UNIFIED GEODYNAMICS EARTH SCIENCE COMPUTING ENVIRONMENT John Yu, Thorsten W Becker University of Southern California, Los Angeles CA UTIG, JSG, UT Austin (c) 2012, 2015, 2016 --- Abstract --- This customized Linux virtual machine is intended to provide easy access to a range of freely available Earth science software and data to illustrate the capabilities of such open source tools, and assist in teaching map making, data analysis, and modeling. It is focused on geodynamics and seismology, but can be used for any Earth science application. The package is provided in the hope that it will be useful, but without any warranties. Copyright for the software and data lies with the original authors whose work should be cited as appropriate. --- Technical details --- All of the software we re-packaged here should be fairly straightforward to install on any Linux or OS-X platform, but the devil is in the details. We therefore provide a platform-independent way of using the Linux tools we like; this involves downloading a huge file (because you'll be running a second operating system, it's like a second hard drive), but we think that the benefits of having one consistent installation outweigh the drawbacks. Depending on your application, you might actually do your work entirely within the virtual machine, or you might eventually want to install the software you like the most on your own OS. We chose to run Fedora 14 Linux, with yum-installed packages, for the most part, and our own GMT 4.5.7. For a complete list of currently included software, see http://www-udc.ig.utexas.edu/external/becker/ugesce.html the main UGESCE page --- REQUIREMENTS --- - A 64BIT MACHINE. Sorry, VirtualBox won't work with 32bit hardware. - A VirtualBox software install, which is freely available for Windows, OS-X, and Linux at https://www.virtualbox.org/wiki/Downloads - A copy of our Computing Environment virtual box "hard drive" Available as (version 0.3, May 2015) * gzipped (might cause problems on Windows) http://www-udc.ig.utexas.edu/external/becker/ugesce/SEATREE64-2015.vdi.tgz (This file is 5.2 GB large.) * bzipped (might cause problems on Windows) http://www-udc.ig.utexas.edu/external/becker/ugesce/SEATREE64-2015.vdi.bz2 (This file is 4.4 GB large.) * zipped (for Windows) http://www-udc.ig.utexas.edu/external/becker/ugesce/SEATREE64-2015.zip (This file is 5.2 GB large.) - Enough disk space, and enough memory (shouldn't be a problem on modern machines, including laptops). --- Downloading the virtual machine --- Given the large size of the file, download via a browser might be a problem and timeouts might occur depending on your connection. You therefore might want to use a download tool such as "curl" or "wget" (obtain the latter from http://gnuwin32.sourceforge.net/packages/wget.htm if not installed). This will allow restarting from interrupted downloads. From a terminal (on Mac OS-X Applications-Utilities-Terminal) type something akin to curl -C -L -O http://www-udc.ig.utexas.edu/external/becker/ugesce/SEATREE64-2015.zip or wget -c http://www-udc.ig.utexas.edu/external/becker/ugesce/SEATREE64-2015.zip --- Installing our virtual Linux machine within VirtualBox --- - start VirtualBox - select "new" from menu - choose Linux-Fedora (64bit) as operating system, and use something like "SEATREE-2015" as a name - choose some memory that leaves enough for your other operating system, depending on hardware. 2GB should be enough. Use defaults if at any stage you're not sure. - select "use existing disk" and pick the .vdi file you downloaded (best to put it close to wherever your VirtualBox install likes to put those "hard drives") - if this step is successful, your new Linux virtual machine should show within VirtualBox as "SEATREE-2015". --- Troubleshooting if your image will not boot --- - Make sure the visualization setting for you CPU is enable in your BIOS. - Make sure PAE/NX is enabled in VirtualBox [SEATREE IMAGE > SETTINGS > SYSTEM PROCESSOR ******************************************************************************** - IMPORTANT - Making your VirtualBox install access the network and regular files ******************************************************************************** If you want your virtual box Linux to use your machine's Internet access (very useful to download data, for example), you'll need to go into virtual box settings (by selecting your Linux drive), then select "network", go to adapter 1 (which should be enabled and be attached to "NAT"), then select the "advanced" tab and enter as MAC address 08002701FCBD There is a way to setup your install to access all local files (e.g. UGESCE will be able to read your Mac OS-X files), or use shared folders. Instructions to follow. To enable the image to access your local (Mac or Windows) files, highlight the SEATREE VM in VirtualBox, [SETTINGS > SHARED FOLDERS] - Now, try to start up the virtual machine by clicking on the green arrow within VirtualBox. (Whenever you need to make changes to settings such as virtual box' network access, the machine needs to be shut down). --- Using the Linux machine (LOGIN) --- - If the machine is running, you should see a Fedora/Linux login screen with one user, the "Seatree User". Click on the user icon, and login User: seatreeuser Password: seatree (There might a security warning, disregard it.) The GNOME graphical user interface should load and you're presented with your user desktop. There are several program icons, on which you can click, including some of our own stuff If, at some point, you need to be root (superuser) to change administrative settings within UGESCE, the password for root is the same, seatree. --- General instructions on using UNIX, LINUX, and the like --- Can be found on the web. My lecture notes at http://www-udc.ig.utexas.edu/external/becker/unix_rome.html might also be of use --- Some comments on installed software --- For an up to date list with version numbers, see the main UGESCE page at http://www-udc.ig.utexas.edu/external/becker/ugesce.html - GMT - The Generic Mapping Tools http://gmt.soest.hawaii.edu/ - iGMT - a graphical user interface for mapping using GMT http://www-udc.ig.utexas.edu/external/becker/projects.i.html - SEATREE - The Solid Earth Research and Teaching Environment http://geosys.usc.edu/projects/seatree/ And some example for other nice free software, including - Octave - a free matlab alternative - g3data - a plot digitizer - gnuplot - a simple x-y plotter - Paraview - a 3D visualization tool, e.g. for VTK files - GRASS - a free GIS system The machine also comes preloaded with a range of earth science datasets, which you can access via the folders that are on the desktop, as well as a number of other scientific software/libraries, including GMT, netcdf, gnuplot, BLAS, LAPACK, g3data, and Paraview. To make sure everything works, click on the iGMT and SEATREE icons which should open GUIs to run the respective software. You are now running a full Linux installation which has been customized to do some Earth science mapping and modeling. You can customize your copy of the software as you like. -- Installing additional software -- For example, if we missed out on a popular package, chances are you might be able to install it (as root) using yum install my_favorite_software assuming you have network access set up. --- Feedback, comments, requests, bug reports --- Please direct any comments to twb@usc.edu. In particular, please let us know if you like us to install additional software or data.