Graphics mode

Some of the Linux cluster machines display a plain-text login screen, instead of a graphical user interface. You can login easily enough, but how to start up the graphics?

The answer: type startx; if you're a bit more confident with X issues, you can use xinit.

Incidentally, the reason why some older systems do not initially have a graphical login screen is that, in the early days of the Redhat Linux distribution (versions 8 and earlier), it was by no means certain that the operating system would be compatible with the graphics card in the computer. It was much easier to configure the system with a text-based login, so that if any graphics problems developed, they could be debugged. Nowadays this is not as much of an issue, and I tend to enable the graphical login screens with current versions of Fedora Core.

By the way, if you're reading this on a text-based system, you must know how to use a text-based web browser such as lynx, links, or elinks. Good for you!

Speed issues

• Here's a tip if it seems to take a long time to login to the cluster.

• If the machine with your home directory is not working properly, it will take a long time to read your mail.

• Another reason it takes a long time to read your mail: Are you running a mail reader on two different machines at once? Before you come into work, quit your mail reader at home (and vice versa).

• If the network seems slow, you can monitor the traffic.

• If your machine seems slow, check if there's a program running that you did not expect. The top, w, ps, and pstree commands can be helpful. The free command can tell you if you're running low on memory; the df command can tell you if you're running low on disk space, and the du command can tell you which files and directories are taking up space.

The "setup" command

• I tried to use the setup command, but it doesn't work.

  ..or..

  I'm told that the variable ${NevisAppBase} points to the application directory. But when I try to use it, it doesn't have a value.

  Some things to check:

  • Are using using setup or ${NevisAppBase} in a batch script? This alias and variable are normally only defined in interactive or login shells.

    The solution is to add the -l option to the shell invocation in the first line of your script; e.g., change

    #!/bin/bash to
    #!/bin/bash -l

    Be careful! If your login setup scripts do things that you don't want done in your batch scripts, use the -t 1 test to see if you're in an interactive environment; see the section on the less command below for more information.

  • If you're using tcsh as your shell, make sure you have the following command in your ~/.cshrc file: source ${NevisAppBase}/adm/nevis-init.csh Or, if you're using an sh-style shell, make sure you have the following command in your ~/.profile file: source ${NevisAppBase}/adm/nevis-init.sh If the initialization command is not there, then the system will not be able to find setup at all.

  • Are you using additional software (e.g., the D0 software suite) that also defines a setup command? If so, that command will override the Nevis version.

Using ssh or sftp without typing a password

This guide contains the information you need.

• What is the different between a password and and a passphrase?
  • The term "password" is normally used for the text you type in to identify yourself to a computer system.

  • The term "passphrase" is typically used to identify yourself to a particular program. For ssh, the "passphrase" refers to a code to verify your identity when you use a particular ssh key.

• Why would you use a passphrase instead of a password?

  A passphrase would protect you if the files in your ~/.ssh directory were stolen. Without your passphrase, the contents of ~/.ssh/identity or ~/.ssh/id-rsa are useless. If you use your computer in an environment where it's reasonable to assume, for example, that strangers would use your unguarded terminal to copy your files while you walked away for lunch, then passphrases are good idea.

  However, they are also cumbersome to use; ssh and sftp need your passphrase every time you use your private ssh key. If you want to create an automated job to transfer files via ssh (with rsync. for example) the use of a passphrase can make things complicated. To some extent, you can simply the use of passphrases via the program ssh-agent.

  Another possiblity is to just hit RETURN when ssh-keygen prompts you for a passphrase. This is the most convenient setup, but not necessarily the most secure; remember the "wandering stranger" example above. Also, although the contents of ~/.ssh are protected from casual viewers, they are not protected from system administrators, and (at least in theory) can be copied from the backup disks.

  So the decision to use passphrases boils down to: How paranoid do you wish to be?

Connecting to Linux from a Windows machine

• I have a Windows machine. I want to connect to the Linux cluster, run programs that create windows (like ROOT or emacs), and see those windows on my machine. How do I set this up?

  You need two things:

  1. An X-windows emulator for Windows;
  2. A way to forward X11 connections via SSH.

  There are a number of programs that can do this. Most of them cost money. At Nevis, we have a site license for two programs, Exceed 7.0 (an X-windows emulator) and SecureCRT (a terminal program with SSH); instead of the latter, many people prefer Putty, which is available for free.

