbody

See Simbody's User Guide for a step-by-step explanation of this example.

Features

  • Wide variety of joint, constraint, and force types; easily user-extended.
  • Forward, inverse, and mixed dynamics. Motion driven by forces or prescribed motion.
  • Contact (Hertz, Hunt and Crossley models).
  • Gradient descent and interior point optimizers.
  • A variety of numerical integrators with error control.
  • Visualizer, using OpenGL.

You want to...

Dependencies

Simbody depends on the following:

  • cross-platform building: CMake 2.8.6 or greater
  • compiler: Visual Studio 2013 or later (Windows only), gcc (typically on Linux), or Clang (typically on Mac)
  • linear algebra: LAPACK and BLAS
  • visualization (optional): FreeGLUT, Xi and Xmu
  • API documentation (optional): Doxygen 1.7.6 or later; we recommend at least 1.8.8.

Installing

Simbody works on Windows, Mac, and Linux. For Windows, you must build from source. For Mac and Linux, you can use a package manager or build from source. In this file, we provide instructions for 4 different ways of installing Simbody:

  1. Windows: build from source using Microsoft Visual Studio
  2. Mac: install with Homebrew
  3. Ubuntu: install with apt-get
  4. UNIX (Mac, Linux): build from source using gcc or Clang with Makefile's

These are not the only ways to install Simbody, however. For example, on a Mac, you could use CMake and Xcode.

Windows and Visual Studio

Get the dependencies

We give the linear algebra dependencies to you, and Windows comes with the visualization dependencies.

  1. Download and install Microsoft Visual Studio. If using an Express (free) version, use Visual Studio Express 2013 for Windows Desktop.
  2. Download and install CMake.
  3. If you want to build API documentation, download and install Doxygen as well.

Download the Simbody source code

  • Method 1: Download the source code from https://github.com/simbody/simbody/releases. Look for the highest-numbered release, click on the .zip button, and unzip it on your computer. We'll assume you unzipped the source code into C:/Simbody-source.
  • Method 2: Clone the git repository.

    1. Get git. There are many options: Git for Windows (most advanced), TortoiseGit (intermediate; good for TortoiseSVN users), GitHub for Windows (easiest).

    2. Clone the github repository into C:/Simbody-source. Run the following in a Git Bash / Git Shell, or find a way to run the equivalent commands in a GUI client:

       $ git clone https://github.com/simbody/simbody.git C:/Simbody-source
 $ git checkout Simbody-3.5

    3. In the last line above, we assumed you want to build a released version. Feel free to change the version you want to build. If you want to build the latest development version ("bleeding edge") of Simbody off the master branch, you can omit the checkout line.

Configure and generate project files

  1. Open CMake.
  2. In the field Where is the source code, specify C:/Simbody-source.
  3. In the field Where to build the binaries, specify something like C:/Simbody-build, just not inside your source directory. This is not where we will install Simbody; see below.
  4. Click the Configure button.
    1. Choose a "generator" that corresponds to the Visual Studio you're using. For Visual Studio 2013, select Visual Studio 12. To build as 64-bit (recommended), select an option that ends with Win64.
    2. Click Finish.
  5. Where do you want to install Simbody on your computer? Set this by changing the CMAKE_INSTALL_PREFIX variable. We'll assume you set it to C:/Simbody. If you choose a different installation location, make sure to use yours where we use C:/Simbody below.
  6. Play around with the other build options:
    • BUILD_EXAMPLES to see what Simbody can do. On by default.
    • BUILD_TESTING to ensure your Simbody works correctly. On by default.
    • BUILD_VISUALIZER to be able to watch your system move about! If building remotely, you could turn this off. On by default.
    • BUILD_STATIC_LIBRARIES builds the three libraries as static libraries, whose names will end with _static. Off by default.
    • BUILD_TESTS_AND_EXAMPLES_STATIC if static libraries, and tests or examples are being built, creates statically-linked tests/examples. Can take a while to build, and it is unlikely you'll use the statically-linked libraries.
    • BUILD_TESTS_AND_EXAMPLES_SHARED if tests or examples are being built, creates dynamically-linked tests/examples. Unless you know what you're doing, leave this one on.
  7. Click the Configure button again. Then, click Generate to make Visual Studio project files.

Build and install

  1. Open C:/Simbody-build/Simbody.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 and visualizer names end with _d.
    • RelWithDebInfo: debugger symbols; optimized. This is the configuration we recommend.
    • Release: no debugger symbols; optimized. Generated libraries and executables are smaller but not faster than RelWithDebInfo.
    • MinSizeRel: minimum size; optimized. May be slower than RelWithDebInfo or Release.

