====== 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. \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 //\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 ===== VcXsrv Windows X Server ===== VcXsrv is now pre-installed on your Windows machine instead of [[#cywin-x|Cygwin-X]]. It should work more reliably with the LSCE servers, but does not provide all the resources of Cygwin-X. You may want to install Cygwin-X as well, in some special cases Web & Download: http://vcxsrv.sourceforge.net/ ==== Setup ==== * 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! * FIXME 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 ==== Notes ==== * 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 ===== Cygwin-X ===== Cygwin/X used to be pre-installed on your LSCE machine but the connection with the obelixN servers in XDMCP mode became unreliable\\ The Windows machines now use [[#vcxsrv_windows_x_server|VcXsrv]] but you may still need to install Cygwin-X in some special cases\\ 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. :\Scratch\\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...) ==== 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 [[other:win7apps#installing_cygwin-x|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 ('':\Scratch\\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 ==== 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 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 @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 ==== 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 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'' ==== 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 * [[http://ubuntu-tutorials.com/2008/01/10/gconftool-2-gconf-editor-from-the-shell/|Using gconftool-2]] * [[http://aaron-kelley.net/blog/2013/03/cygwinx-xwin-causes-nvidia-optimus-to-run-all-of-the-time/|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 * [[http://www.mesa3d.org/envvars.html|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// ([[http://en.wikipedia.org/wiki/MIT-SHM|MIT Shared Memory Extension ]])? * http://x.cygwin.com/docs/ug/using-shared-memory.html ===== Panoply ==== 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/ {{:pmip3:database:visualizing_netcdf_panoply_seidenglanz.pdf|User manual}} (courtesy of Anne Seidenglanz)\\ [[http://www.geo.uni-bremen.de/Interdynamik/images/stories/pdf/visualizing_netcdf_panoply.pdf|Link to the original version]] ===== GIMP ==== Web: http://www.gimp.org/ Download: http://www.gimp.org/downloads/ ===== Gnu emacs + GnuWin DiffUtils ===== ==== Download ==== - Emacs installer for Windows: http://vgoulet.act.ulaval.ca/emacs/windows - Recompiled diff programs for Windows (needed for the //ediff// mode): http://gnuwin32.sourceforge.net/packages/diffutils.htm - JYP's .emacs file: {{:other:emacs_win_7_64_140408.zip|for Windows}} - {{:other:emacs_linux_150806.tar|for Linux}} - Annotated reference card of the emacs text editor: {{:other:newppl:emacs_jyp.pdf}} ==== Configuration ==== - Create a Home directory for Windows, in your user directory\\ :\Users\\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. /@ssh1.lsce.ipsl.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 ==== Misc. emacs related notes ==== === Windows specific 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 === Other notes === * 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! FIXME ===== 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'' ===== Samsung utilities ===== * Smart Switch: http://www.samsung.com/fr/support/smartswitch/ * Kies & Kies3, for older phones: http://www.samsung.com/fr/support/usefulsoftware/KIES/JSP ===== Malwarebytes Anti-Malware ===== Web & Download: https://www.malwarebytes.org/ ===== 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//) More information: http://ciclad-web.ipsl.jussieu.fr/data/documents/ssh_putty_v2_2011-1.pdf ==== Configuring and using pageant ==== FIXME ==== 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\\ \\ Using synctoy is very similar to using Linux //rsync// 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\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. '' Windata_'' * 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 ===== BlueScreenView ===== 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 ===== HTTrack Website Copier ===== 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 /* standard page footer */ \\ \\ \\ ---- [ [[pmip3:|PMIP3 Wiki Home]] ] - [ [[pmip3:wiki_help|Help!]] ] - [ [[wiki:syntax|Wiki syntax]] ]