• Software Requirements and Installation

SimVascular Software Requirements and Installation

After a review of the platforms we currently support or plan to support, two scenarios for SimVascular use are presented. If you are not modifying SimVascular source code, please follow the first section for Users.

Platforms

• Windows -- Used within Stanford's Taylor lab. Currently the best supported platform.

• Linux -- This platform is scheduled for support within 2007.

• MacOS X -- The Mac platform is scheduled for support shortly after Linux. You can use SimVascular on a Mac by using the Parallels Virtual Machine or VMWare Fusion with Windows XP or Vista. The newer Parallels 3.0 virtual machine supports OpenGL hardware acceleration, which is an integral part of SimVascular's visualization ability.

Installation for Users

Basic Steps to Install SimVascular for Users (developers see below)

1. If running Windows, download Cygwin, a Linux-like environment for Windows. Install the full cygwin environment. A snapshot of the complete Cygwin install is available at Simtk.org.

2. Go to the SimVascular Application Download web page at Simtk.org.

3. Download the SimVascular base install tarball. (A tarball is an archive that can be opened using tar zxvf my-archive.tar.gz.) Separate tarballs are available for academic and commercial users, so download one of the following:

     simvascular-x86-academic-install.<Date>.tar.gz
       or
     simvascular-x86-commercial-install.<Date>.tar.gz
   

   This tarball includes precompiled x86 binaries for libraries like VTK, MPICH2, Tcl/TK, and support libraries for Fortran and Visual Studio C++.

4. Open a cygwin shell and type something like the following:

     % cd directory-where-you-put-tarballs
     % tar zxvf simvascular-x86-academic-install-Aug-30-2007.tar.gz
     % cd remote_install_simvascular
    

   Note that unpacking the tarball will create a remote_install_simvascular directory.

5. Download the SimVascular licensed install tarball

     simvascular-licensed-x86.<Date>.tar.gz
   

   into the remote_install_simvascular directory. This tarball contains libraries that won't be usable until you obtain licensing keys from Simmetrix and AcuSim. See the Licensing Process.

6. Download the SimVascular Parasolid Driver tarball from a UGS FTP site. Your account and password for the UGS ftp site will be provided after licensing Parasolid from UGS. This tarball, like the tarball in #5, should be placed in the remote_install_simvascular.

7. In the cygwin shell where you are still in the remote_install_simvascular directory, execute the install script:

     % ./simvascular-x86-install.sh
    

Installation for Developers

Required Open Source Packages

• Tcl/Tk - This is included in the download

• VTK

• Subversion source control client if you want to checkout code from the SimVascular source code repository. We recommend TortoiseSVN for Windows development.

• MPICH2 is a freely available, portable implementation of MPI, a standard for message-passing libraries useful for parallel computing applications. It implements both MPI-1 and MPI-2.

Compilers required for development

• Microsoft Visual Studio 2005 C++ (if running Windows)
• Intel Fortran (Version 9.1) for 3-D flow solver compilation

Basic Steps to Install SimVascular for Developers

1. If running Windows, download Cygwin, a Linux-like environment for Windows. Install the full cygwin environment. A snapshot of the complete Cygwin install is available at the same location as the SimVascular binaries below.

2. Install a subversion client if you don't have one already installed. We recommend TortoiseSVN for Windows developers.
3. Checkout or download all the necessary source code you'll be modifying. This includes:

   1. The SimVascular code from public trunk. The repository URL is https://simtk.org/svn/simvascular/trunk.

   2. The external open source code necessary to run SimVascular. Binaries and source code for VTK, Tcl/TK, MPICH2, and some other useful libraries are available at:

      • A subversion repository, cardio_external, which includes both binaries and source code. These are versions that have worked with internal builds.

      • The various open source project websites. This would give you the most recent versions of these open source packages if you prefer not to work with older versions in the subversion repository.
4. Contact the three commercial vendors - UGS, Simmetrix, and AcuSim - and obtain licensing. The solid modeling and meshing components will be available from UGS via a webkey. Place these files in the SimVascular directory.
5. The source code for the meshing object can be obtained from Taylor lab after you have completed Simmetrix licensing.

6. Follow the compilation instructions in the appropriate README file at the SimVascular subversion repository.

Suggested Computational Resources

The amount of compute power required by SimVascular varies greatly with the type of modeling and simulation you are performing. Modeling is usually performed on one (typically Windows) computer. Simulations have been run on a gamut of compute power, from a single computer to thousands of processors in a BlueGene compute farm.

We will eventually populate this section with benchmarks. A benchmark will include (1) necessary data files, (2) a description of compute environment including number of nodes and their OS, networking, and storage configurations, and (3) timing data. By sharing this information, SimVascular users will be able to assess cost-effective platforms and possibly suggest code improvements.