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Alba Box

This page contains information for users of the ALBA Box. The ALBA Box is a Virtual Machine with preinstalled scientific software for users of the ALBA Synchrotron.

 

Installing Alba Box:

 

Note: The Alba Box needs at least 1Gb of RAM and ~16Gb of disk in the host system.

 

  1. Get the AlbaBox file (AlbaBox-XXXXXXXX.ova)
  2. Install VirtualBox if not already installed (tested with version 4.0).
    1. For Linux: recent distros already include Virtualbox4.0 in their repositories. If not, see  http://www.virtualbox.org/wiki/Linux_Downloads
    2. For Windows and OSX: see http://www.virtualbox.org/manual/ch02.html
  3. Open VirtualBox and go to File-->Import Appliance (select AlbaBox-XXXXXXXX.ova)

 

Using Alba Box:

  1. Open VirtualBox
  2. Select the AlbaBox and click on "Start"
  3. You can log into it using the following default user (alba) and password (albapass). I strongly recommend changing the default password immediately after the first login
  4. If this is the first time, you may need to change the keyboard layout to match your own: Start Menu (K)-->Settings-->System Settings-->InputDevices-->KeyBoard-->Layouts
  5. All the sci-soft programs packed in Albabox are ready to be launched (either from a command line or from the system menu)
  6. You can find links to help for the installed programs in the bookmarks of the Firefox browser.

 

 

Creation of the box

The following is a description of how the Alba Box was created.

This is not important from the user point of view.

The purpose of the following instructions is to log the creation process for knowing how to re-create the box (or as a guide on how to install some of these programs in your own PC)

