Simbody: High-performance C++ Multibody Dynamics/physics Library

Simbody  

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:

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.
    system.setUseUniformBackground(true);
    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);
}

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, interior point, and global (CMA) optimizers.
• A variety of numerical integrators with error control.
• Visualizer, using OpenGL

You want to...

• install Simbody.
• use Simbody in your own program.
• view API documentation.
• learn the theory behind Simbody.
• extend Simbody.
• get support at the Simbody Forum.
• report a bug or suggest a feature.

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Dependencies

Simbody depends on the following:

• cross-platform building: CMake 2.8.10 or later (3.1.3 or later for Visual Studio).
• compiler: Visual Studio 2015, 2017, or 2019 (Windows only), gcc 4.9.0 or later (typically on Linux), Clang 3.4 or later, or Apple Clang (Xcode) 8 or later.
• linear algebra: LAPACK 3.6.0 or later and BLAS
• visualization (optional): FreeGLUT, Xi and Xmu
• API documentation (optional): Doxygen 1.8.6 or later; we recommend at least 1.8.8.

Using Simbody

• Creating your own Simbody-using project with CMake To get started with your own Simbody-using project, check out the cmake/SampleCMakeLists.txt file.

Installing

Simbody works on Windows, Mac, and Linux. For each operating system, you can use a package manager or build from source. In this file, we provide instructions for 6 different ways of installing Simbody:

1. Windows: build from source using Microsoft Visual Studio.
2. Linux or Mac (make): build from source using gcc or Clang with make.
3. Mac (Homebrew): automated build/install with Homebrew.
4. Ubuntu/Debian: install pre-built binaries with apt-get.
5. FreeBSD: install pre-built binaries with pkg.
6. Windows using MinGW: build from source using MinGW.
7. Windows/Mac/Linux: install pre-built binaries with the Conda package manager.
8. Install using vcpkg: download and install simbody using the vcpkg dependency manager

If you use Linux, check Repology to see if your distribution provides a package for Simbody.

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

C++11 and gcc/Clang

Simbody 3.6 and later uses C++11 features (the -std=c++11 flag). Simbody 3.3 and earlier use only C++03 features, and Simbody 3.4 and 3.5 can use either C++03 or C++11; see the SIMBODY_STANDARD_11 CMake variable in these versions. Note that if you want to use the C++11 flag in your own project, Simbody must have been compiled with the C++11 flag as well.

Windows using Visual Studio

Get the dependencies

All needed library dependencies are provided with the Simbody installation on Windows, including linear algebra and visualization dependencies.

1. Download and install Microsoft Visual Studio, version 2015, 2017, or 2019. The Community edition is free and sufficient.

• 2015: By default, Visual Studio 2015 does not provide C++ support; when installing, be sure to select Custom, and check Programming Languages > Visual C++ > Common Tools for Visual C++ 2015. If you have already installed Visual Studio without C++ support, simply re-run the installer and select Modify.
• 2017 and later: In the installer, select the Desktop development with C++ workload.
• Any other C++ code you plan to use with Simbody should be compiled with the same compiler as used for Simbody.

1. Download and install CMake, version 3.1.3 or higher.
2. (optional) If you want to build API documentation, download and install Doxygen, version 1.8.8 or higher.

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.

Get git. There are many options:

• Git for Windows (most advanced),
• TortoiseGit (intermediate; good for TortoiseSVN users),
• GitHub Desktop (easiest).

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-3.7

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.

To see the set of releases and checkout a specific version, you can use the following commands:

 $ git tag
 $ git checkout Simbody-X.Y.Z

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. When prompted to select a generator, in the dropdown for Optional platform for generator, choose x64 to build 64-bit binaries or leave blank to build 32-bit binaries. In older versions of CMake, select a generator ending with Win64 to build 64-bit binaries (e.g., Visual Studio 14 2015 Win64 or Visual Studio 15 2017 Win64), or select one without Win64 to build 32-bit binaries (e.g., Visual Studio 14 2015 or Visual Studio 15 2017).
   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_DYNAMIC_LIBRARIES builds the three libraries as dynamic libraries. On by default. Unless you know what you're doing, leave this one on.
   • BUILD_STATIC_LIBRARIES builds the three libraries as static libraries, whose names will end with _static. Off by default. You must activate either BUILD_DYNAMIC_LIBRARIES, BUILD_STATIC_LIBRARIES, or both.
   • 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

Open C:/Simbody-build/Simbody.sln in Visual Studio.