    You at least want optimized libraries (all configurations but Debug are optimized), but you can have Debug libraries coexist with them. To do this, go through the full installation process twice, once for each configuration.

  3. Build the project ALL_BUILD by right-clicking it and selecting Build.

  4. Run the tests by right-clicking RUN_TESTS and selecting Build. Make sure all tests pass. You can use RUN_TESTS_PARALLEL for a faster test run if you have multiple cores.

  5. (Optional) Build the project doxygen to get API documentation generated from your Simbody source. You will get some warnings if your doxygen version is earlier than Doxygen 1.8.8; upgrade if you can.

  6. Install Simbody by right-clicking INSTALL and selecting Build.

Play around with examples

Within your build in Visual Studio (not the installation):

  1. Make sure your configuration is set to a release configuration (e.g., RelWithDebInfo).
  2. Right click on one of the targets whose name begins with Example - and select Select as Startup Project.
  3. Type Ctrl-F5 to start the program.

Set environment variables and test the installation

If you are only building Simbody to use it with OpenSim, you can skip this section.

  1. Allow executables to find Simbody libraries (.dll's) by adding the Simbody bin/ directory to your PATH environment variable.
    1. In the Start menu (Windows 7) or screen (Windows 8), 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:/Simbody/bin; to the front of the text field. Don't forget the semicolon!
  2. Allow Simbody and other projects (e.g., OpenSim) to find Simbody. In the same Environment Variables window:
    1. Under User variables for..., click New....
    2. For Variable name, type SIMBODY_HOME.
    3. For Variable value, type C:/Simbody.
  3. Changes only take effect in newly-opened windows. Close any Windows Explorer or Command Prompt windows.
  4. Test your installation by navigating to C:/Simbody/examples/bin and running SimbodyInstallTest.exe or SimbodyInstallTestNoViz.exe.

Note: Example binaries are not installed for Debug configurations. They are present in the build environment, however, so you can run them from there. They will run very slowly!

Layout of installation

How is your Simbody installation organized?

  • bin/ the visualizer and shared libraries (.dll's, used at runtime).
  • doc/ a few manuals, as well as API docs (SimbodyAPI.html).
  • examples/
    • src/ the source code for the examples.
    • bin/ the examples, compiled into executables; run them! (Not installed for Debug builds.)
  • include/ the header (.h) files; necessary for projects that use Simbody.
  • lib/ "import" libraries, used during linking.
  • cmake/ CMake files that are useful for projects that use Simbody.

Mac and Homebrew

If using a Mac and Homebrew, the dependencies are taken care of for you.

With this method, Simbody is built with C++11 (the -std=c++11 compiler flag). Thus, any projects you build on top of Simbody must also use C++11. See issue #125.

Install

  1. Install Homebrew.

  2. Open a terminal.

  3. Add the Open Source Robotics Foundation's list of repositories to Homebrew:

    $ brew tap osrf/simulation

  4. Install the latest release of Simbody.

    $ brew install simbody

    To install from the master branch instead, append --HEAD to the command above.

Where is Simbody installed?

Simbody is now installed to /usr/local/Cellar/simbody/<version>/, where <version> is either the version number (e.g., 3.5), or HEAD if you specified --HEAD above.

Some directories are symlinked (symbolically linked) to /usr/local/, which is where your system typically expects to find executables, shared libraries (.dylib's), headers (.h's), etc. The following directories from the Simbody installation are symlinked:

  • include/simbody -> /usr/local/include/simbody
  • lib -> /usr/local/lib
  • share/doc/simbody -> /usr/local/share/doc/simbody

Layout of installation

What's in the /usr/local/Cellar/simbody/<version>/ directory?

  • include/simbody/ the header (.h) files; necessary for projects that use Simbody.
  • lib/ shared libraries (.dylib's), used at runtime.
    • cmake/simbody/ CMake files that are useful for projects that use Simbody.
    • pkgconfig/ pkg-config files useful for projects that use Simbody.
    • simbody/examples/ the examples, compiled into executables; run them! (Not installed for Debug builds.)
  • libexec/simbody/ the simbody-visualizer executable.
  • share/doc/simbody/ a few manuals, as well as API docs (SimbodyAPI.html).
    • examples/ source code for the examples.

Ubuntu and apt-get

You can currently get Simbody via the Open Source Robotics Foundation's Debian repositories. We are currently working on getting Simbody directly into the Debian repositories. apt-get will take care of getting the necessary dependencies.

With this method, Simbody is built with C++11 (the -std=c++11 compiler flag). Thus, any projects you build on top of Simbody must also use C++11. See issue #125.

Install

  1. Setup your computer to accept software from packages.osrfoundation.org. This step depends on your version of Ubuntu. For more detailed instructions, see OSRF's installation instructions.

