= [http://geosys.usc.edu/projects/seatree/wiki/ SEATREE] distribution = [[PageOutline]] == License and availability == SEATREE is distributed under the [http://geosys.usc.edu/projects/seatree/browser/trunk/COPYING GNU public license] without any warranties whatsoever. Computational modules as included with SEATREE might hold different copyrights, please refer to the module documentation for references to original scientific work. If you use SEATREE, please cite [http://geodynamics.usc.edu/~becker/preprints/mbbssw08.pdf this Eos report]. SEATREE is now released as version 1.0. == Downloads == Most users will want to follow the fully automated install procedure; for system software requirements, see below. For users familiar with the untar-make-make install cycle, we suggest to download the tar ball and follow the SEATREE installation procedure. Given that SEATREE is in active development, users familiar with [http://svnbook.red-bean.com/en/1.4/svn-book.html SVN] might prefer to subscribe to the development version which we use. [https://geosys.usc.edu/projects/seatree/browser/trunk Our repository] holds all codes, including the 3-D tomography and earthquake location modules, which are not included in the 1.0 release yet. === Fully automated installation === Download the [http://geosys.usc.edu/projects/seatree/browser/trunk/install_seatree?format=raw install_seatree script] and execute from a directory where you wish to place the SEATREE source code, such as $HOME/progs/ or /usr/local/src. {{{ sh -x install_seatree }}} This will attempt to download the most recent tar ball from the web, unpack it, and run the SEATREE installation process for you (see below). === Tar-ball with source === The most recent release of SEATREE in a single tar file which includes the GUI and the most stable modules is available from [http://geodynamics.usc.edu/~becker/software/seatree.recent.tgz http://geodynamics.usc.edu/~becker/software/seatree.recent.tgz]. The last release is version 1.0 {{{ -rw-rw-r-- 1 becker becker 8844396 2009-02-03 13:50 seatree-1.0.0-020309.tgz }}} The release includes a [wiki:screenshots fully functional GUI] and drivers for [wiki:hc_docu hc], [wiki:larry_docu larry], [wiki:syn2d_docu syn2D]. You will need this file if you do not choose to subscribe to our SVN version, and either obtain it manually or by running the fully automated installer. === Developer source code access === You can inspect the current source code through our [http://geosys.usc.edu/projects/seatree/browser source browser], or checkout the [http://svnbook.red-bean.com/en/1.4/svn-book.html SVN] repository by {{{ svn co http://geosys.usc.edu/svn/seatree/trunk/ seatree }}} To install, then follow the SEATREE installation procedure below. == Installation == === Required Software Packages === All individual computational modules should compile and work fine when run from the command line. For the compilation, C (for [wiki:hc_docu hc] and [wiki:nonlinloc nonlinloc]) and Fortran (for [wiki:conman ConMan], [wiki:larry_docu larry], larry3d, and [wiki:syn2d_docu syn2d]) compilers (such as GNU gcc and gfortran, which we use for development) need to be available, of course. Compilers will typically be available on a regular Linux install, and can be added easily to Mac OS-X (see, e.g., [http://www.eecs.wsu.edu/~schneidj/mac-os-x-10.3.html#compiler this page]). However, the GUI and scripting functionality (i.e. the main contribution of SEATREE) will require further software. Often all of this can be installed very easily on a OS-X or Linux system using [http://www.finkproject.org/ fink] (for Mac OS-X), [http://fedoraproject.org/wiki/Tools/yum yum] (e.g. Fedora Linux), or [http://wiki.linuxhelp.net/index.php/Apt-get_Guide apt-get] (e.g. Ubuntu Linux). We are also working on a packaged, virtual machine type of install DVD. You will have to have these individual packages installed: * [http://www.python.org/ Python]: Python alone will give you more sophisticated scripting capabilities, - for the graphical user interface, you'll also need to add [http://www.pygtk.org/ pygtk] - [http://matplotlib.sourceforge.net/ matplotlib] is needed for additional plotting functionality The simplest approach may be to obtain the [https://www.enthought.com/products/getepd.php Enthought Python Distribution]. This software package is free for academic users and contains all of the individual packages below. It is available for Mac-OSX, Windows, and Linux. * [http://gmt.soest.hawaii.edu/ Generic Mapping Tools (GMT) 3.4.5 or 4.x.x] including Coastline Data Used for generating postscript plots to visualize output. * [http://www.unidata.ucar.edu/software/netcdf/ NetCDF, including Development Kit] Used by GMT. * Must have the following files/libraries: * libnetcdf.a * netcdf.h * netcdf.inc * libnetcdf.so * [http://www.imagemagick.org/ ImageMagick] Used to convert postscript to PNG for display. === Fully automated installation === The [http://geosys.usc.edu/projects/seatree/browser/trunk/install_seatree?format=raw install_seatree script] will download the tar file for you and attempt the next step. === SEATREE installation === 1. Download the tar file, unpack and change into the directory where you unpackaged SEATREE. Here, I will use my install directory {{{ ~/tmp/seatree-1.0.0-082108/ }}} as an example directory from which the python scripts are run. Replace the version string "1.0.0-082108" with whatever version you are using. 