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.

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

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.

(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.

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 10) 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.

Linux or Mac using make

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

Check the compiler version

Simbody uses recent C++ features, that require a modern compiler. Before installing Simbody, check your compiler version with commands like that:

• g++ --version
• clang++ --version

In case your compiler is not supported, you can upgrade your compiler.

Upgrading GCC to 4.9 on Ubuntu 14.04

Here are some instructions to upgrade GCC on a Ubuntu 14.04 distribution.

$ sudo add-apt-repository ppa:ubuntu-toolchain-r/test
$ sudo apt-get update
$ sudo apt-get install gcc-4.9 g++-4.9

If one wants to set gcc-4.9 and g++-4.9 as the default compilers, run the following command

$ sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9

Remember that when having several compilers, CMake flags CMAKE_C_COMPILER and CMAKE_CXX_COMPILER can be used to select the ones desired. For example, Simbody can be configured with the following flags:

$ cmake -DCMAKE_C_COMPILER=gcc-4.9 -DCMAKE_CXX_COMPILER=g++-4.9

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.

LAPACK version 3.6.0 and higher may be required for some applications (OpenSim). LAPACK can be downloaded from http://www.netlib.org/lapack/, and compiled using the following method. It is sufficient to set LD_LIBRARY_PATH to your LAPACK install prefix and build Simbody using the -DBUILD_USING_OTHER_LAPACK:PATH=/path/to/liblapack.so option in cmake.

cmake ../lapack-3.6.0 -DCMAKE_INSTALL_PREFIX=/path/to/new/lapack/ -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_SHARED_LIBS=ON
make
make install

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.

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.

Clone the github repository into ~/simbody-source.

 $ git clone https://github.com/simbody/simbody.git ~/simbody-source
 $ git checkout Simbody-3.7

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.

To see the set of releases and checkout a specific version, you can use the following commands:

 $ git tag
 $ git checkout Simbody-X.Y.Z

Configure and generate Makefiles

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

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 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.

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. 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_DYNAMIC_LIBRARIES builds the three libraries as dynamic libraries. 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.

Build and install

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

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

 $ make -j8

Run the tests.

 $ ctest -j8

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.

Allow executables to find Simbody libraries (.dylib's or so's) by adding the Simbody lib directory to your linker path. On Mac, most users can skip this step.

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

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

Open a new terminal.

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 did NOT install to /usr/local/ and varies by platform. 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).
  • 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/src source code for the examples.
  • examples/bin symbolic link to the runnable examples.

Mac and Homebrew

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

Install

Install Homebrew.

Open a terminal.

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

$ brew tap osrf/simulation

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., 3.6.1), 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/src source code for the examples.
  • examples/bin symbolic link to executable examples.

Ubuntu and apt-get

Starting with Ubuntu 15.04, Simbody is available in the Ubuntu (and Debian) repositories. You can see a list of all simbody packages for all Ubuntu versions at the Ubuntu Packages website. The latest version of Simbody is usually not available in the Ubuntu repositories; the process for getting a new version of Simbody into the Ubuntu repositories could take up to a year.

Install

Open a terminal and run the following command:

 $ sudo apt-get install libsimbody-dev simbody-doc

Layout of installation

Simbody is installed into the usr/ directory. The directory [x86_64-linux-gnu] varies by platform.

• usr/include/simbody/ the header (.h) files; necessary for projects that use Simbody.
• usr/lib/[x86_64-linux-gnu] shared libraries (.so's).
  • cmake/simbody/ CMake files that are useful for projects that use Simbody.
  • pkgconfig/ pkg-config files useful for projects that use Simbody.
• usr/libexec/simbody/ the simbody-visualizer executable.
• usr/share/doc/simbody/ a few manuals, as well as API docs (SimbodyAPI.html).
  • examples/src source code for the examples.
  • examples/bin symbolic link to executable examples.

FreeBSD and pkg

Simbody is available via the FreeBSD package repository.

Install

Open a terminal and run the following command:

 $ sudo pkg install simbody

Windows using MinGW

Warning: The MinGW generation and build is experimental!

