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
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.
- 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 simplify 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.
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
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"
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
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 /usr/nevis/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
See this
page.