Installing extra applications

Web & Download: https://www.enthought.com/products/canopy/

• The full version of Canopy is free for students and staff at degree-granting institutions. You just have to create an account and request an Academic license
  https://store.enthought.com/#canopy-academic
• Download the installer of the free Canopy Express installer
  https://store.enthought.com/#canopy-individual
• Create a directory that you will use for the second part of the installation process. You should use a partition where you have some space (possibly a scratch disk that's not backed up)
  e.g. <MY_SCRATCH_PARTITION>\Enthought_Canopy
• Start the installer, accept the License Agreement, choose Install just for you… and click Install to perform the base installation
• When you get the Canopy environment setup window, click on Change to select the <MY_SCRATCH_PARTITION>\Enthought_Canopy directory that you created earlier, and click on Continue.
• Accept Canopy as your default Python environment and click on Start using Canopy
• Click on Log in (just below 'Hi, welcome to Canopy!') and enter the email and password that you used for requesting the Academic license
• Start the Package manager from Tools → Package Manager
• In the Package Manager, click on Updates NN in the left window and then on Install all Updates
• Click on Available Packages if you need to install extra packages
  You may want to install the following:
  • from Canopy Packages (note: if you know that you have an academic license, but you only get Subscribe instead of Install next to the packages available in Canopy Packages, just quit and restart Canopy): basemap, basemap_ld, cartopy, netCDF4
• Click on Updates NN again, and install them, if some new updates are available

Web & Download: http://vcxsrv.sourceforge.net/

• Start XLaunch to configure VcXsrv
• Select One large window, then Next
• Select Open session via XDMCP, then Next
• Select Connect to host obelix and Terminate on server reset, then Next
• Use the settings specified below, then Next
  • Select Clipboard
  • Unselect Native opengl, unless you know what you are doing!
    • We should try to keep it selected and check if glxgears works correctly, with and without setting the LIBGL_ALWAYS_INDIRECT environment variable
• Click on Save configuration to save the settings on the Windows desktop (e.g obelix_VcXsrv.xlaunch), then Finish. VcXsrv will automatically start.
  The next time you want to start VcXsrv, just click on the obelix_VcXsrv.xlaunch file that you have saved on your desktop

• Once you have started VcXsrv and logged in with you account on one of the obelix servers, it is highly suggested to activate the windows wireframe moving mode by typing:
  gconftool-2 --set /apps/metacity/general/reduced_resources --type bool true
• If you just need to run an X server (instead of using XDMCP), e.g. when you are outside LSCE, just start VcXsrv from the Windows Start Menu

Web & Download: http://x.cygwin.com/

• Make sure that Cygwin-X is not running (if you have a previous installation of Cygwin)
• Get the 64-bit installer (setup-x86_64.exe) and start it (use the regular installer if you have a Win7 32-bit)
• Accept the default Install from Internet mode
• Accept the default Root/install directory (C:\cygwin64) and install for All Users
• Select a scratch directory for downloading the installation packages
  e.g. <disk>:\Scratch\<your_login>\CygwinX
• Accept the Direct Connection
• Select a nearby mirror
  e.g. http://mirror.easyname.at
• The Select Packages window should start with the Category view. If this is not the case, click several times on the View button to select the Category view
  • When you select a package, the dependencies will automatically be selected as well
  • View ⇒ Pending will display the selected packages and the dependencies that will be downloaded
• Select the following packages, from:
  • X11: xorg-server, xinit, xterm, all the font-* packages, font-config, showfont, xlsfonts, xdpyinfo
  • X11 optional: mesa-demos, x11perf
  • Net: openssh
• Click Next and accept the suggested extra packages (dependencies)
• Click Next and wait for the download
• Accept the default icons creations and exit

Note: You can remove the installation packages directory once you have checked that the installation was correct, unless you want to use the CygwinX directory to perform a network-less installation on another computer. The content of this directory is possibly used when upgrading Cygwin-X, so you may want to keep it (it's less than 130 Mb…)

• Get the latest version of the installer from the Cygwin-X web site.
  The version number of the installer is not included in the installer file name (setup-x86_64.exe), so it's impossible to know if you already have the latest version. But the installer will display warnings after the mirror download site selection (see Select a nearby mirror in Installing Cygwin-X above) if the installer is out-of-date
• Follow all the Installation steps detailed above till the Select Packages step.
  Cygwin-X seems to remember the settings of the previous installation, but maybe this is just the case when the download directory of the previous installation (<disk>:\Scratch\<your_login>\CygwinX) still exists…
• Click on the View button till it displays Pending, and the list of packages requiring an update are displayed (with the Current (installed) and the New version number)
• Click Next and accept the suggested extra packages (dependencies)
• Click Next and wait for the download and installation
  • Warning! If you get the unable to extract /usr/bin/cygwin1.dll error message during the installation, open the task manager, go to the Services (not Processes) tab, kill the cygserver process, then click on Retry
• Accept the default icons creations and exit

