SEATREE distribution

  1. SEATREE distribution
    1. License and availability
    2. Downloads
      1. Fully automated installation
      2. Tar-ball with source
      3. Developer source code access
    3. Installation
      1. Required Software Packages
      2. Fully automated installation
      3. SEATREE installation
    4. Documentation
      1. [http://geodynamics.usc.edu/~becker/preprints/mbbssw08.pdf Brief EOS …
      2. User documentation
      3. Developer documentation
      4. Mac OSX comments
      5. Bug reports, feedback, and release history

License and availability

SEATREE is distributed under the 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 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 SVN might prefer to subscribe to the development version which we use. 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 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.

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 fully functional GUI and drivers for hc, larry, 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 source browser, or checkout the 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 hc and nonlinloc) and Fortran (for ConMan, larry, larry3d, and 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., 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 fink (for Mac OS-X), yum (e.g. Fedora Linux), or 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:

  • Python: Python alone will give you more sophisticated scripting capabilities,
    • for the graphical user interface, you'll also need to add pygtk
    • matplotlib is needed for additional plotting functionality

The simplest approach may be to obtain the 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.

Fully automated installation

The 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 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 "<string>", line 1, in <module>
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

Brief EOS report

User documentation

Developer documentation

Mac OSX comments

The simplest approach may be to obtain the 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, 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

Bug reports, feedback, and release history

See our SEATREE version history page for recent changes.