Installing MBDyn - zanoni-mbdyn/blendyn GitHub Wiki

Chances are, if you are here, that you already are an MBDyn user, and thus you don't need to install it. This section was written for the convenience of the inexperienced users. It is be also useful to highlight which is the recommended MBDyn configuration that allows to get the most out of Blendyn.

• MacOS (outdated, last tested on 10.15.7) installation guide
• Windows installation guide
• GNU/Linux [Ubuntu] installation guide (same as before: what you do in the WSL is what you would do in a Debian/Ubuntu terminal)
• GNU/Linux [Arch] installation guide: follow along...

Since June 2023, the AUR package mbdyn-git is available. The package will automatically build MBDyn following the process described below, and is optimized for the use of Blendyn by default. The latest version of the develop branch is downloaded.

You install it in the usual way you install AUR packages. For example:

$ git clone https://aur.archlinux.org/mbdyn-git.git
$ cd mbdyn-git/
$ makepkg -si

or with your distribution AUR manager (yay, pamac, etc...)

MBDyn is a software that is designed and developed mostly by people using GNU/Linux and it is distributed only in source code form. It is compiled from the source code using GNU's autotools. It can be built also on Windows using MinGW or, under Windows 10 and above, the Windows Subsystem for Linux. Look here for a complete guide to install both MBDyn and Blendyn under Windows 10 using the WSL. Note that the same guide contains also, in practical terms, MBDyn installation instructions for Debian/Ubuntu.

In this guide I'll assume that you are working in a GNU/Linux environment. I'll use my currently preferred distribution, Arch as a reference for the commands. Differences with other distributions, as it pertains to this guide, are only related to the package manager: for example, Arch relies on pacman, Debian/Ubuntu and OpenSUSE on Apt, Fedora on dnf, etc... So the name of the packages and the commands might change a bit for you if you do not use Arch, but the general procedure remains the same.

The basic packages needed to be able to compile MBDyn are GNU's autotools, GNU's autoconf, GNU's libtool, and a fortran compiler, for example gfortran.

In Arch, you can install all of them with

$ sudo pacman -S base-devel gcc-fortran

The MBDyn package is highly modular: it allows the user (you) to customize a lot the installation by requiring only a minimal set of external libraries in the baseline configuration, and optionally enabling more functionalities if the required additional libraries are found. Here, I will list the ones that are useful for Blendyn, and a few more not directly related to Blendyn that I recommend you to install before building MBDyn.

To to get the most out of Blendyn, it is recommended to at least enable the binary (NetCDF) output feature of MBDyn. This is accomplished by installing the NetCDF/C++ library.

The related packages in Arch are the netcdf and netcdf-cxx packages:

$ sudo pacman -S netcdf netcdf-cxx

If you use a different distribution, keep in mind that often library packages are available in two versions: one without headers, the other with the headers, usually having a name containing a suffix dev or devel. This is not the case in Arch: all the Arch packages contain header files (and are therefore directly available to be linked by other software during builds).

If you are interested in performing eigenanalyses in MBDyn and visualize the eigensolutions (i.e., the vibration modes) in Blendyn, you need to install one of the libraries that MBDyn relies on for this particular problem.

The recommended one is LAPACK. You can install it in Arch with

$ sudo pacman -S lapack

Optionally, you can also install ARPACK, which gives you an alternative to LAPACK:

$ sudo pacman -S arpack

Remember than in other distributions it might be needed to install the development version of the library.

MBDyn functionalities are often extended through run-time modules , i.e. libraries that are loaded during the execution, only if they are requested by the specific problem MBDyn is asked to solve.

To enable modules , the GNU Libtool library has to be made available.

In Arch, the related package is called libtool, and can be installed with

sudo pacman -S libtool

other frequently used names for the same package contain the acronym ltdl: for example, the Debian/Ubuntu equivalent package is libltdl-dev.

MBDyn default linear solver, naive, is very reliable and very efficient in solving the vast majority of the linear systems that MBDyn has to tackle during the integration of multibody systems. However, it is always nice to have alternatives available when things start to go South.

MBDyn has built-in support for some of the most widespread
(free) linear solver packages available. Among them, I recommend to install the SuiteSparse package, providing the UMFPACK and KLU linear solvers.

You do this in Arch with

$ sudo pacman -S suitespase

and, as usual, in other distribution things might chance: it is libsuitesparse-dev in Debian/Ubuntu, suitesparse-devel in Fedora, etc...

Now that we have installed everything we need, we are ready to download the MBDyn source code, configure the package, and compile it.

Head over to the Gitlab repository page at https://public.gitlab.polimi.it/DAER/mbdyn. Dowload the repository code with the download button (left of the blue Clone button). It is recommended to first switch to the develop branch, in order to obtain the most recent code. Download and extract the archive, and cd into the MBDyn directory:

$ tar -xzf mbdyn-develop.tar.gz
$ cd mbdyn-develop/

Alternatively, if you have Git installed, you can clone the repository:

$ git clone https://public.gitlab.polimi.it/DAER/mbdyn.git
$ cd mbdyn/

by default, you will be placed on the develop branch. If you want, you can check that this is the case using git status.

You first have to execute the bootstrap.sh script, to generate the configure scripts

& sh bootstrap.sh

Now you need to configure the package, using the just created configure script (you can copy and paste the whole command, or copy everything in one line, removing the backslashes \):

$ LDFLAGS="-rdynamic -lsuitesparseconfig" \
  CPPFLAGS="-I/usr/include/suitesparse/" \
  ./configure \
 --prefix=/usr/local \
 --enable-netcdf=yes \
 --with-umfpack=yes \
 --with-lapack=yes \
 --with-arpack=yes \
 --with-module="hfelem muscles" \
 --enable-runtime-loading

the choice of changing the prefix to /usr/local is arbitrary: one can choose to keep the default prefix /usr/local/mbdyn and add the /usr/local/mbdyn/bin directory to the systems' PATH environment variable (look here, for example, for more information). This is setting the folder in which the MBDyn binaries and libraries will be placed.