     $ sudo sh -c 'echo "deb http://packages.osrfoundation.org/gazebo/ubuntu `lsb_release -cs` main" > /etc/apt/sources.list.d/gazebo-latest.list'
 $ wget http://packages.osrfoundation.org/gazebo.key -O - | sudo apt-key add -
 $ sudo apt-get update

  2. Install Simbody.

     $ sudo apt-get update
 $ sudo apt-get install libsimbody-dev

Layout of installation

Simbody is installed into the usr/ directory.

  • usr/include/simbody/ the header (.h) files; necessary for projects that use Simbody.
  • usr/lib/ shared libraries (.so's), used at runtime.
    • cmake/simbody/ CMake files that are useful for projects that use Simbody.
    • pkgconfig/ pkg-config files useful for projects that use Simbody.
    • simbody/examples/ the examples, compiled into executables; run them! (Not installed for Debug builds.)
  • usr/libexec/simbody/ the simbody-visualizer executable.
  • usr/share/doc/simbody/ a few manuals, as well as API docs (SimbodyAPI.html).

UNIX and Makefiles

These instructions are for building Simbody from source on either a Mac or on Ubuntu.

Get dependencies

On a Mac, the Xcode developer package gives LAPACK and BLAS to you via the Accelerate framework. Mac's come with the visualization dependencies.

On Ubuntu, we need to get the dependencies ourselves. Open a terminal and run the following commands.

  1. Get the necessary dependencies: $ sudo apt-get install cmake liblapack-dev
  2. If you want to use the CMake GUI, install cmake-qt-gui.
  3. For visualization (optional): $ sudo apt-get install freeglut3-dev libxi-dev libxmu-dev
  4. For API documentation (optional): $ sudo apt-get install doxygen

Get the Simbody source code

There are two ways to get the source code.

  • Method 1: Download the source code from https://github.com/simbody/simbody/releases. Look for the highest-numbered release, click on the .zip button, and unzip it on your computer. We'll assume you unzipped the source code into ~/simbody-source.
  • Method 2: Clone the git repository.

    1. Get git.

      • Mac: You might have it already, especially if you have Xcode, which is free in the App Store. If not, one method is to install Homebrew and run brew install git in a terminal.
      • Ubuntu: run sudo apt-get install git in a terminal.

    2. Clone the github repository into ~/simbody-source.

       $ git clone https://github.com/simbody/simbody.git ~/simbody-source
 $ git checkout Simbody-3.5

    3. In the last line above, we assumed you want to build a released version. Feel free to change the version you want to build. If you want to build the latest development version ("bleeding edge") of Simbody off the master branch, you can omit the checkout line.

Configure and generate Makefiles

  1. Create a directory in which we'll build Simbody. We'll assume you choose ~/simbody-build. Don't choose a location inside ~/simbody-source.

     $ mkdir ~/simbody-build
 $ cd ~/simbody-build

  2. Configure your Simbody build with CMake. We'll use the cmake command but you could also use the interactive tools ccmake or cmake-gui. You have a few configuration options to play with here.

    • If you don't want to fuss with any options, run:

        $ cmake ~/simbody-source

    • Where do you want to install Simbody? By default, it is installed to /usr/local/. That's a great default option, especially if you think you'll only use one version of Simbody at a time. You can change this via the CMAKE_INSTALL_PREFIX variable. Let's choose ~/simbody:

        $ cmake ~/simbody-source -DCMAKE_INSTALL_PREFIX=~/simbody

    • Do you want to use C++11? By default, Simbody assumes yes. If you plan to use Simbody in a project that DOES use C++11, then you must build Simbody with C++11 as well. You can change this via the SIMBODY_STANDARD_11 variable:

        $ cmake ~/simbody-source -DSIMBODY_STANDARD_11=off

    • Do you want the libraries to be optimized for speed, or to contain debugger symbols? You can change this via the CMAKE_BUILD_TYPE variable. There are 4 options:

      • Debug: debugger symbols; no optimizations (more than 10x slower). Library and visualizer names end with _d.
      • RelWithDebInfo: debugger symbols; optimized. This is the configuration we recommend.
      • Release: no debugger symbols; optimized. Generated libraries and executables are smaller but not faster than RelWithDebInfo.
      • MinSizeRel: minimum size; optimized. May be slower than RelWithDebInfo or Release.

      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 full installation process twice, once for each configuration. It is typical to use a different build directory for each build type (e.g., ~/simbody-build-debug and ~/simbody-build-release).

