Installing extra applications

Enthought Canopy (python)

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

Installing 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

Cygwin-X

Cygwin/X should already be installed on your LSCE machine This section covers the reinstallation/update, or installation from scratch

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

Installing Cygwin-X

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.switch.ch

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...)

Updating Cygwin-X

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 Processes tab, kill the cygserver process, then click on Retry

Accept the default icons creations and exit

Testing Cygwin-X

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 asterix 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>@asterix1.saclay.cea.fr' to login to asterix1

do the 'xterm' test

do the 'glxinfo|grep -i opengl' test

exit asterix

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

Cygwin-X tips and tricks

Where are the directories?

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)

Solving Cygwin directories access rights

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

Uninstalling Cygwin-X

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

Using Cygwin-X at LSCE

We use XDMCP query on asterix in order to open a full Linux environment running on one of the asterix 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 asterix -terminate

Note: the -wgl argument is optional. It may (or not) give you some increased performance

Select a name for the shorcut: Asterix64, Asterix, etc...

Once you have started Cygwin and logged in with you account on one of the asterix 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

Trying to have Cygwin-X work faster on Win7+Intel HDxxx cards

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

Gnu emacs + GnuWin DiffUtils

Download

http://vgoulet.act.ulaval.ca/emacs/windows (Emacs installer for Windows)

http://gnuwin32.sourceforge.net/packages/diffutils.htm (Recompiled diff programs for Windows)

emacs_win_7_64_140408.zip (JYP's .emacs file)

Configuration

Create a Home directory for Windows, in your user directory
<disk>:\Users\<your_login>\HOME_WIN

Extract the .emacs file (from emacs.zip above) to HOME_WIN

Configure Windows so that it will look for configuration files in HOME_WIN

Right-click on the Computer icon and choose Properties

Click on Advanced systm parameters on the left

Click on Environment variables

Select or create the HOME variable and give it the location of the HOME_WIN directory

Save the configuration

Install emacs and the diffutils binaries (no need to install diffutils documentation and sources)

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

Testing the tramp mode

Try to open a remote file, in order to check if tramp works correctly
e.g. /<your_login>@idefix1.saclay.cea.fr:.emacs

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

In that case:

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”)

Execute the line with Ctrl-Meta-x

Exit Emacs

Delete Tramp cache: HOME_WIN/.emacs.d/tramp

Start Emacs

Notes

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

QtGrace

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

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

Installing

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

Kies (Samsung)

Web & Download: http://www.samsung.com/fr/support/usefulsoftware/KIES/JSP

Putty

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)

Configuring and using pageant

Notes

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

SciDAVis

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

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

Microsoft synctoy

This is a free and easy to install backup program that will only copy new/modified files

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

Configuration

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\<your_computer_model>\Windata_<your_login>

Click Next and choose Echo, because we want the backup to be an exact copy of the original 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

Google Drive

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

VLC

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

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

WinSCP

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

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

XnView

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

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

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