Nguyen Lab Wiki

Table of Contents

Installing the ACCESS Libraries - step 1

You will need to install the ACCESS libraries if you plan to use the exodus binary file format for the finite element geometry and output files. Do this before installing Tahoe.

Compiling ACCESS for Mac

Install Dependencies. These instructions are for the bash shell. If you're running a different shell, simply type bash at the prompt to work in the bash shell. Homebrew is the best way to install SEACAS dependencies on the Mac. Install Homebrew, tools and compilers:

$ ruby -e “$(curl -fsSL https://raw.github.com/mxcl/homebrew/go/install)”

Add the homebrew/bin directory to your path in your .chsrc or .bashrc files. Then source the files or log out and log back in for it to take effect. Otherwise your shell won't be able find the executables like install. You will also have to do this for the /sw directory if you're using fink instead of homebrew,.

  • $ brew install git
  • $ brew install cmake
  • $ brew install gcc
  • $ brew install wget

Download SEACAS source code from git repository:

Download and build HDF5

Go to http://www.hdfgroup.org/HDF5/release/obtainsrc.html and download latest source code. The latest version as of this date is 5-1.10.5. There may be later versions by the time you get to install. If so, change all of the 5-1.10.5 to the latest version number.

Direct link: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.bz2

Extract to seacas/TPL/hdf5. (If you get error in ./configurem, check that you have two hyphens)

Download and Build NetCDF

Go to http://www.unidata.ucar.edu/downloads/netcdf/index.jsp and download latest source code. The latest version as of this date is 4.5.0. There may be later versions by the time you get to install. If so, change all of the 4.5.0 to the latest version number.

Build the library

  • $ export CFLAGS=“$CFLAGS -I${ACCESS}/include”; export LDFLAGS=“$LDFLAGS -L${ACCESS}/lib”; ./configure –enable-netcdf-4 –enable-shared –disable-fsync –prefix=${ACCESS} –disable-dap –disable-cdmremote
  • $ make && make install

Download and Build MatIO

Build SEACAS with Exodus (Tahoe Dependency)

  • $ cd $ACCESS
  • $ mkdir build
  • $ cd build

Change the flag for the directory for hdf5 include and lib

  • $ vi ../cmake-exodus

Modify the following line: -D HDF5_ROOT:PATH=${H5DIR}

  • $ ../cmake-exodus
  • $ make
  • $ make install

Installing TAHOE - MAC

1) A few preliminaries

Set your $ACCESS shell variable to the seacas directory. You can do this in your ~/.cshrc or ~/.bashrc file then source the files or log out and log back in. Also, set the CVS_RSH to ssh and the DYLD_LIBRARY_PATH to $ACCESS/lib the same way. If you don't have cvs, then install using fink or homebrew.

If you're using the tcsh shell, include the following in your ~/.cshrc file

  • setenv CVS_RSH ssh
  • setenv ACCESS [path to seacas]/seacas
  • setenv DYLD_LIBRARY_PATH $ACCESS/lib

If you're using the bash shell, write this in your ~/.bashrc file

  • export CVS_RSH=ssh
  • export ACCESS=[path to seacas]/seacas
  • export DYLD_LIBRARY_PATH=$ACCESS/lib

To set these variables, log back in and log back out. If you don't want to do that, then type source ~/.cshrc (or source ~`/.bashrc) in your current window. These variables will be defined for that window only.

  • $ cd $ACCESS
  • $ ln -s include/ inc
  • $ cd lib
  • $ ln -s libexodus.dylib libexoIIv2c.dylib
  • $ ln -s libexodus.a libexoIIv2c.a

1) You can download TAHOE from sourceforge as an anonymous user, who will only have read privileges, or as a developer, who will have read and write privileges and can modify the code in the repository. If you think you will be a developer, register for a username and password on sourceforge.net and send me your username so I can give you write privileges.

2) If you plan on installing the development project, you will need a developer's account. Email me (vicky.nguyen@jhu.edu) your source forge username, and I will create for you an account on codesion and add you to the Tahoe project. Wait for an email with your codesion password before going ton to step 3.

3) Download TAHOE from sourceforge.net (http://sourceforge.net/projects/tahoe/)

Direct link: http://downloads.sourceforge.net/project/tahoe/tahoe-install/tahoe-install%201.2/tahoe-install.tar.gz

4) $ tar xpfv tahoe-install.tar.gz

You will obtain two files after unzipping the folder downloaded in step 3: ReadMe and tahoe-manager

5) tahoe-manager is a perl script that manages the build options. The text ReadMe file contains instructions and runtime options for tahoe-manager. If you don't have perl, then install it using homebrew ($ brew install perl) or Fink.

6) Run tahoe-manager on command prompt:

  • $ cd tahoe-install
  • $ ./tahoe-manager

running tahoe-manager script at Mon Apr 5

17:06:46 2010

*

creating default config file ./.tahoe_config

*

found CVS_RSH env var, using cvs connection

Sourceforge server username [anonymous]:

7) Enter your sourceforge username (developer) or hit return to download as anonymous.

8) Enter your codesion username (tahoe.username). Hit return if you don't have a codehsion account. 9) Setup the configuration options in the building process.

  • Macros are shell script for plat-form specific compiling and linking option.
    • select: DARWIN-GCC4.X for fast execution on a Mac or DARWIN-GCC4.debug for execution with additional error checks for debugging on a mac.
    • select yes to: do you want this to be the default architecture for all modules?
  • Tahoe is installed with the following default modules:
    • macros - shell scripts for compiling and linking
    • expat - code to create and read XML inputs
    • toolbox - data structures, advance math functions, data I/O, MPI communication
    • tahoe - main.cpp, shape functions, boundary controllers, element models, and material models.
  • You will need to install additional optional modules
    • select: benchmark_XML, contrib (utility scripts and programs), f2c (fortran to C translator), and
    • spooles (Linear solver)
    • select access if you want to use the exodus binary file formate
    • select development and development_benchmark_xml if you plan to install the development module.
    • select metis and spoolesMPI if you plan to compile Tahoe for parallel execution.
    • the remaining modules are libraries for solving linear systems.

10) At this point, tahoe-manager will checkout each module from sourceforge using svn. You will need to type your sourceforge password. The script ends when all the modules are successfully downloaded.

11) Build Tahoe by typing tahoe-manager build.

12) After successful build, an executable file called tahoe will appear in tahoe-install/bin. If you received errors during the build, try looking at the build.log or init.log files for the affected modules to figure out the problem. You can also build each module separately using Make (see Building Tahoe Using Make section below). 13) Add the tahoe-install/bin directory to your path to either your .bashrc using “export path” or .cshrc using “set path” command.

Installing Tahoe for Linux Ubuntu

1) You can install some libraries (svn, openmpi, etc.) that you might need in order to install Tahoe on your Linux system by downloading “Install-tahoe-pre.sh” from:

install-tahoe-pre.sh

Make the file executable and execute the shell script: 

chmod +x Install-tahoe-pre.sh
    ./Install-tahoe-pre.sh

Note: In the process of the installation of some the libraries, you might need to press enter.

Note: This script was tested on ubuntu-12.04.3 32 bit

Note: You can change to tcsh by this command: chsh -s /bin/tcsh

2) Download and compile SEACAS. Follow the same procedure as listed in the MAC session

3) Download and compile tahoe. All the procedure is same as in MAC except two things: a. In your shell script, set the environment variable LD_LIBRARY_PATH (rather than DYLD_LIBRARY_PATH). b. When select macros, choose GNU-GCC-9.3 or GNU-GCC-mpi-9.3 for parallel execution.

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