// -*- text -*- Congratulations! You are reading the README file for a software package you downloaded! You are now officially an *advanced* software installer. This is the README file for OOF3D, describing how to build and install it with the Python distutils utility. This README file is for OOF3D version 3.2.0 or later. Disclaimer: ---------- 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@list.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: ------------ 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 oof3d-.tar.gz > cd oof3d- > python setup.py build --3D > python setup.py install --3D 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@list.nist.gov. It's diagnostically useful to include all the output from setup.py. OOF3D has been built and tested on Linux and Macintosh OS X. OOF3D does *not* work on Microsoft Windows, but should work within a Linux virtual machine on Windows. Details: ------- 0. What You Should Already Have: A computer running a variant of the Unix operating system, including Linux and macOS (Macintosh OS X). A C++ compiler. The following external programs and libraries and the header files ("includes") associated with these programs and libraries. These are usually available as part of a "development" version of the library software. Python (2.6 or 2.7) http://www.python.org gtk+-2.0 (2.6 or later) http://www.gtk.org/download/ pygtk2 (2.6 or later) http://www.pygtk.org vtk (8.1.1 or later) http://www.vtk.org Please note that the words "or later" do not include later major versions. OOF3D will not work with Python 3.x or gtk+ 3.x. VTK 9.x is ok. Linux users should already have an X11 server. Macintosh users can build OOF3D either to use X11 or native Mac graphics. 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). Detailed instructions for installing the OOF3D prerequisites on a number of different operating systems can be found at http://www.ctcms.nist.gov/oof/oof3d/prerequisites.html. 1. What You Got From Us: The file "oof3d-.tar.gz". Procedure: --------- (Macintosh OS X users can install OOF2 from either a Terminal or xterm window, or the equivalent.) 0. Unpack Unpack the .tar.gz file. The usual way is to run "tar -xf" on the file you want to unpack. This will create a subdirectory named "oof2-" in the directory where you run tar. 1. Build the OOF2 libraries and Python extension modules Switch to the newly-created directory, and run % python setup.py build --3D Macintosh users who prefer not to use X11 should add "--cocoa" to the command line ("cocoa" being the name of the Apple GUI API). Because we've been having trouble getting VTK to work properly with X11 on recent Mac operating systems, using cocoa is recommended: % python setup.py build --3D --cocoa The build command will create a "build" subdirectory in the top OOF2 directory. Within "build" it will create subdirectories with system-dependent names. There are three options to the build command that are special to OOF3D and aren't discussed with the generic build options below. (a) --3D must be provided. (b) If your vtk installation isn't in a standard location, you will need to add --vtkdir= to the command line, replacing with the base of the directory tree containing vtk. For example, if the vtk files are located in /usr/unusual/include/vtk-8.1.1 and /usr/unusual/lib, then you'd build OOF3D this way: % python setup.py build --3D --vtkdir=/usr/unusual (c) As mentioned above, --cocoa must be provided to build a macOS version that uses native Mac graphics instead of X11. 1.1 Getting more control over the build 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, liboof3dcommon.so, etc, that contain most of the low-level OOF3D machinery. "build_ext" builds the OOF3D 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 --3D or in combination % python setup.py build_shlib build_ext --3D 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 (except that this *doesn't* include the all-important --3D option!). 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" For "build_ext" or "build": --with-swig Specify the name of the swig executable. Swig is a tool that generates the code that allows communication between python and C++. OOF3D ships with a modified copy of swig, because we rely on an old version (swig 1.1 build 883, to be precise). If you have another version of swig that you'd like to use, you can name it here, like this: pyton setup.py build --with-swig=myswig Be advised that it probably won't work with the OOF3D source code. --swig, --swig-cpp, --swig-opts Do NOT use these options. They will be ignored. They're leftover from the raw distutils swigging mechanism, which we don't use. 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. 2. Install To install OOF3D, run % python setup.py install --3D This will install OOF3D 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 OOF3D 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: a) Get a system administrator to run the installation step. b) Tell distutils to install oof3D in a different place, like this: % python setup.py install --3D --prefix= where is a directory that you can write to, such as your home directory. The installation procedure will create an executable script called "oof3d" in /bin, a bunch of shared libraries called "liboof3d*.so" or "liboof3d*.dylib" in /lib, a directory called "oof3d" in /lib/python2.x/site-packages (where 2.x is your python version number), and some example files in /share/oof3d/examples. The default value of , if you haven't used --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 something in /sw or /opt/local if you're using fink or macports. (It's possible to use --home= instead of --prefix when installing oof3d. The only difference is that --home will put the python libraries in /lib/python instead of /lib/python2.x/site-packages.) 2.1. Set environment variables If /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 /bin/oof3d). (Typing "echo $PATH" will print the current value of your path. The method for setting environment variables depends on which Unix shell you're using.) If /lib is not in the list of directories that the dynamic linker searches for libraries, you'll have to add it by setting the LD_LIBRARY_PATH environment variable. Setting LD_LIBRARY_PATH is not necessary on Macintosh OS X. If /lib/python2.x/site-packages is not in your Python path, you'll have to add it to the PYTHONPATH environment variable. (Running the command % python -c "import sys; print sys.path" will print your Python path.) If you're using the common "bash" shell, you can set environment variables by putting the following lines in a file called .profile in your home directory: export PATH=/bin:$PATH export PYTHONPATH=/lib/python2./site-packages:$PYTHONPATH export LD_LIBRARY_PATH=/lib:$LD_LIBRARY_PATH replacing and python2. with the appropriate values. To find out if you're using the bash shell, type "echo $SHELL" in a terminal window. If it replies "/bin/bash", you're using bash. Setting environment variables in .profile doesn't actually change their values in your current terminal session. To start using the new values, you will need to open a new terminal window. Running OOF3D: ------------ At this point, you should have an executable file named "oof3d" in a bin directory in your execution path. You can now simply type "oof3d" at your shell prompt, and OOF3D will start up. OOF3D also has many options, and you can get a summary of them by typing "oof3d --help". Most of the OOF2 manual also applies to OOF3D. The manual can be found at http://www.ctcms.nist.gov/~langer/oof2man/ The OOF3D web page includes a summary of differences between OOF2 and OOF3D. Be sure to go through the tutorials provided in the OOF3D help menu. Bugs: ---------- If you encounter bugs in the program, please use the OOF error reporting tool, which can be accessed via the "Report" button on the OOF3D error dialog, or the "Report Error" item in the "Help" menu. This will create a file which you can e-mail to oof_bugs@list.nist.gov. If the file is too large for e-mail, send a message to oof_bugs@list.nist.gov and we can arrange another way to transfer the file. If for some reason you can't use the error reporting tool, please send e-mail to oof_bugs@list.nist.gov including what version of OOF3D you're using, what operating system you're using, and *exactly* what you did to encounter the error. It is helpful to include an OOF3D 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 ourselves. Contact Us: --------- Other communications, including requests for help and suggestions for new features, can be sent to oof_manager@list.nist.gov.