  Here's how to set up the connection with those two programs:

  • In Exceed, start the configuration program. You can do this by opening the "Xconfig" icon in the Hummingbird folder; alternatively, you can start Exceed, right-click on the program tab in the taskbar, and select Config under the Tools menu.
  • Double-click on the "Communications" icon. Select "PASSIVE" from the pop-up menu.
  • Close all the Exceed windows; click "OK" if the program asks if it should restart the server. From now on, when you run Exceed the only change you'll see is the Exceed tab in the taskbar.
  • Start SecureCRT. Don't make any connections; click "Cancel" on any dialog boxes.
  • Under the "Options" menu, select "Global Options".
  • Select "Default Sessions" in the left-hand pane.
  • Click the "Edit Default Settings" button.
  • In the left-hand pange, click on "X11" under "Port Forwarding".
  • Make sure "Forward X11 packets" is checked.
  • Click "OK" and "Accept" on all dialog boxes to close the above windows and accept the settings.

  Fortunately, this is a one-time-only setup; hopefully you won't have to do this again. In the future, just start Exceed, then start SecureCRT. Any new sessions you create in SecureCRT will be able to display X-windows using Exceed.

  If you're using Putty instead of SecureCRT, look through the Connection options; you must turn on "X11 Forwarding".

• OK, I did everything you said, but it doesn't work.

  If you created and saved any sessions with SecureCRT before you changed the X11 forwarding, those sessions probably still have X11 forwarding turned off.

  Under the "Options" menu, select "Session options". Turn on X11 port forwarding as in the above instructions. Then select select "Save settings" from the "Options" menu. Log off, quit SecureCRT, then start it again.

Transferring files between Linux and Windows machines

• I have files on a Windows machine. I want to copy them to one of the Linux systems, but that system isn't running FTP. Will you turn on FTP for me?

  Only in the most extreme cases. It is much secure for you to install SSH or SCP on your Windows system.

  Two popular options are:

  • Putty, a command-line interface for SSH and SCP.
  • WinSCP, with an Explorer-like interface for transferring files.

• Do you have Samba available on any of the Linux systems?

  There is a Linux SMB server named tango.nevis.columbia.edu that acts a central file server for the Windows systems at Nevis. Contact a systems amdministrator if you need to have files shared on this server.

Java web-browser plugin

• I want to use java from my web browser. I've tried setup java, and I've tried the installing the plug-in following the directions in the browser, and it still doesn't work.

  The command setup java only sets up a version of Sun's Java Development Kit; it doesn't have anything to with your web browser. The instructions for installing the plug-in generally won't work properly unless you have administrator access to your Linux system; even then, there's one crucial step that a lot of people forget. (Let's be honest: it's a step that I always forget.)

  That step is to create a link in your browser's plug-ins directory. In most cases, you don't actually have to install or use setup or anything else, other than the following commands:

  # Create the plugins directory if it's not already there mkdir -p ~/.mozilla/plugins cd ~/.mozilla/plugins # Link the java plugin from the Nevis applications server ln -sf /usr/nevis/java/default/jre/plugin/i386/ns7/libjavaplugin_oji.so . Don't forget that final separate period (".") at the end of the last command.

  Note that these instructions only work for Mozilla-style browsers (Firefox, Mozilla, Seamonkey, Netscape, etc.). If you're running a more exotic browser, you'll have to search Sun's web site for specific instructions.

The "less" command

• When I try to use the less command, instead of seeing the contents of a file I see messages that I usually see only when I log in. How do I fix this?

  If the .cshrc, .profile, or any other shell start-up file in your home directory prints any text, less will display that text instead of your file.

  To get rid of this behavior, test to see if you can write to standard output before you actually print anything. For example, assume you're using tcsh shell, and you've put the following statements in your .cshrc file:

  echo ".cshrc here" echo "I am logged on to machine $hostname" Replace this with: # "-t 1" is true only if standard output is enabled; # if not, then don't write any messages. if ( -t 1 ) then echo ".cshrc here" echo "I am logged on to machine $hostname" endif An equivalent test in an sh-style shell: if [ -t 1 ]; then echo ".profile here" echo "I am logged on to machine $hostname" fi

• A FAQ within a FAQ: Why does less do this?

  In RedHat Linux, less has a facility to display other types of files in addition to plain text. For example, if you type:

  less ${NevisAppBase}/src/archive-tar/gcc-2.95.2.tar.gz you will see a list of the compressed files in gcc-2.95.2.tar.gz, instead of binary garbage. However, to enable this facility, less has to invoke a sub-shell. If that sub-shell writes anything to standard output, you'll see that output instead of your file.

Kerberos

• How do I use Kerberos from the Nevis Linux cluster?

  See this page.

AFS

• I want to access files via AFS from the Nevis Linux cluster. How do I arrange this?

  Ask a systems amdministrator to install the AFS client software on your machine. See the Nevis AFS page for more information.

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