  1. Install VirtualBox. Note: initially I used the official ubuntu repo (sudo apt-get install  virtualbox-ose virtualbox-guest-additions), but then I needed to use some tools from vbox4 version, so I added the oracle repo (important, since vbox-4 the vbox from oracle is free!). To install vbox4.0:
    1. for ubuntu >=11.04, it is in the official repos. For ubuntu <11.04, add the oracle repo (e.g., "deb http://download.virtualbox.org/virtualbox/debian maverick contrib") and get the signing key ($ wget -q http://download.virtualbox.org/virtualbox/debian/oracle_vbox.asc -O- | sudo apt-key add -). See more info in http://www.virtualbox.org/wiki/Linux_Downloads
    2. $sudo apt-get install virtualbox-4.0
  2. Download Kubuntu iso (11.04-32b)
  3. Create Virtual Machine (all standard except choosing 1Gb RAM and 16Gb hard disk and mounting the kubuntu iso as cd)
  4. Start the VM and install kubuntu using default settings. Use alba/albapass as user/password
  5. Enable keyboard layouts: Start Menu (K)-->Settings-->System Settings-->InputDevices-->KeyBoard-->Layouts
  6. Customize desktop:
    1. Add shortcut for konsole to panel
    2. Change start menu icon to classic mode
    3. Install firefox and add shortcut to panel
    4. change wallpaper to alba_wallpaper.jpg (can be found in storage00/temp/cpascual/albabox/, and put in ~/)
  7. Create ~/alba_settings.sh and call it from ~/.bashrc  (put PATH=~/.local/bin:~/bin:$PATH)
  8. install several needed packages
    1. $sudo apt-get install openssh-server subversion gksu tcsh python-setuptools build-essential unrar ipython pyqt4-dev-tools qt4-dev-tools libqt4-dev python-qt4-dev gfortran python-qwt5-qt4 python-qwt5-doc libqwt5-qt4-dev libhdf5-serial-dev hdfview hdf5-tools python-h5py python-dev python-sphinx python-qscintilla2 python-scipy python-ply codeblocks
    2. *install the guest additions if not already done (Virtualbox-->Devices-->Install Guest Additions and then go to the GUESTADDITIONS CD and run Autorun.sh)(SCRIPT FAILED. COULD NOT INSTALL (this is a bug in vbox guest-additions with linux kernel 2.6.38))
  9. Install scisoft packages
    1. Some scisoft packages from repos: $sudo apt-get install pymca qtiplot gnuplot spyder g3data scilab octave qtoctave imagej xmaxima kile
    2. install nexus (see instructions here)
    3. guidata & guiqwt: easy_install --user guidata && easy_install --user guiqwt
    4. imagej TOMO pluggins: 
      1. get tomo plugins collection from https://www.cells.es/Members/cpascual/files/public/scisoft_files/imagej-tomo-plugins/at_download
      2. uncompress imagej-tomo-plugins.rar and copy the contents to ~/.imagej/plugins
    5. fit2d:
      1. download  http://ftp.esrf.eu/pub/expg/FIT2D/fit2d_12_081_i686_linux2.4.20 (linked from http://www.esrf.eu/computing/scientific/FIT2D/)
      2. save it as ~/.local/bin/fit2d
      3. chmod +x ~/.local/bin/fit2d
    6. bsl: download from http://www.small-angle.ac.uk/dms/small-angle/linux/bsl-tar/bsl.tar.gz and untar it in ~/.local/bin/  (seems to work, but needs testing with real data)
    7. xotoko: download from http://www.small-angle.ac.uk/dms/small-angle/linux/xotoko-tar/xotoko.tar.gz and untar it in ~/.local/bin/  (seems to work, but needs testing with real data)
    8. GSAS + EXPGUI (seems to work, but needs testing with real data):
      1. download from ftp://ftp.ncnr.nist.gov/pub/cryst/gsas/LINUX_gsas+expgui.tar.gz
      2. $untar in ~/.local/
      3. $ln -s ~/.local/gsas/GSAS ~/.local/bin/gsas
      4. $echo '~/.local/gsas/exe/ncnrpack ~/.local/gsas/expgui/expgui' > ~/.local/bin/expgui
      5. $chmod +x ~/.local/bin/expgui
      6. $cd ~/.local/gsas/expgui/ && ln -s Geo_Viewer.tcl geo_viewer.tcl
    9. FullProf ( wfp2k seems to work, but needs testing with real data. )
      1. download from http://www.ill.eu/sites/fullprof/
      2. $md ~/local/FullProf_Suite
      3. untar in  ~/local/FullProf_Suite
      4. add envvar to ~/albabox_settings.sh (export FULLPROF=~/local/FullProf_Suite ) and also add it to the PATH
  10. Install Sardana packages
    1. Install Tango
      1. sudo add-apt-repository ppa:tango-controls/tango
      2. sudo echo 'deb-src http://ftp.debian.org/debian/ unstable main' >> /etc/apt/sources.list.d/tango-controls-debian.list
      3. upgrade the system: sudo apt-get update ; sudo apt-get upgrade
      4. $sudo apt-get install mysql-server  (use albapass as the mysql root password when asked)
      5. $sudo apt-get install tango-db tango-test omninotify libtango-java (use albabox as TANGO HOST when asked, and answer yes to question on whether to auto-configure the mysql Tango server. When prompted for a password, give "albapass" always)
      6. $apt-src -bi install pytango (we install pytango from the debian sources because it is not yet available for ubuntu)
      7. comment out the contents of /etc/apt/sources.list.d/tango-controls-debian.list (in order not to leave the debian src repo)
    2. Install Taurus
      1. $cd ~/src  && svn co http://tango-cs.svn.sourceforge.net/svnroot/tango-cs/gui/taurus/trunk taurus
      2. $cd ~/src/taurus && python setup.py build_resources
      3. add ~/src/taurus/lib to PYTHONPATH in  ~/alba_settings.sh and export it
    3. Install Sardana
      1. $sudo apt-get install libltdl-dev
      2. $cd ~/src && svn co http://tango-cs.svn.sourceforge.net/svnroot/tango-cs/share/Sardana/trunk sardana
      3. $cd ~/src/sardana && ./configure --prefix=/home/alba/.local --with-omni-prefix=/usr --with-tango-prefix=/usr
      4. make
      5. make install
  11. create bookmarks in Firefox for installed programs
  12. Update everything: $sudo apt-get update && sudo apt-get upgrade
  13. clean downloaded packages cache (sudo apt-get clean)
  14. clean browser cache and info
  15. shut down the box and export the VM (VirtualBox-->File-->Export Appliance )