Start ⇒ All programs ⇒ Cygwin-X ⇒ xterm

• An xterm should appear
  • Note: this will NOT work if you already have a running X server connected to the LSCE obelix servers in XDMCP mode
• Type 'xterm' and check you get a new xterm window
• In the notification zone, right-click on the X icon and choose About. You should get Version 1.16.1 (2014-10-17) or higher
• Type 'glxgears' and check that you get a window with rotating gears
• Type 'glxinfo|grep -i opengl' and check the vendor string: it should be the same as your computer's graphics card
• Type 'ssh -Y <your_login>@obelix2.lsce.ipsl.fr' to login to obelix2
  • do the 'xterm' test
  • do the 'glxinfo|grep -i opengl' test
  • exit obelix
• More tests with x11perf??

Start ⇒ All programs ⇒ Cygwin ⇒ Cygwin Bash shell

• cygcheck -c : list of installed packages
• cygcheck -s : system information and list of installed packages

Notes:

• Log files are in: C:\cygwin64\var\log\xwin\XWin.0.log
  • You can find the installed version of Cygwin at the top of the file (e.g. Release: 1.16.0.0)
• Discussion: http://blog.gmane.org/gmane.os.cygwin.xfree

• You can use df -h to get information about the partitions
• The Linux root (/) directory is located in C:\cygwin or C:\cygwin64 (depending if you are using a 32bit or 64bit Windows).
  e.g. /home is actually in C:\cygwin64\home
• The C: Windows partition (accessible with cd c: from cygwin) is in /cygdrive/c (from cygwin)

You may encounter Windows access rights problem when using cygwin:

• you don't have the correct ownership or enough rights to remove c:\cygwin
• when starting cygwin/X, you get an error message saying that you can't write/access /var/log/xwin/XWin.0.log
• …

These problems can be solved with cygwin!

• Start a cygwin shell with administrator rights
  Start ⇒ All Programs ⇒ Cygwin Bash Shell ⇒ right-click and choose to run as administrator
• Use standard Linux commands to check and fix the access rights
  • ls -l, chmod, chown, chgrp, …
    • e.g., to solve the XWin.0.log above, you can use: chmod a+rwx /var/log/xwin

You may have to uninstall Cygwin-X if you want to really restart from scratch, or because of some unforeseen technical problems

• Official uninstall instructions: https://cygwin.com/faq/faq.html#faq.setup.uninstall-all
• An interesting thread about uninstall: http://superuser.com/questions/167219/how-to-completely-uninstall-remove-cygwin-from-windows-7
  • Look for hints in there if you get some weird access rights problems!
    • Some Windows command lines have some potential: takeown, icacls

We use XDMCP query on obelix in order to open a full Linux environment running on one of the obelix server, displayed in a full-screen window on the local desktop

Use the following steps to create a shortcut on your desktop that you can use to start Cygwin-X in XDMCP mode:

• Right-click on the desktop and choose New –> Shortcut
• Choose the target of the shortcut: C:\cygwin64\bin\XWin.exe
  • Do not forget to add the extra options to the shortcut, so that it looks like:
    C:\cygwin64\bin\XWin.exe -wgl -query obelix -terminate
  • Note: the -wgl argument is optional. It may (or not) give you some increased performance
• Select a name for the shorcut: Obelix64, Obelix, etc…

Once you have started Cygwin and logged in with you account on one of the obelix servers, it is highly suggested to activate the windows wireframe moving mode by typing:
gconftool-2 --set /apps/metacity/general/reduced_resources --type bool true

• Activate wireframe mode
  gconftool-2 --set /apps/metacity/general/reduced_resources --type bool true
• Check if other metacity parameters should be set?
  • http://www.yolinux.com/TUTORIALS/GNOME.html#GCONF
  • Using gconftool-2
• Should we disable OpenGL ?
  • Start with -nowgl option, or use the GLWIN_NO_WGL_EXTENSIONS environment variable
• Check the performance and basic parameters with: glxgears -info
• Should we play with the Mesa 3D Graphics Library environment variables
• Have we forgotten to install some optional cygwin packages?
• Search the cygwin mailing lists: https://cygwin.com/lists.html
  • https://sourceware.org/cgi-bin/search.cgi?wm=wrd&form=extended&m=all&s=D&ul=%2Fml%2Fcygwin-xfree%2F%25&q=
• What can we do with cygserver-config ?
• Enable MIT-SHM extension (MIT Shared Memory Extension )?
  • http://x.cygwin.com/docs/ug/using-shared-memory.html

You can use Panoply to work with NetCDF data (and some other geo-referenced data) if you just need a quick-look or you are not familiar with NetCDF