This build is still experimental, because of :

• the various MinGW versions available (Thread model, exception mechanism)
• the compiled libraries Simbody depends on (Blas, Lapack and optionnaly glut).

Below are three sections that gives a list of supported versions, command line instructions, and reasons why is it not so obvious to use MinGW.

Supported MinGW versions

If you do not want to go into details, you need a MinGW version with :

• a Posix thread model and Dwarf exception mechanism on a 32 bit computer
• a Posix thread model and SJLJ exception mechanism on a 64 bit computer

Other versions are supported with additional configurations.

The table below lists the various versions of MinGW versions tested:

	OS	Thread	Exception	Comment	URL
1	64 Bits	Posix	SJLJ	All features supported, all binary included (Recommended version)	MinGW64 GCC 5.2.0
2	64 Bits	Posix	SEH	Needs to be linked against user's Blas and Lapack	MinGW64 GCC 5.2.0
3	32 Bits	Posix	Dwarf	No visualization, all binary included	MinGW64 GCC 5.2.0
4	32 Bits	Posix	SJLJ	No visualization, needs to be linked against user's Blas and Lapack	MinGW64 GCC 5.2.0

We recommend to use the first configuration where all features are supported and does not need additional libraries to compile and run. The URL allows to download directly this version. The second version needs to be linked against user's Blas and Lapack (A CLI example is given below). Blas and Lapack sources can be downloaded from netlib. For the 3rd and 4th versions that run that target a 32 bit behaviour, visualization is not possible for the time being. (It is due to a compile and link problem with glut). Moreover for the 4th one, one needs to provide Blas and Lapack libraries.

Please note that only Posix version of MinGW are supported.

If your version is not supported, CMake will detect it while configuring and stops.

Instructions

Below are some examples of command line instructions for various cases. It is assumed you are running commands from a build directory, that can access Simbody source with a command cd ..\simbody.

It is recommended to specify with the installation directory with flag CMAKE_INSTALL_PREFIX (e.g. -DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody"). If not used, the installation directory will be C:\Program Files (x86)\Simbody on a 64 bit computer. This might be confusing since it is the 32 bit installation location.

Example of instructions where one uses Blas and Lapack libraries provided (to be used in a Windows terminal, where MinGW is in the PATH):

rem CMake configuration
cmake ..\simbody -G "MinGW Makefiles" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody"
rem Compilation
mingw32-make
rem Test
mingw32-make test
rem Installation
mingw32-make install

Example of instructions where one uses Blas and Lapack libraries provided (to be used in a Windows terminal, where MinGW is NOT in the PATH):

rem Variable and path definition
set CMAKE="C:\Program Files\CMake\bin\cmake.exe"
set MinGWDir=C:\Program Files\mingw-w64\i686-5.2.0-posix-sjlj-rt_v4-rev0\mingw32
set PATH=%MinGWDir%\bin;%MinGWDir%\i686-w64-mingw32\lib
rem CMake configuration
%CMAKE% ..\simbody -G"MinGW Makefiles" -DCMAKE_BUILD_TYPE=Release ^
 -DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody" ^
 -DCMAKE_C_COMPILER:PATH="%MinGWDir%\bin\gcc.exe" ^
 -DCMAKE_CXX_COMPILER:PATH="%MinGWDir%\bin\g++.exe" ^
 -DCMAKE_MAKE_PROGRAM:PATH="%MinGWDir%\bin\mingw32-make.exe"
rem Compilation
mingw32-make
rem Test
mingw32-make test
rem Installation
mingw32-make install

Example of instructions where one uses Blas and Lapack libraries provided (to be used in a MSYS terminal with MinGW in the PATH):

# CMake configuration
cmake ../simbody -G "MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody"
# Compilation
make
# Test
make test
# Installation
make install

Example of instructions where one provides our own Blas and Lapack libraries (to be used in a MSYS terminal with MinGW in the PATH):

# CMake configuration
cmake ../simbody -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody" \
-DCMAKE_C_COMPILER:PATH="C:\Program Files\mingw-w64\i686-5.2.0-posix-sjlj-rt_v4-rev0\mingw32\bin\gcc.exe" \
-DCMAKE_CXX_COMPILER:PATH="C:\Program Files\mingw-w64\i686-5.2.0-posix-sjlj-rt_v4-rev0\mingw32\bin\g++.exe" \
-DBUILD_USING_OTHER_LAPACK:PATH="C:\Program Files\lapack-3.5.0\bin\liblapack.dll;C:\Program Files\lapack-3.5.0\bin\libblas.dll"
make
# Test
make test
# Installation
make install

MinGW details

This paragraph explains the reason why one can not use any MinGW version.