2. Run the automated installer. This can be done with {{{ becker@walter:~/tmp/seatree-1.0.0-082108 > ./configure }}} but this script mainly only loads the actual installer, which is [source:trunk/python/seatree/install/install.py python/seatree/install/install.py] {{{ install_seatree: installing in seatree-1.0.0-082108/ by running configure script... configure: SEATREE installation process configure: This script assumes you have C and F77 compilers and the regular flags set to usable values configure: CC: gcc CFLAGS: -O2 -Wall -funroll-loops -fomit-frame-pointer -DLINUX_SUBROUTINE_CONVENTION -DUSE_GZDIR configure: F77: gfortran FFLAGS: -x f77-cpp-input -O2 -Wall -funroll-loops -fomit-frame-pointer -DLINUX_SUBROUTINE_CONVENTION configure: running install.py in python/seatree/install subdirectory Setting up GMT GMT appears to be in your system path already... Specify another path (y/n default: n)? Loading Modules... Parsing /home/walter/becker/tmp/seatree-1.0.0-082108/python/conf/install/hc.xml Found FlowCalc Parsing /home/walter/becker/tmp/seatree-1.0.0-082108/python/conf/install/larry.xml Found Invert Parsing /home/walter/becker/tmp/seatree-1.0.0-082108/python/conf/install/nll.xml Found NonLinLoc Parsing /home/walter/becker/tmp/seatree-1.0.0-082108/python/conf/install/syn2d.xml Found Syn2D Installing Module: FlowCalc Installing FlowCalc Build HC (note: you must do this once) (y/n default: y)? GMT Home: /usr/local/src//GMT4.3.1/ NetCDF Home: /usr/geosys/x86_64/netcdf-3.6.0-p1/ HC Directory: /home/walter/becker/tmp/seatree-1.0.0-082108/modules/mc/hc 1) GMT 3.4.5 2) GMT 4.x.x Select GMT version from above (default: 2): CPU Architecture (default: x86_64): Building HC... Success! Installing Module: Invert Installing Larry-Invert Build Larry (note: you must do this once) (y/n default: y)? Larry Directory: /home/walter/becker/tmp/seatree-1.0.0-082108/modules/seismo/larry Building Larry... COMMAND: cd /home/walter/becker/tmp/seatree-1.0.0-082108/modules/seismo/larry; make clean COMMAND: cd /home/walter/becker/tmp/seatree-1.0.0-082108/modules/seismo/larry; make Success! Installing Module: NonLinLoc Traceback (most recent call last): File "python/seatree/install/install.py", line 95, in installModule exec(execstr) File "", line 1, in ImportError: No module named nllInstaller NonLinLoc installer missing or not needed Installing Module: Syn2D Installing Syn2D Build Syn2D Binaries (note: you must do this once) (y/n default: y)? Syn2D Directory: /home/walter/becker/tmp/seatree-1.0.0-082108/modules/seismo/syn2d Detected GNU Fortran Compiler, checking $FFLAGS for fixed line length flag Building Syn2D... COMMAND: cd /home/walter/becker/tmp/seatree-1.0.0-082108/modules/seismo/syn2d; make clean COMMAND: cd /home/walter/becker/tmp/seatree-1.0.0-082108/modules/seismo/syn2d; make build_only Success! }}} Note how the installer automatically configures default setting for the python SEATREE GUI, checks for existing modules, and then loops through all modules to install then. In this case, the installer configured and compiled hc and larry. If everything works OK, you should end up with a link to the main python script in (at least) the installation directory {{{ becker@walter:~/progs/src/seatree> more seatree #!/bin/sh /home/walter/becker/progs/src/seatree/install/../py-drivers/py-gui/SEATREE.py }}} == Documentation == === [http://geodynamics.usc.edu/~becker/preprints/mbbssw08.pdf Brief EOS report] === === [wiki:UserDocs User documentation] === === [wiki:DevDocs Developer documentation] === === Mac OSX comments === The simplest approach may be to obtain the [https://www.enthought.com/products/getepd.php Enthought Python Distribution]. This software is free for academic users and contains all of the required, python-related packages below. Should you wish to install the individual packages, and are having problems installing PyGTK, [http://developer.imendio.com/node/175 this thread] may help. Other installation comments (from Marc Spiegelman, LDEO) 1. have a reasonably recent python from http://www.python.org/ e.g. python2.4 2. if not installed, use Fink to install * GMT * netCDF * gtk * pygtk these will normally be installed in /sw (and the path for GMT and netCDF will be /sw ) 3. make sure PYTHONPATH includes /sw/lib/python2.4/site-packages (for pygtk) (and anywhere else) 4. If you need a fortran complier (i.e. to build Larry) install gfortran http://gcc.gnu.org/wiki/GFortranBinaries 5. when building Larry setenv F77 gfortran setenv F90 gfortran === [wiki:bugs Bug reports, feedback, and release history] === See our [wiki:bugs SEATREE version history page] for recent changes.