Web & Download: http://www.giss.nasa.gov/tools/panoply/

User manual (courtesy of Anne Seidenglanz)
Link to the original version

Web: http://www.gimp.org/

Download: http://www.gimp.org/downloads/

1. Emacs installer for Windows: http://vgoulet.act.ulaval.ca/emacs/windows
2. Recompiled diff programs for Windows (needed for the ediff mode): http://gnuwin32.sourceforge.net/packages/diffutils.htm
3. JYP's .emacs file: for Windows - for Linux
4. Annotated reference card of the emacs text editor: emacs_jyp.pdf

1. Create a Home directory for Windows, in your user directory
   <disk>:\Users\<your_login>\HOME_WIN
2. Extract the .emacs file (from emacs.zip above) to HOME_WIN
3. Configure Windows so that it will look for configuration files in HOME_WIN
   1. Right-click on the Computer icon and choose Properties
   2. Click on Advanced systm parameters on the left
   3. Click on Environment variables
   4. Select or create the HOME variable and give it the location of the HOME_WIN directory
   5. Save the configuration
4. Install emacs and the diffutils binaries (no need to install diffutils documentation and sources)
5. If you use tramp to edit remote files, you will need the Putty package, but this should have been already installed as part as the standard LSCE installation

Try to open a remote file, in order to check if tramp works correctly
e.g. /<your_login>@ssh1.lsce.ipsl.fr:.emacs

You will probably get the following error: Couldn't find a proper `ls' command

In that case:

1. Paste the following line in a buffer and select it
   (byte-compile-file “C:\\Program Files (x86)\\GNU Emacs 24.3\\lisp\\net\\tramp-sh.el”)
2. Execute the line with Ctrl-Meta-x
3. Exit Emacs
4. Delete Tramp cache: HOME_WIN/.emacs.d/tramp
5. Start Emacs

• Installing the DiffUtils packages makes it possible to use the emacs Tools ⇒ Compare (ediff) menu
• If you get the following error when starting emacs
  error: The directory `~/.emacs.d/server' is unsafe
  Use the following solution: http://stackoverflow.com/a/2944197

• Commenting/commenting lines (in a python script, or anything) : M-;
• Improving python support: https://samrelton.wordpress.com/2013/09/16/emacs-and-python/
  • Not tested!

Web & Download: http://sourceforge.net/projects/qtgrace/

Note: for interactive scientific graphics on Windows, see also scidavis

• Download and unzip the Windows binary distribution to \somewhere\qtgrace_windows_binary_024
• Go to qtgrace_windows_binary_024\bin and double-click on qtgrace.exe

• Smart Switch: http://www.samsung.com/fr/support/smartswitch/

• Kies & Kies3, for older phones: http://www.samsung.com/fr/support/usefulsoftware/KIES/JSP

Web & Download: https://www.malwarebytes.org/

Web: http://www.chiark.greenend.org.uk/~sgtatham/putty/

Download: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html (Get the Windows installer for everything except PuTTYtel)

More information: http://ciclad-web.ipsl.jussieu.fr/data/documents/ssh_putty_v2_2011-1.pdf

Add here some information about ssh, public/private keys, etc…

Web & Download: http://scidavis.sourceforge.net/

Note: for interactive scientific graphics on Windows, see also qtgrace

Web & Download: http://www.microsoft.com/en-us/download/details.aspx?id=15155

The idea is to create pairs of folders (left folder and right folder) and to keep them synchronized

• Click on Create New Folder Pair
• Choose a Left Folder on the computer
  e.g. F:\Users\jypeter
• Choose a Right Folder on the backup disk
  e.g. J:\Backup_JYP\Dell_Precision_T1700\Windata_jypeter
• Click Next and choose Echo, because we want the backup to be an exact copy of the original folder
  • Warning! Exact copy means that if something is removed in the left folder and you run synctoy, synctoy will also erase the same thing in the right folder
• Click Next and give a meaningful name to the folder pair
  e.g. <your_computer_model> Windata_<your_login>
• Finish…
• Select the folder pair and click on Change options
  • Enable Exclude system files
  • Disable Save overwritten files in the Recycle Bin
• Click on Preview and check the list of actions that the backup program will use
• Click on Run

Web & Download: https://www.google.com/drive/download/

Web: http://www.videolan.org/vlc/index.html

Download: http://www.videolan.org/vlc/download-windows.html

Web: http://winscp.net/eng/docs/introduction

Download: http://winscp.net/eng/download.php

Web: http://www.xnview.com/

Download: http://www.xnview.com/en/xnview/#downloads

This utility makes it possible to display information about previous crashes of a Win computer. Use this if your PC has experienced a BSOD (Blue Screen of Death) and you want to know what happened

Web & Download: http://www.nirsoft.net/utils/blue_screen_view.html

This utility makes it possible to download a web site for backup (e.g. HTML backup/export of a Joomla web site) or offline usage

Web & Download: http://www.httrack.com/page/1/en/index.html

[ PMIP3 Wiki Home ] - [ Help! ] - [ Wiki syntax ]