MinGW is available with two thread models :

• Win32 thread model
• Posix thread model

One has to use the Posix thread model, since all thread functionalities (e.g. std:mutex) are not implemented.

To ease building on Windows, Simbody provides compiled libraries for Blas and Lapack :

• On Windows 32 Bits, these were compiled with a Dwarf exception mechanism,
• On Windows 64 Bits, these were compiled with a SJLJ exception mechanism.

If one chooses a MinGW compilation, we need to respect this exception mechanism. A program can not rely on both mechanisms. This means that if we want to use the compiled libraries, our MinGW installation should have the same exception mechanism. Otherwise, we need to provide our own Blas and Lapack libraries.

To see which exception mechanism is used, user can look at dlls located in the bin directory of MinGW. The name of mechanism is present in the file libgcc_XXXX.dll, where XXXX can be dw, seh or sjlj. For some MinGW versions, this information is also available by looking at the result of gcc --version.

CMake will check the version of your MinGW, and if the exception mechanism is different, then the configuration stops because of this difference. If one provides Blas and Lapack libraries with the CMake variable BUILD_USING_OTHER_LAPACK, compilation with MinGW is always possible.

Windows, Mac, and Linux Using Conda

Conda is a cross platform package manager that can be used to install Simbody on Windows, Mac, or Linux. To install Simbody using Conda you must first install Miniconda or Anaconda. Either of these will provide the conda command which can be invoked at the command line to install Simbody from the Conda Forge channel as follows:

$ conda install -c conda-forge simbody

This command will install Simbody (both the libraries and headers) into the Miniconda or Anaconda installation directory as per the standard layout for each of the operating systems described above. The Conda Forge Simbody recipe can be found in Conda Forge's feedstock repository.

Installing simbody(vcpkg)

You can download and install simbody using the vcpkg dependency manager:

git clone https://github.com/Microsoft/vcpkg.git
cd vcpkg
./bootstrap-vcpkg.sh
./vcpkg integrate install
./vcpkg install simbody

The simbody port in vcpkg is kept up to date by Microsoft team members and community contributors. If the version is out of date, please create an issue or pull request on the vcpkg repository.

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.

---

Download Details:

Author: Simbody
Source Code: https://github.com/simbody/simbody 
License: Apache-2.0 license

#machinelearning #cpluplus #robotics #physics #engine 

What is GEEK

Buddha Community

Simbody: High-performance C++ Multibody Dynamics/physics Library

Simbody  

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:

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.
    system.setUseUniformBackground(true);
    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);
}

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, interior point, and global (CMA) optimizers.
• A variety of numerical integrators with error control.
• Visualizer, using OpenGL

You want to...

• install Simbody.
• use Simbody in your own program.
• view API documentation.
• learn the theory behind Simbody.
• extend Simbody.
• get support at the Simbody Forum.
• report a bug or suggest a feature.

---

Dependencies

Simbody depends on the following:

• cross-platform building: CMake 2.8.10 or later (3.1.3 or later for Visual Studio).
• compiler: Visual Studio 2015, 2017, or 2019 (Windows only), gcc 4.9.0 or later (typically on Linux), Clang 3.4 or later, or Apple Clang (Xcode) 8 or later.
• linear algebra: LAPACK 3.6.0 or later and BLAS
• visualization (optional): FreeGLUT, Xi and Xmu
• API documentation (optional): Doxygen 1.8.6 or later; we recommend at least 1.8.8.

Using Simbody

• Creating your own Simbody-using project with CMake To get started with your own Simbody-using project, check out the cmake/SampleCMakeLists.txt file.

