This is the README file for OOF2, describing how to build and install it with the Python distutils utility.
This README file is for OOF2 version 2.1.12 or later.
OOF2 is designed to help materials scientists calculate macroscopic properties from images of real or simulated microstructures. It reads an image, assigns material properties to features in the image, and conducts virtual experiments to determine the macroscopic properties of the microstructure.
The programs are written in C++ and Python and benefit from an object-oriented design. The underlying numerical solutions rely on finite element technology. Hence the name OOF, for object-oriented finite element analysis.
This software provided is provided by NIST as a public service. You may use, copy and distribute copies of the software in any medium, provided that you keep intact this entire notice. You may improve, modify and create derivative works of the software or any portion of the software, and you may copy and distribute such modifications or works. Modified works should carry a notice stating that you changed the software and should note the date and nature of any such change. Please explicitly acknowledge the National Institute of Standards and Technology as the source of the software. To facilitate maintenance we ask that before distributing modified versions of this software, you first contact the authors at oof_manager@nist.gov.
The software is expressly provided "AS IS". NIST MAKES NO WARRANTY OF ANY KIND, EXPRESS, IMPLIED, IN FACT OR ARISING BY OPERATION OF LAW, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT AND DATA ACCURACY. NIST NEITHER REPRESENTS NOR WARRANTS THAT THE OPERATION OF THE SOFTWARE WILL BE UNINTERRUPTED OR ERROR-FREE, OR THAT ANY DEFECTS WILL BE CORRECTED. NIST DOES NOT WARRANT OR MAKE ANY REPRESENTATIONS REGARDING THE USE OF THE SOFTWARE OR THE RESULTS THEREOF, INCLUDING BUT NOT LIMITED TO THE CORRECTNESS, ACCURACY, RELIABILITY, OR USEFULNESS OF THE SOFTWARE.
You are solely responsible for determining the appropriateness of using and distributing the software and you assume all risks associated with its use, including but not limited to the risks and costs of program errors, compliance with applicable laws, damage to or loss of data, programs or equipment, and the unavailability or interruption of operation. This software is not intended to be used in any situation where a failure could cause risk of injury or damage to property. The software was developed by NIST employees. NIST employee contributions are not subject to copyright protection within the United States.
Installation is similar to other Python libraries. If your system is well-set-up, and has the required libraries, there should be no difficulties.
The executive summary of steps is:
tar -xzf oof-<version>.tar.gz
cd oof-<version>
python setup.py build
python setup.py install
but please read the rest of this file before proceeding.
If something goes wrong, your system adminstrator may be able to help you, or you can contact the oof developers at oof_manager@nist.gov. It's diagnostically useful to include all the output from setup.py.
OOF2 has been built and tested on Linux (Debian, CentOS, Ubuntu, and, OpenSUSE), and Macintosh OS X.
A computer running a variant of the Unix operating system, including Linux and Macintosh OS X, and an X11 server. OOF2 currently does not run on Microsoft Windows.
The following external programs and libraries must be present before you can run OOF2. To compile OOF2 from sources, you will also require the header files ("includes") associated with these programs and libraries. These are usually available as part of a "development" version of the library software.
Please note that the words "or later" do not include later major versions. OOF2 will not work with Python 3.x or gtk+ 3.x.
Macintosh OS X users will need to install an X11 server.
You should also have the ability to run lapack and the "blas" basic linear algebra subroutines. On Macintosh OS X, they are built in to the Accelerate framework in the OS, and no special libraries are required. On Linux and commercial Unix systems, they may have to be installed, and you may require headers (sometimes provided as part of a "-dev" package).
OOF2 will use the tcmalloc library for efficient memory allocation if it is available, but it will also work without it (although it will be slower). It can be obtained from https://github.com/gperftools/gperftools and many package managers.
Detailed instructions for installing the OOF2 prerequisites on a number of different operating systems can be found at http://www.ctcms.nist.gov/oof/oof2/prerequisites.html.
(Macintosh OS X users can install OOF2 from either a Terminal or xterm window, or the equivalent.)
Unpack the .tar.gz file. The usual way is to run tar -xzf on the
file you want to unpack. This will create a subdirectory named
"oof2-" in the directory where you run tar.
Switch to the newly-created directory, and run
% python setup.py build
The build_ext command will create a "build" subdirectory in the top OOF2 directory. Within "build" it will create a subdirectory with a system-dependent name.
You can ignore this section unless something went wrong when building OOF2 in step 1. setup.py tries to be intelligent about choosing options, but it's not perfect.
The distutils "build" command actually runs a bunch of separate subcommands, each of which has its own options. The relevant subcommands are "build_shlib", "build_ext", "build_scripts", and "build_py". "build_shlib" builds the shared libraries, liboof2common.so, etc, that contain most of the low-level OOF2 machinery. "build_ext" builds the OOF2 Python extension modules that provide the interface betweeen C++ and Python. "build_py" copies the Python files from the source directory to the build directory, and "build_scripts" copies the start-up script into the build directory and makes it executable. OOF2 installers will probably only have to worry about "build_shlib" and "build_ext".
