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Category: Configuration

To access weekly online backup on canopus last updated 2024 August

Newest update 2024 Aug to reflect that backups are have been stored on canopus: for several years:

Go to canopus:/thuban2-backups

Bruce has an automatic (cron) job do a weekly backup of thuban onto canopus.

On canopus,

df -h gives the various mount points, incl
“Filesustem” /dev/mapper/centos_canopis-thuban2–backups”\
” Mounted on”  /thuban2/backups

Navigate down to whatever file you’re looknig for, and copy over to a safe place (Careful: do not overwrite newer file of same name on thuban!)

See also post on root superuser privileges on thuban2  (although current post you are reading deals with canopus, which is where weekly backups are stored).

–joel

aastex setup (latex) and emulateapj

1. download aastex.cls  and emulateapj.cls from the web and place  in /usr/share/texmf/tex/latex/misc/

(you will probably need superuser privileges to do this [or sudo]).

2. type texconfig rehash.  This updates the paths where tex looks for files; eg the above.

3. that should be it! I got aastex to run on mirzam.

4. Note that /usr/share is NOT SHARED ACROSS OUR COMPUTERS, so the above needs to be done on any computer on which one wishes to use aastex. (A simpler workaround is to just put aastex.cls and emulateapj.cls in whatever directory the user has the .tex source file.)

(there are a variety of tools to find the latex default paths, etc. See the web, as I already forgot the many I had to use to figure out the above.)

(note that tex and latex files tend to be in (NONSHARED) /usr/share/texmf/.)

At the top of the .tex file, place one of the  commands:

\documentclass[12pt,preprint]{aastex} or
\documentclass[manuscript]{aastex}

which use the asatex.cls file to generate typewriter-like preprint or manuscript files; or 

\documentclass{emulateapj}

[This emulates apj format: see http://hea-www.harvard.edu/~alexey/emulateapj/ ]
In either case, a useful command to put a comment on leading page is:

\slugcomment{Draft 2011 Aug 21 skeleton from Joel and  Andrew}

which is placed after abstract and keywords.
–Joel

 

Quota Check

Added a script to the bashrc, zshrc, and csh.cshrc files that automatically checks if you are over your quota.

Every time you open a new terminal, run an xterm, or ssh into a computer it should echo “Quotacheck OK (/home/$USER is <used/softcap>% full)” if you are under quota. If you are over quota it will tell you, so either delete files or talk to Joel about increasing your quota size.

Install Mathematica 7

Put in Mathematica 7 CD, ensuring that it appeared on the desktop.
Open a terminal window and cd to /media/Mathematica/Unix/Installer
Run ./MathInstaller.
(For some reason the Mathematica Installer won’t open unless you run it from the terminal)
Note, if it throws an error that says “/bin/sh: bad interpreter” point the shell directly at MathInstaller by typing:
/bin/bash ./MathInstaller

Choose default install directory:

/usr/local/Wolfram/Mathematica/7.0/

Allow selinux modification

Choose default script directory:

/usr/local/bin

For password configuration choose option (1):

(1) Single machine
Install a password specific to this machine. Mathematica will launch,
and you can enter your password.

This is what the Installer does upon selection of option (1).

xxxxxxxxxxxxxxxx
Configuring Single-Machine password…

Mathematica 7.0 for Linux x86 (32-bit)
Copyright 1988-2009 Wolfram Research, Inc.

You will need to get a password from your
license certificate or from Wolfram Research
(http://register.wolfram.com).
Machine name:   antigone.Physics.Carleton.edu
MathID: 7108-71426-20286

You will need a valid license ID and password in order
to proceed. Go to http://register.wolfram.com or
consult your Getting Started documentation.
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

Then, go to (http://register.wolfram.com) and type in the information the Installer gave you; Machine Name, MathID, and Carleton’s License (L3125-8812). The registration web page will ask for the name of the person registering, supply either Joel Weisberg or Nelson Christensen, but give Bruce’s email address (or your own email, just forward the forthcoming email to Bruce).
So it will look like:

Name: Joel Weisberg
Organization: Carleton College
Department: Physics and Astronomy
Email address: bduffy@carleton.edu

This will cause an email to be sent the email address you entered with the password needed to finish the installation.

Here are the contents of the email I received:

xxxxxxxxxxxxxxxxxxxxxx
Version 7.0 password(s) were generated for license: L3125-8812

Here is the content for your mathpass file:

antigone.Physics.Carleton.edu
7108-71426-20286
L3125-8812
5157-617-135:2:8:20080701

Requestor information:

Name: Joel Weisberg
Organization: Carleton College
Department: Physics and Astronomy
Email address: bduffy@carleton.edu

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

The install script then asked for:

Carleton’s License (L3125-8812)
The Requestor (Nelson Christensen/Joel Weisberg)
The organization (Carleton College)

Then the Installer asked for the password (the one from the email I received was 5157-617-135:2:8:20080701).