Installing

Simbody works on Windows, Mac, and Linux. For each operating system, you can use a package manager or build from source. In this file, we provide instructions for 6 different ways of installing Simbody:

1. Windows: build from source using Microsoft Visual Studio.
2. Linux or Mac (make): build from source using gcc or Clang with make.
3. Mac (Homebrew): automated build/install with Homebrew.
4. Ubuntu/Debian: install pre-built binaries with apt-get.
5. FreeBSD: install pre-built binaries with pkg.
6. Windows using MinGW: build from source using MinGW.
7. Windows/Mac/Linux: install pre-built binaries with the Conda package manager.
8. Install using vcpkg: download and install simbody using the vcpkg dependency manager

If you use Linux, check Repology to see if your distribution provides a package for Simbody.

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

C++11 and gcc/Clang

Simbody 3.6 and later uses C++11 features (the -std=c++11 flag). Simbody 3.3 and earlier use only C++03 features, and Simbody 3.4 and 3.5 can use either C++03 or C++11; see the SIMBODY_STANDARD_11 CMake variable in these versions. Note that if you want to use the C++11 flag in your own project, Simbody must have been compiled with the C++11 flag as well.

Windows using Visual Studio

Get the dependencies

All needed library dependencies are provided with the Simbody installation on Windows, including linear algebra and visualization dependencies.

1. Download and install Microsoft Visual Studio, version 2015, 2017, or 2019. The Community edition is free and sufficient.

• 2015: By default, Visual Studio 2015 does not provide C++ support; when installing, be sure to select Custom, and check Programming Languages > Visual C++ > Common Tools for Visual C++ 2015. If you have already installed Visual Studio without C++ support, simply re-run the installer and select Modify.
• 2017 and later: In the installer, select the Desktop development with C++ workload.
• Any other C++ code you plan to use with Simbody should be compiled with the same compiler as used for Simbody.

1. Download and install CMake, version 3.1.3 or higher.
2. (optional) If you want to build API documentation, download and install Doxygen, version 1.8.8 or higher.

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.

Get git. There are many options:

• Git for Windows (most advanced),
• TortoiseGit (intermediate; good for TortoiseSVN users),
• GitHub Desktop (easiest).

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-3.7

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.

To see the set of releases and checkout a specific version, you can use the following commands:

 $ git tag
 $ git checkout Simbody-X.Y.Z

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. When prompted to select a generator, in the dropdown for Optional platform for generator, choose x64 to build 64-bit binaries or leave blank to build 32-bit binaries. In older versions of CMake, select a generator ending with Win64 to build 64-bit binaries (e.g., Visual Studio 14 2015 Win64 or Visual Studio 15 2017 Win64), or select one without Win64 to build 32-bit binaries (e.g., Visual Studio 14 2015 or Visual Studio 15 2017).
   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_DYNAMIC_LIBRARIES builds the three libraries as dynamic libraries. On by default. Unless you know what you're doing, leave this one on.
   • BUILD_STATIC_LIBRARIES builds the three libraries as static libraries, whose names will end with _static. Off by default. You must activate either BUILD_DYNAMIC_LIBRARIES, BUILD_STATIC_LIBRARIES, or both.
   • 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

Open C:/Simbody-build/Simbody.sln in Visual Studio.

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.

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

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.

(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.

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 10) 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.

Linux or Mac using make

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

Check the compiler version

Simbody uses recent C++ features, that require a modern compiler. Before installing Simbody, check your compiler version with commands like that:

• g++ --version
• clang++ --version

In case your compiler is not supported, you can upgrade your compiler.

Upgrading GCC to 4.9 on Ubuntu 14.04

Here are some instructions to upgrade GCC on a Ubuntu 14.04 distribution.

$ sudo add-apt-repository ppa:ubuntu-toolchain-r/test
$ sudo apt-get update
$ sudo apt-get install gcc-4.9 g++-4.9

If one wants to set gcc-4.9 and g++-4.9 as the default compilers, run the following command

$ sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9

Remember that when having several compilers, CMake flags CMAKE_C_COMPILER and CMAKE_CXX_COMPILER can be used to select the ones desired. For example, Simbody can be configured with the following flags:

$ cmake -DCMAKE_C_COMPILER=gcc-4.9 -DCMAKE_CXX_COMPILER=g++-4.9

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.