The four commands must be run in order: build_shlib must precede build_ext, and build_ext must precede build_py.
Each command can be run separately, for example
% python setup.py build_ext
or in combination
% python setup.py build_shlib build_ext
and options can be provided to each one
% python setup.py build_shlib --debug build_ext --include_dirs=/sw/include
You can see the full set of options by running
% python setup.py --help <command name>
Here are the options most likely to be useful:
For "build_shlib" or "build":
-
--library-dirs
Specify a non-standard location for libraries. Multiple directories should be separated by colons, like this: --library-dirs=/strange/spot:/out/of/theway
-
--libraries
Specify libraries to load. Due to a bug in distutils, it's only possible to specify a single library. For example --libraries=abc will load libabc.so. If you need to load more than one library in this way, please contact us.
-
--blas-libraries
Specify libraries to use for blas and lapack. Multiple library names should be separated by spaces, like this: --blas-libraries="myblas mylapack"
-
--blas-link-args
Specify additional link arguments required by blas and lapack, for example: --blas-link-args="-faltivec -framework vecLib"
The following arguments can appear anywhere after "setup.py" in the command line, and apply to both the build and install steps. Tf you run the build and install steps separately, you must provide these arguments in both steps if you provide them in one.
-
--disable-gui
Don't include any components of the graphical user interface. When this option is used, it's not necessary to have the gtk, pygtk, or libgnomecanvas libraries installed.
-
--enable-openmp
Turn on OpenMP code in OOF2 for parallel execution. This will only work if your compiler supports OpenMP, which the Macintosh clang compiler does not. (In OOF2 2.1.12 only the matrix construction and pixel autogroup operations are parallelized.)
Prior to version 2.1.12, setup.py accepted the arguments --skip-swig and --with-swig to control swig, which is used to generate some of the OOF2 code. The OOF2 distribution now includes its own copy of swig, and those arguments are unnecessary.
To install OOF2, run
% python setup.py install
This will install OOF2 in the standard location for Python extensions on your system. This is good, because then you won't have to do anything special to get OOF2 to run. It's also bad, because unless you are the system administrator, you probably don't have permission to install anything in that directory. You have two options:
-
Get a system administrator to run the installation step.
-
Tell distutils to install oof2 in a different place, like this:
% python setup.py install --prefix=<prefix>where <prefix> is a directory that you can write to. The default value of <prefix> is usually /usr/local. On OS X it may be something like /Library/Frameworks/Python.framework/Versions/2.7 if you're using the system Python, or /sw or /opt/local if you're using fink or macports.
The installation procedure will create an executable script called "oof2" in <prefix>/bin, a bunch of shared libraries called "liboof2*.so" or "liboof2*.dylib" in <prefix>/lib, a directory called "oof2" in <prefix>/lib/python2.x/site-packages (where 2.x is your python version number), and some example files in <prefix>/share/oof2/ examples.
(It's possible to use --home=<home> instead of --prefix when installing oof2. The only difference is that --home will put the python libraries in <home>/lib/python instead of <prefix>/lib/python2.x/site-packages.)
If <prefix>/bin is not in your Unix command path, you'll need to
add it to the PATH environment variable, or create a symbolic link
from a directory that is in your path (or start OOF2 the hard way
by by typing <prefix>/bin/oof2). (Typing echo $path will print
the current value of your path. The method for setting
environment variables depends on which Unix shell you're using.)
If <prefix>/lib is not in the list of directories that the dynamic linker searches for libraries, you'll have to add it by setting the LD_LIBRARY_PATH environment variable. This should not be necessary on Macintosh OS X.
If <prefix>/lib/python2.x/site-packages is not in your Python
path, you'll have to add it to the PYTHONPATH environment
variable. Running the following command will print your Python
path. python -c "import sys; print sys.path" will print your
Python path.
At this point, you should have an executable file named "oof2" in a
bin directory in your execution path. You can now simply type oof2
at your shell prompt, and OOF2 will start up.
OOF also has many options, and you can get a summary of them by typing
oof2 --help.
By default, OOF runs in graphics mode, opening a couple of windows to
get you started. If you don't want this, you can use the --text
option to run it in command-line mode.
Be sure to read the OOF manual and to go through the tutorials provided in the OOF2 help menu.
If you encounter bugs in the program, please send e-mail to oof_bugs@nist.gov. Tell us what version of OOF2 you're using, what operating system you're using, and exactly what you did to encounter the error. It is helpful to include an OOF2 script (which you can save with the "File/Save/Python Log" menu item) and a copy of any input files (images, oof data files, etc) required to run the script. It is extremely difficult for us to fix a bug if we can't reproduce it here.
Other communications, including requests for help and suggestions for new features, can be sent to oof_manager@nist.gov.