    • There are a few other variables you might want to play with:

      • BUILD_EXAMPLES to see what Simbody can do. On by default.
      • BUILD_TESTING to ensure your Simbody works correctly. The tests take a long time to build, though. If you need to build Simbody quickly, maybe turn this off. On by default.
      • BUILD_VISUALIZER to be able to watch your system move about! If building on a cluster, you could turn this off. On by default.
      • BUILD_STATIC_LIBRARIES builds the three libraries as static libraries, whose names will end with _static.
      • BUILD_TESTS_AND_EXAMPLES_STATIC if tests or examples are being built, creates statically-linked tests/examples. Can take a while to build, and it is unlikely you'll use the statically-linked libraries.
      • BUILD_TESTS_AND_EXAMPLES_SHARED if tests or examples are being built, creates dynamically-linked tests/examples. Unless you know what you're doing, leave this one on.

      You can combine all these options. Here's another example:

        $ cmake ~/simbody-source -DCMAKE_INSTALL_PREFIX=~/simbody -DCMAKE_BUILD_TYPE=RelWithDebInfo -DBUILD_VISUALIZER=off

Build and install

  1. Build the API documentation. This is optional, and you can only do this if you have Doxygen. You will get warnings if your doxygen installation is a version older than Doxygen 1.8.8.

     $ make doxygen

  2. Compile. Use the -jn flag to build using n processor cores. For example:

     $ make -j8

  3. Run the tests.

     $ ctest -j8

  4. Install. If you chose CMAKE_INSTALL_PREFIX to be a location which requires sudo access to write to (like /usr/local/, prepend this command with a sudo .

     $ make -j8 install

Just so you know, you can also uninstall (delete all files that CMake placed into CMAKE_INSTALL_PREFIX) if you're in ~/simbody-build.

$ make uninstall

Play around with examples

From your build directory, you can run Simbody's example programs. For instance, try:

    $ ./ExamplePendulum

Set environment variables and test the installation

If you are only building Simbody to use it with OpenSim, you can skip this section.

  1. Allow executables to find Simbody libraries (.dylib's or so's) by adding the Simbody lib directory to your linker path.

    • If your CMAKE_INSTALL_PREFIX is /usr/local/, run:

        $ sudo ldconfig

    • If your CMAKE_INSTALL_PREFIX is neither /usr/ nor /usr/local/ (e.g., ~/simbody'):

      • Mac:

          $ echo 'export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:~/simbody/lib' >> ~/.bash_profile

      • Ubuntu:

          $ echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/simbody/lib/x86_64-linux-gnu' >> ~/.bashrc

      These commands add a line to a configuration file that is loaded every time you open a new terminal. If using Ubuntu, you may need to replace x86_64-linux-gnu with the appropriate directory on your computer.

  2. Allow Simbody and other projects (e.g., OpenSim) to find Simbody. Make sure to replace ~/simbody with your CMAKE_INSTALL_PREFIX.

    • Mac:

        $ echo 'export SIMBODY_HOME=~/simbody' >> ~/.bash_profile

    • Ubuntu:

        $ echo 'export SIMBODY_HOME=~/simbody' >> ~/.bashrc

  3. Open a new terminal.

  4. Test your installation:

     $ cd ~/simbody/share/doc/simbody/examples/bin
 $ ./SimbodyInstallTest # or ./SimbodyInstallTestNoViz

Layout of installation

The installation creates the following directories in CMAKE_INSTALL_PREFIX. The directory [x86_64-linux-gnu] only exists if you're using a recent version of Ubuntu (e.g., 13.10) and did NOT install to /usr/local/. Even in that case, the name of your directory may be different.

  • include/simbody/ the header (.h) files; necessary for projects that use Simbody.
  • lib/[x86_64-linux-gnu]/ shared libraries (.dylib's or .so's), used at runtime.
    • cmake/simbody/ CMake files that are useful for projects that use Simbody.
    • pkgconfig/ pkg-config files useful for projects that use Simbody.
    • simbody/examples/ the examples, compiled into executables; run them! (Not installed for Debug builds.)
  • libexec/simbody/ the simbody-visualizer executable.
  • share/doc/simbody/ a few manuals, as well as API docs (SimbodyAPI.html).
    • examples/ source code for the examples.

Acknowledgments

We are grateful for past and continuing support for Simbody's development in Stanford's Bioengineering department through the following grants:

  • NIH U54 GM072970 (Simulation of Biological Structures)
  • NIH U54 EB020405 (Mobilize Center)
  • NIH R24 HD065690 (Simulation in Rehabilitation Research)
  • OSRF subcontract 12-006 to DARPA HR0011-12-C-0111 (Robotics Challenge)

Prof. Scott Delp is the Principal Investigator on these grants and Simbody is used extensively in Scott's Neuromuscular Biomechanics Lab as the basis for the OpenSim biomechanical simulation software application for medical research.