LAPACK version 3.6.0 and higher may be required for some applications (OpenSim). LAPACK can be downloaded from http://www.netlib.org/lapack/, and compiled using the following method. It is sufficient to set LD_LIBRARY_PATH to your LAPACK install prefix and build Simbody using the -DBUILD_USING_OTHER_LAPACK:PATH=/path/to/liblapack.so option in cmake.

cmake ../lapack-3.6.0 -DCMAKE_INSTALL_PREFIX=/path/to/new/lapack/ -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_SHARED_LIBS=ON
make
make install

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.

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.

Clone the github repository into ~/simbody-source.

 $ git clone https://github.com/simbody/simbody.git ~/simbody-source
 $ git checkout Simbody-3.7

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.

To see the set of releases and checkout a specific version, you can use the following commands:

 $ git tag
 $ git checkout Simbody-X.Y.Z

Configure and generate Makefiles

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

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 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.

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. 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_DYNAMIC_LIBRARIES builds the three libraries as dynamic libraries. 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.

Build and install

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

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

 $ make -j8

Run the tests.

 $ ctest -j8

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.

Allow executables to find Simbody libraries (.dylib's or so's) by adding the Simbody lib directory to your linker path. On Mac, most users can skip this step.

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

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

Open a new terminal.

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 did NOT install to /usr/local/ and varies by platform. 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).
  • 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/src source code for the examples.
  • examples/bin symbolic link to the runnable examples.

Mac and Homebrew

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

Install

Install Homebrew.

Open a terminal.

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

$ brew tap osrf/simulation

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., 3.6.1), 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/src source code for the examples.
  • examples/bin symbolic link to executable examples.

Ubuntu and apt-get

Starting with Ubuntu 15.04, Simbody is available in the Ubuntu (and Debian) repositories. You can see a list of all simbody packages for all Ubuntu versions at the Ubuntu Packages website. The latest version of Simbody is usually not available in the Ubuntu repositories; the process for getting a new version of Simbody into the Ubuntu repositories could take up to a year.

Install

Open a terminal and run the following command:

 $ sudo apt-get install libsimbody-dev simbody-doc

Layout of installation

Simbody is installed into the usr/ directory. The directory [x86_64-linux-gnu] varies by platform.

• usr/include/simbody/ the header (.h) files; necessary for projects that use Simbody.
• usr/lib/[x86_64-linux-gnu] shared libraries (.so's).
  • cmake/simbody/ CMake files that are useful for projects that use Simbody.
  • pkgconfig/ pkg-config files useful for projects that use Simbody.
• usr/libexec/simbody/ the simbody-visualizer executable.
• usr/share/doc/simbody/ a few manuals, as well as API docs (SimbodyAPI.html).
  • examples/src source code for the examples.
  • examples/bin symbolic link to executable examples.

FreeBSD and pkg

Simbody is available via the FreeBSD package repository.

Install

Open a terminal and run the following command:

 $ sudo pkg install simbody

Windows using MinGW

Warning: The MinGW generation and build is experimental!

This build is still experimental, because of :

• the various MinGW versions available (Thread model, exception mechanism)
• the compiled libraries Simbody depends on (Blas, Lapack and optionnaly glut).

Below are three sections that gives a list of supported versions, command line instructions, and reasons why is it not so obvious to use MinGW.

Supported MinGW versions

If you do not want to go into details, you need a MinGW version with :

• a Posix thread model and Dwarf exception mechanism on a 32 bit computer
• a Posix thread model and SJLJ exception mechanism on a 64 bit computer

Other versions are supported with additional configurations.

The table below lists the various versions of MinGW versions tested:

	OS	Thread	Exception	Comment	URL
1	64 Bits	Posix	SJLJ	All features supported, all binary included (Recommended version)	MinGW64 GCC 5.2.0
2	64 Bits	Posix	SEH	Needs to be linked against user's Blas and Lapack	MinGW64 GCC 5.2.0
3	32 Bits	Posix	Dwarf	No visualization, all binary included	MinGW64 GCC 5.2.0
4	32 Bits	Posix	SJLJ	No visualization, needs to be linked against user's Blas and Lapack	MinGW64 GCC 5.2.0

We recommend to use the first configuration where all features are supported and does not need additional libraries to compile and run. The URL allows to download directly this version. The second version needs to be linked against user's Blas and Lapack (A CLI example is given below). Blas and Lapack sources can be downloaded from netlib. For the 3rd and 4th versions that run that target a 32 bit behaviour, visualization is not possible for the time being. (It is due to a compile and link problem with glut). Moreover for the 4th one, one needs to provide Blas and Lapack libraries.