 

TODO:

  • Install programs for Xaloc

  • use nexus ppa packages to install nexus (instead of compiling)

  • test each program installed (with the person who asked for it)

  • create web page showing info of all sci-soft installed

  • create a pool for demo

 

Notes

Packages that have been proposed (and person who proposed them):

  1. cpascual (ALL DONE):
    1. PyMca
    2. qtiplot
    3. gnuplot
    4. guiqwt
    5. matplotlib
    6. spyder
    7. nexus lib
    8. h5py
    9. hdfview
    10. g3data
    11. octave + qtoctave
    12. scilab
    13. maxima
    14. gimp
  2. jbordas
    1. - fit2d (DONE, we got permission from author for re-distributing it)
    2. - bsl (DONE)
    3. -fortran compiler (DONE, gfortran)
  3. mvalvidares:
    1. qtiplot (DONE)
    2. Calculator (DONE, Kcalc, ipython, spyder,...)
    3. Editor/powerpoint compatible with word, such as open office (DONE, libreoffice)
    4. LaTex compiler (DONE, installed  kile with all deps)
    5. Image viewer with some capabilities (DONE, imagej, gimp, gwenview,...)
    6. Quick plotting tool if there is one develop by you (DONE, installed qtiplot, gnuplot,...)
  4. epereiro
    1. imagej + tomo plugins (see magnycour01) (DONE)
  5.  vperez
    1.   "Igor Pro"(NONFREE)
    2. - "SPECS Casa XPS". http://www.casaxps.com/ (NONFREE)
  6.  ggelabert
    1. FEFF9 (NONFREE)
    2. CCDB  (NONFREE)
  7.  abarla
    1. Origin (NONFREE)
    2. Igors   (NONFREE)
  8. iperal
    1. gsas : https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro (free), (DONE)
    2. fullprof: http://www.ill.eu/sites/fullprof/ (looks free, but RE-CHECK), (DONE)
    3. powdercell (WINDOWS ONLY. In theory it can be run on wine: http://www.ccp14.ac.uk/solution/wine/powdercell_wine_linux.html, but Installation FAILED)
  9.  jbenach & juanhuix:(jbenach offers to install them)
    1. MX suite as installed in neptu02 in /local/mxsoft:  (CHECK ALL LICENSES BEFORE INSTALLING!!!)
    2. programs in /home/jbenach/xsoft  (CHECK ALL LICENSES BEFORE INSTALLING!!!) (note that some of them may be available as deb packages... eg. "sudo apt-get install povray")
    3.  sharp: http://www.globalphasing.com/sharp/ (NONFREE, free for non-profit BUT DOES NOT ALLOW REDISTRIBUTION)
    4. arp/warp: http://www.embl-hamburg.de/ARP/ (NONFREE, free for non-profit BUT DOES NOT ALLOW REDISTRIBUTION)
    5. BnP: http://www.hwi.buffalo.edu/BnP/ (NONFREE, free for non-profit BUT DOES NOT ALLOW REDISTRIBUTION)
    6. solve: https://solve.lanl.gov/download.html (NONFREE one time $600 license fee)
    7. buster: http://www.globalphasing.com/buster/ (NONFREE, free for non-profit  BUT DOES NOT ALLOW REDISTRIBUTION)
    8. como: http://como.bio.columbia.edu/tong/Public/Download/ (free)
    9.  phaser: http://www.phaser.com/main/download.html (NONFREE one time $90 license fee)
    10.  hkl: http://www.hkl-xray.com/ (NONFREE first fee $24,000, later on $8,000 annually)
  10. asvensson:
    1. XOTOKO: http://www.small-angle.ac.uk/small-angle/Software.html
    2. ATSAS2.2:  http://www.small-angle.ac.uk/small-angle/Software.html (NONFREE, free for non-profit BUT DOES NOT ALLOW REDISTRIBUTION)
    3. Also BSL & Fit2d (already requested and installed)
    4. CCP13 repository (not needed for now)
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