1.3 Connecting to the servers of CSC
You can connect the servers of CSC either by using the web based Scientist's User Interface extranet service or through linux terminal connections. While the Scientist's User Interface provides an easy and intuitive way to connect to CSC, it allows you to use only a very limited set tools for working with your data. Terminal connections and Linux command line usage still provides the most versatile and efficient tools to manage and analyze data in the servers of CSC. If you want to work with graphical user interfaces we recommend using the NoMachine remote desktop, which is described below.
Scientist's User Interface is an extranet service that allows the customers of CSC to access the CSC computing environment through a normal web browser. The URL of the Scientist's User Interface (SUI) is https://sui.csc.fi and it can be used for following tasks
- monitoring and managing you user account at CSC (please use my.csc.fi instead)
- managing files in the servers of CSC
- managing files in the IDA storage service
- Launch SSH console sessions
- Use Lemmie language bank corpora interface and DMA -Digital Morphology Archive
- Use PaITuli Geospatial Data Service
- Download software and data sets provided by CSC
- Create and execute batch job scripts for the computing servers of CSC.
- Manage and store grid certificates
You can use either your HAKA account (local university account) or CSC user account to log into Scientist's User Interface. The My Files file manager is discussed more in detail in chapter 5.1 of this guide.
Figure 1.2: Scientist's User Interface extranet service.
A terminal connection to CSC should be opened using a secure terminal program that encrypts the data traffic between the user and CSC. In Linux and Mac OSX systems you can use ssh program to connect to CSC. In Windows machines you can use for example the PuTTY open source program to open the connection to CSC. If you don't want install a local ssh terminal program, you can use the SSH console tool in Scientist's User Interface (more details in chapter 5.1.2).
For example to log into Taito, open a new terminal screen and give command:
ssh taito.csc.fi -l csc_username
If you wish to use also X11 based graphical tools give command:
ssh taito.csc.fi -X -l csc_username
or in some cases, if the command above does not work, try:
ssh taito.csc.fi -Y -l csc_username
When you stop working at the servers of CSC, you should first close the connections to CSC with command:
In addition to the plain text based terminal connections you may need be able to use also X-term connections. X-term connection can be used to enable viewing image files or launching a graphical interface on the servers of CSC. To be able to use X-term based tools your local computer must have an X11 server (often called as X window server program) installed and running. In linux machines X11 is normally installed and running automatically. In Mac OSX machines the X11 software is not installed by default, but it can be installed from the Mac OSX installation disks. In Windows machines, an X server program must be installed to the users local machine. In addition to several commercial xterm programs there are also some free ones like Xming, but CSC recommends using the NoMachine remote desktop, see below.
Once your X server program is running, open a terminal connection to CSC ( remember to use the -X or -Y option or Tunnel X11 setting), and test by running command:
This should open a new xterm connection to your screen.
Figure 1.3 Linux terminal window
NoMachine Remote Desktop provides an alternative way to use remotely graphical interfaces at the servers of CSC. The service works with a NoMachine client which is installed on the researcher's computer. No X-term software is needed in the local computer.
We recommend NoMachine for remote usage of graphical interfaces instead of X11 connections. It often speeds up the graphical response even 10 fold with respect to the normal X11 connections. Further, the NoMachine client is often easier to install to a Windows machine, than an X-emulator. The NoMachine remote desktop can also be suspended, so that while you close your connection or reboot your computer, you can continue from where you left off without the connections from the NoMachine server to CSC servers being closed or the running processes stopped.
Figure 1.4 The NoMachine server setup at CSC. The blue line means the connection established from the NoMachine client installed on your computer, which gives good performance even with slow connection. The solid red line is an ssh connection from the NoMachine server to a CSC compute server. Connections within a location are fast (within Kajaani).
When you open a connection to CSC, the NoMachine client first connects to a NoMachine server nxkajaani.csc.fi, which is located in Kajaani. After the login, a remote desktop opens to your screen. From this remote desktop you need to further connect to the actual computing servers (by right clicking the desktop) and then start the applications with normal terminal commands. You can also start some applications directly from the right-click menu.
To start e.g. Mercury in Taito (taito-shell), right click with the mouse in the Desktop area, choose taito-shell from the pull down menu, add your password, and you are logged in Taito. Then go to your working directory with cd $WRKDIR, initialize the CSD package with module load ccdc and then start the GUI with mercury.
To exit from NX close the Desktop. Point the top right corner with your mouse to access the peel menu and left-click. Click the small "power" button at the right lower corner of the options. Then choose terminate. If you want to close the connection to the remote desktop, but want to leave the connections from the desktop to the servers alive, choose 'Disconnect' or 'Suspend'.
Figure 1.5 Matlab opened in the NoMachine remote desktop.
First download the NoMachine Enterprise client (not the Desktop, which is first on the list) for your operating system from here:
Installing the client requires admin privileges. For Windows start the installer, accept the agreement and default installation location. For Linux see the instructions on the download page and continue here for the configuration.
You may need to grant some nx* applications to access to the internet for your anti-virus/firewall software.