Please note that only Posix version of MinGW are supported.

If your version is not supported, CMake will detect it while configuring and stops.

Instructions

Below are some examples of command line instructions for various cases. It is assumed you are running commands from a build directory, that can access Simbody source with a command cd ..\simbody.

It is recommended to specify with the installation directory with flag CMAKE_INSTALL_PREFIX (e.g. -DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody"). If not used, the installation directory will be C:\Program Files (x86)\Simbody on a 64 bit computer. This might be confusing since it is the 32 bit installation location.

Example of instructions where one uses Blas and Lapack libraries provided (to be used in a Windows terminal, where MinGW is in the PATH):

rem CMake configuration
cmake ..\simbody -G "MinGW Makefiles" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody"
rem Compilation
mingw32-make
rem Test
mingw32-make test
rem Installation
mingw32-make install

Example of instructions where one uses Blas and Lapack libraries provided (to be used in a Windows terminal, where MinGW is NOT in the PATH):

rem Variable and path definition
set CMAKE="C:\Program Files\CMake\bin\cmake.exe"
set MinGWDir=C:\Program Files\mingw-w64\i686-5.2.0-posix-sjlj-rt_v4-rev0\mingw32
set PATH=%MinGWDir%\bin;%MinGWDir%\i686-w64-mingw32\lib
rem CMake configuration
%CMAKE% ..\simbody -G"MinGW Makefiles" -DCMAKE_BUILD_TYPE=Release ^
 -DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody" ^
 -DCMAKE_C_COMPILER:PATH="%MinGWDir%\bin\gcc.exe" ^
 -DCMAKE_CXX_COMPILER:PATH="%MinGWDir%\bin\g++.exe" ^
 -DCMAKE_MAKE_PROGRAM:PATH="%MinGWDir%\bin\mingw32-make.exe"
rem Compilation
mingw32-make
rem Test
mingw32-make test
rem Installation
mingw32-make install

Example of instructions where one uses Blas and Lapack libraries provided (to be used in a MSYS terminal with MinGW in the PATH):

# CMake configuration
cmake ../simbody -G "MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody"
# Compilation
make
# Test
make test
# Installation
make install

Example of instructions where one provides our own Blas and Lapack libraries (to be used in a MSYS terminal with MinGW in the PATH):

# CMake configuration
cmake ../simbody -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody" \
-DCMAKE_C_COMPILER:PATH="C:\Program Files\mingw-w64\i686-5.2.0-posix-sjlj-rt_v4-rev0\mingw32\bin\gcc.exe" \
-DCMAKE_CXX_COMPILER:PATH="C:\Program Files\mingw-w64\i686-5.2.0-posix-sjlj-rt_v4-rev0\mingw32\bin\g++.exe" \
-DBUILD_USING_OTHER_LAPACK:PATH="C:\Program Files\lapack-3.5.0\bin\liblapack.dll;C:\Program Files\lapack-3.5.0\bin\libblas.dll"
make
# Test
make test
# Installation
make install

MinGW details

This paragraph explains the reason why one can not use any MinGW version.

MinGW is available with two thread models :

• Win32 thread model
• Posix thread model

One has to use the Posix thread model, since all thread functionalities (e.g. std:mutex) are not implemented.

To ease building on Windows, Simbody provides compiled libraries for Blas and Lapack :

• On Windows 32 Bits, these were compiled with a Dwarf exception mechanism,
• On Windows 64 Bits, these were compiled with a SJLJ exception mechanism.

If one chooses a MinGW compilation, we need to respect this exception mechanism. A program can not rely on both mechanisms. This means that if we want to use the compiled libraries, our MinGW installation should have the same exception mechanism. Otherwise, we need to provide our own Blas and Lapack libraries.

To see which exception mechanism is used, user can look at dlls located in the bin directory of MinGW. The name of mechanism is present in the file libgcc_XXXX.dll, where XXXX can be dw, seh or sjlj. For some MinGW versions, this information is also available by looking at the result of gcc --version.

CMake will check the version of your MinGW, and if the exception mechanism is different, then the configuration stops because of this difference. If one provides Blas and Lapack libraries with the CMake variable BUILD_USING_OTHER_LAPACK, compilation with MinGW is always possible.

