Nevis Linux Cluster FAQ

The answers to many Frequently Asked Questions about the Nevis Linux cluster. It covers subjects not addressed by the other Linux cluster pages.

If you're looking for answers to questions about mail, try the mail page. For questions about printers and printing, try the printing page.

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.
    • The du command can tell you which files and directories are taking up space.

The "module" command

I tried to use environment modules (the module command), but it doesn't work.

Some things to check:

  • Are using using module in a batch script? The Nevis set up is 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 -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 /usr/nevis/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 /usr/nevis/adm/
    If the initialization command is not there, then the system will not be able to find the Nevis software environments at all.

  • Are you using additional software (e.g., the LArSoft software framework) that uses the same packages (e.g., ROOT, Geant4) than the Nevis versions? If so, the software versions will likely conflict.

Using ssh or sftp without typing a password

This guide contains the information you need.

What's 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 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

If you want to connect to Linux and run X11 programs on a Windows machine, I recommend MobaXterm.

Transferring files between Linux and Windows machines

Popular options are:

  • MobaXterm can copy files, in addition to its SSH and X-window functions.
  • Putty, a command-line interface for SSH and SCP.
  • WinSCP, with an Explorer-like interface for transferring files.

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

Java web-browser plugin

With the recent security problems associated with Java, please consider using some other method to accomplish your task.

Now that you've been warned: If you want to run Java via a web browser in Linux, it should work. All of the systems on the Linux cluster have a version of Sun's Java Development Kit installed; as of Dec-2009 this is JDK version 1.6.0. If you're running the standard web browsers on these systems (e.g., Firefox), the Java plug-in should work without any additional changes by you.


less displays login messages instead of a file.

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"
An equivalent test in an sh-style shell:
if [ -t 1 ]; then
   echo ".profile here"
   echo "I am logged on to machine $hostname"

Why does less do this?

In Redhat-flavored 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.


See this page.


To access files via AFS from your system, ask a systems administrator to install the AFS client software on your machine.

Topic revision: r3 - 2015-02-03 - WilliamSeligman
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