Open NoMachine Enterprise Client. (In windows from Start menu). If this is the first time you open the Client, your screen will look a bit different. If it does, choose the "Create a new connection" icon.
... or click "new" at the top menu.
Choose NX as the protocol and click continue.
Fill in "nxkajaani.csc.fi" as the Host. The default port is ok. Click continue.
Choose "Password" and click continue.
In most cases you don't want the proxy. If the connection fails, consult your IT-support in case you need to connect via proxy.
Give your configuration some name. If you want a Desktop shortcut, click that too. Click done.
Double click the new connection icon (or the shortcut on your Desktop).
Give your CSC username and CSC password (which you use to log in e.g. Taito) and click OK. If this is the first time you connect to nxkajaani.csc.fi you will be asked if you trust the server identity. Click yes.
Now there are few options. If you didn't have a session open, you'll be taken to remote desktop, which is blank. Right click to proceed. Alterntively, you (may) now see a number of other connections on the NX-server. If you have a previous session open (suspended) on nxkajaani, search for it in the search box at the top with your username and double click it. If you don't have a session to choose, create a new one by choosing the "new Desktop" and then choose "Create new GNOME desktop".
The first time you connect to nxkajaani, you'll be introduced to the icons and menus of the NXclient. Take a moment to learn them and click "Don't show again" to speed up getting access next time. The first few items in the next list are highly recommended additional improvements.
Deselect "Match the client resolution upon reconnection" -option from the Display menu (access from "peel menu"). GUIs will work better.
To get rid of the scroll bars, maximise your NX window and select the 1:1 icon (Resize remote screen) from the "peel menu".
The default font in the terminal is ugly and small. To improve, start gnome-terminal (write
gnome-terminal on the command line) as the first thing, when you have a terminal in either Taito or Sisu. The font is then resizable on the fly.
In Windows7, if you have problems in the installation, try disabling "direct draw" from the advanced settings.
If you get an error in logging into nxkajaani, that is likely due to corrupted ssh-key (extra line breaks or spaces). Redo the ssh-key determination step above, but use the key from the plain text file available in SUI. See below for keyboard layout, to fix logging in from nxkajaani to Sisu/Taito.
If copy/paste does not work with the middle mouse button, try ctrl-alt-c / ctrl-alt-v.
If right-click does not bring up the server/application menu on the remote desktop, you can try to exit from the session and create a new desktop (in the last screen capture shown above) instead of reconnecting to the old desktop.If Mathematica stalls after the "splash" screen, kill your terminal and start Mathematica again with "--nosplash" on the command line.
If your keyboard becomes unresponsive after using the AltGr key in the NXClient version 4, disable the "alt + ctrl + 0" special meaning from the configuration menu (section input -> uncheck the "alt + ctrl + 0". More details on this page.
The key mappings for Macs are not perfect. If you don't get a dollar sign "$" with alt-4 in the x-terminal, try using the right side alt key. That has worked on all Macs we have tested…
The default keyboard layout may be wrong, and may change between logins. See FAQ. You can change that by right clicking in the background, Choose "fluxbox menu" -> "keyboard layout" and your keyboard. If yours is not listed, contact firstname.lastname@example.org. This affects connections from nxkajaani to compute servers. Don't try too many times because that will cause your username/IP to be banned.
If you get garbled fonts in some (old) applications, it could be due to the old binary not being able to utilize server side fonts, but needs those fonts installed on the client side. This has happened at least with the old emacs version in vuori. To fix this, install additional fonts to the client. The instructions and fonts can be found in here: http://www.nomachine.com/download-package.php?Prod_Id=3565
Small screen size by default the remote desktop screen is quite small. If you want to have a full screen desktop, you may need to change settings in two steps. First open the peel menu (top right corner), choose display, and activate either "full screen" or "resize remote display". Click "done", open the peel menu and choose display again, and select the other option. You may need additional steps, but the options you need are in this menu.
Terminal window handle bar outside desktop. If you open the NoMachine remote connection on a smaller screen than you used last time, some terminal window handle bars (that you can use to drag them) may be outside the screen. You can drag the window my pressing "alt" on your keyboard and dragging with left mouse button directly from the terminal window. Mouse pointer turns to a "hand" symbol when the terminal can be dragged.
Frozen session Sometimes your remote desktop session may "freeze" e.g. due to insufficient memory on the gateway machine. It may then happen, that when you try to make a new session, the client will default to the old frozen session. You may try the following workaround. In the opening dialog click "configure" and change the desktop from e.g. gnome to KDE. Save, and connect. You should now get an option to kill the old session and start a new one. Instead of the KDE desktop you'll get the same fluxbox that is started with the gnome –choice.
Ubuntu 12.10 and 14.10 versions have problems with the Desktop system (Unity). Work is in progress but in the mean time you can try these workarounds: https://www.nomachine.com/AR07K00676 and https://www.nomachine.com/AR0500591
Connection to nxkajaani fails after some tens of seconds with a message "Oops, The connection with the server was lost. Error is 108: Connection reset by peer." Try deleting the cache on your local client machine: https://www.nomachine.com/TR12K04112
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