Windows, Mac, and Linux Using Conda

Conda is a cross platform package manager that can be used to install Simbody on Windows, Mac, or Linux. To install Simbody using Conda you must first install Miniconda or Anaconda. Either of these will provide the conda command which can be invoked at the command line to install Simbody from the Conda Forge channel as follows:

$ conda install -c conda-forge simbody

This command will install Simbody (both the libraries and headers) into the Miniconda or Anaconda installation directory as per the standard layout for each of the operating systems described above. The Conda Forge Simbody recipe can be found in Conda Forge's feedstock repository.

Installing simbody(vcpkg)

You can download and install simbody using the vcpkg dependency manager:

git clone https://github.com/Microsoft/vcpkg.git
cd vcpkg
./bootstrap-vcpkg.sh
./vcpkg integrate install
./vcpkg install simbody

The simbody port in vcpkg is kept up to date by Microsoft team members and community contributors. If the version is out of date, please create an issue or pull request on the vcpkg repository.

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.

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Download Details:

Author: Simbody
Source Code: https://github.com/simbody/simbody 
License: Apache-2.0 license

#machinelearning #cpluplus #robotics #physics #engine 

How to Run C/C++ in Sublime Text?

C and C++ are the most powerful programming language in the world. Most of the super fast and complex libraries and algorithms are written in C or C++. Most powerful Kernel programs are also written in C. So, there is no way to skip it.

In programming competitions, most programmers prefer to write code in C or C++. Tourist is considered the worlds top programming contestant of all ages who write code in C++.

During programming competitions, programmers prefer to use a lightweight editor to focus on coding and algorithm designing. Vim, Sublime Text, and Notepad++ are the most common editors for us. Apart from the competition, many software developers and professionals love to use Sublime Text just because of its flexibility.

I have discussed the steps we need to complete in this blog post before running a C/C++ code in Sublime Text. We will take the inputs from an input file and print outputs to an output file without using freopen file related functions in C/C++.

#cpp #c #c-programming #sublimetext #c++ #c/c++

Dicey Issues in C/C++

If you are familiar with C/C++then you must have come across some unusual things and if you haven’t, then you are about to. The below codes are checked twice before adding, so feel free to share this article with your friends. The following displays some of the issues:

1. Using multiple variables in the print function
2. Comparing Signed integer with unsigned integer
3. Putting a semicolon at the end of the loop statement
4. C preprocessor doesn’t need a semicolon
5. Size of the string matters
6. Macros and equations aren’t good friends
7. Never compare Floating data type with double data type
8. Arrays have a boundary
9. Character constants are different from string literals
10. Difference between single(=) and double(==) equal signs.

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The below code generates no error since a print function can take any number of inputs but creates a mismatch with the variables. The print function is used to display characters, strings, integers, float, octal, and hexadecimal values onto the output screen. The format specifier is used to display the value of a variable.

1. %d indicates Integer Format Specifier
2. %f indicates Float Format Specifier
3. %c indicates Character Format Specifier
4. %s indicates String Format Specifier
5. %u indicates Unsigned Integer Format Specifier
6. %ld indicates Long Int Format Specifier

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A signed integer is a 32-bit datum that encodes an integer in the range [-2147483648 to 2147483647]. An unsigned integer is a 32-bit datum that encodes a non-negative integer in the range [0 to 4294967295]. The signed integer is represented in twos-complement notation. In the below code the signed integer will be converted to the maximum unsigned integer then compared with the unsigned integer.

#problems-with-c #dicey-issues-in-c #c-programming #c++ #c #cplusplus

Extensible dynamic type in C# | Expand Object In C# | C# Bangla Tutorial | Advanced C#

https://youtu.be/YP1yDwYwVLk

#oop in c# #object oriented programming #object oriented concept in c# #learn oop concept #advance c# #extensible dynamic type in c#

C# Performance tips and tricks

Given the vast amount of C# and the explosive growth in data we’re dealing with, some optimization work has been needed at various times. Most of the big gains come from really re-thinking a problem and approaching it from a whole new angle.

Today however, I wanted to share some C# performance tips that have helped in my recent work. Some of these are fairly micro so don’t just charge out and employ everything here.

#c #c# #c++ #programming-c