Also the choice of building the muscles and hfelem modules it is just an example: you can choose which ones are of interest for you, or just remove the --with-module="" switch entirely if you do not wish to build any of them.

The configure script will output the result of a number of checks, designed to enable to proceed to the building phase only if the required software libraries are found, and to enable several optional functionalities if additional libraries are found:

$ ./configure
Configuring MBDyn Devel ...
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
[...]
config.status: creating build/Makefile
config.status: creating include/mbconfig.h
config.status: executing depfiles commands
config.status: executing libtool commands

If something goes wrong, errors will be raised. If instead the script does not find a library that is not strictly required, it will generally just raise a warning. If the configuration step is completed with success, you can proceed to build the package:

$ make -j4

note that the -jN switch it is optional: it instructs make to perform the compilation in parallel mode, using N instances in background. You can adjust N as you wish, with a good choice generally be the one to use the number of cores of your CPU.

When the build is completed, you can install it (i.e. make the binaries available to every user from every location) with

$ sudo make install

Please notice that this command should be issued in superuser mode, if the prefix is in one of the system's directories (that is the default behavior). If you did not use the --prefix=/usr/local option, then the MBDyn binaries will be installed in /usr/local/mbdyn/bin, which is not in the default PATH of the distribution. Therefore, the mbdyn command cannot yet be found by the terminal in any location of the system. You can amend this by adding the /usr/local/mbdyn/bin directory to the default PATH of your terminal. For example, if you are using bash, you can add this line to the .bashrc file that is found in your home directory:

export PATH=${PATH}:/usr/local/mbdyn/bin

The change will take effect at the next session (a log-in, log-out should suffice), or you can force it to have immediate effect using this command

$ source ~/.bashrc

(this will have an effect on a single session of a single terminal window or tab).
Now you can check if everything went smoothly:

$ mbdyn -v

you should get something like this:

MBDyn - MultiBody Dynamics 1.7.3
configured on May 30 2024 at 10:42:17
MBDyn terminated normally

What follows is an eXperimental guide to install MBDyn in a macOS environment. It is based on my experience in building and installing MBDyn on a rather outdated machine, running OsX 10.15.7 and I don't currently have access to most recent version of the OS¹. Be careful that it is still possible that with different versions of macOS YMMV, greatly.

These are the steps I've followed to compile MBDyn with LAPACK, (NetCDF), GiNaC, Suitesparse and runtime-loadable modules support.

This is the procedure that works for me:

1. install Homebrew

IMPORTANT NOTE: it has been noted that the co-inhabitance of the XCode IDE and the CommandLine Tools is problematic to build software from source. If you already installed XCode, please skip the installation of the CommandLine Tools in the homebrew installation.

2. install the following casks:

$ brew install autoconf automake ginac libtool m4 netcdf openblas suite-sparse lapack

3. clone the mbdyn repository and switch to the develop branch:

$ git clone https://public.gitlab.polimi.it/DAER/mbdyn.git
$ cd mbdyn/
$ git checkout develop

4. IMPORTANT we will create a symbolic link to use GNU's Libtool (glibtool) instead of the default XCode one during the MBDyn build (remember to issue this command as superuser, for example preceding it with sudo):

# ln -s /usr/local/bin/glibtool /usr/local/bin/libtool
# ln -s /usr/local/bin/glibtoolize /usr/local/bin/libtoolize

5. generate the configure scripts (from the MBDyn tree root directory, i.e. the mbdyn/ directory in which the repository was cloned at step 3. :

$ sh bootstrap.sh

6. move outside of the mbdyn/ directory and make a new directory for the build, for example called (you guessed it) build

$ cd .. 
$ mkdir build/
$ cd build/

7. from the build/ directory, configure MBDyn, setting all required options for the C/C++ preprocessor (CPPFLAGS), the linker (LDFLAGS), pkgconfig (PKG_CONFIG_PATH) and adding the modules (if any) you want to compile

$ CXXFLAGS="--std=c++14" CPPFLAGS="-I/usr/local/include" LDFLAGS="-L/usr/local/lib -lsuitesparseconfig" PKG_CONFIG_PATH=/usr/local/lib/pkgconfig ../mbdyn/configure --with-module="muscles hid hfelem" --enable-Werror=no

8. if everything goes smoothly, build the package

$ make -j4

9. if everything goes smoothly again, install MBDyn (again with sudo or your preferred way to gain elevated privileges)

# make install

10. add the MBDyn binaries folder to the system's PATH:

$ echo "export PATH=\${PATH}:/usr/local/mbdyn/bin" >> $HOME/.bash_profile

11. test that you can call MBDyn now, after sourcing the modified .bash_profile configuration:

$ . $HOME/.bash_profile
$ mbdyn -v

MBDyn -  Multibody Dynamics develop
configured on Mar  1 2022  at 16:03:11
MBDyn terminated normally

12. IMPORTANT remove the symbolic link that we created earlier (superuser privileges needed also here):

# rm /usr/local/bin/libtool
# rm /usr/local/bin/libtoolize

1: EDIT: thanks to the kind support of Neda Taymourtash, I've been now able to test that the procedure works also on a macOS 12.0.1 machine running clang 13.0.0 (XCode 13.2.1).