The password will be the last string of digits given in the email. (And the only string you didn’t have before the email)

Bumped user quotas due to Firefox disk usage

The /home user quotas for all existing users has been bumped from 80M to 200M to handle Firefox’s big disk footprint.

Our former quota of 80M was insufficient for the latest version of Firefox. By default Firefox uses 50M for file caching and another 30M->90M to stash a per-user copy of an anti-phishing blacklist file. Together, these two things could consume the entire original quota of 80M through normal Firefox usage. Rather than turning off Firefox’s cacheing and anti-phishing features I asked James to bump the quota from 80M to 200M and edited the ‘new user’ checklist post with the new values.

Video Drivers no longer necessary

[Update: ATI open sourced the fglrx drivers, which is why this step is not necessary]

As of RHEL5 kernel version 2.6.18-128.1.6 (Apr 30 2009), Red Hat has inproved their kernel and default ATI drivers to the point where it is no longer necessary, as far as I know, to install ATI’s own drivers. This should now be considered an optional part of the install.

I have removed the ATI drivers from the astronet machines, because they are no longer worth the SELinux and kernel update hassel. To remove the drivers from machines that originally had them, I used these commands:

#>rm -rf /etc/X11/xorg.conf
#>cp /etc/X11/xorg.conf.original-0 /etc/X11/xorg.conf
#>yum -y reinstall xorg* mesa* gnome-screensaver kernel-headers
#>reboot

This should (1) Prevent the kernel and xorg from trying to load the 3rd party driver module and (2) Replace any ATI-compiled xorg and/or rendering libraries with the official Red Hat ones…which are, finally, good.

Denyhosts

A small daemon called Denyhosts has no been installed onto all astronet boxes as of April 15 2009. This will block IP addresses from remote access to linux services (sshd, nfs, samba, etc) after a remote host attempts, but fails, to connect after a certain number of times. This will go a long way to prevent our linux machines from brute force attacks where remote zombies try repeatedly to log in and guess our passwords.

It creates a log file at /var/log/denyhosts
It uses a configuration script at /etc/denyhosts.conf (#>service denyhosts restart if you want changes to take effect!)

I have made the directory /etc/secret/clientconfig/denyhosts to store install files and setup info. The .rpm in this directory which contains “fc3” in its filename is for RHEL4, whereas the .rpm with “fc6” in the filename is for RHEL5. The configuration script, which I copy to /etc/ after rpm installation, is also in this directory.

For more information, an excellent FAQ is maintained by the author at http://denyhosts.sourceforge.net/faq.html

People who are accidentally blocked must contact Bruce or I to be unbanned. If you have your username correct, you shouldn’t be banned until failing to enter your password correctly 10 times in succession.

-James

Note: In addition to the above, you must also edit /etc/hosts.allow and /etc/hosts.deny. Here’s a copy of both files on a properly configured system:
=========================================
hosts.allow:
=========================================

#
# hosts.allow This file describes the names of the hosts which are
# allowed to use the local INET services, as decided
# by the '/usr/sbin/tcpd' server.
#

ALL: localhost.localdomain
#sshd: ALL
ALL: .carleton.edu

 

=========================================
hosts.deny:
=========================================

#
# hosts.deny This file describes the names of the hosts which are
# *not* allowed to use the local INET services, as decided
# by the '/usr/sbin/tcpd' server.
#
# The portmap line is redundant, but it is left to remind you that
# the new secure portmap uses hosts.deny and hosts.allow. In particular
# you should know that NFS uses portmap!

ALL EXCEPT sshd: ALL

# DenyHosts below this line

Cyclic Dependency in Java SDK Packages (RHEL 5.3 only)

As of Feb 2009, the RHEL5.3 yum repository has a cyclic dependency in some java packages that may be installed as dependencies by some openoffice.org packages. This will cause yum to be unable to update.

openoffice.org applications are java-based, and some of them require a java-SDK in addition to the normal java system. RHEL 5 provides a bunch of different java packages from many sources (Sun, IBM, BEA, etc….). If you don’t have an SDK installed when installing some openofice.org packages, yum will select one for you in order to fulfill dependencies. Beginning in RHEL 5.3, yum defaults to choosing the java sdk package from BEA if not instructed otherwise.

The java-1.x.x-bea packages, unfortunately, currently are involved in a cyclic dependency – which makes yum very unhappy when told to update.

To avoid this, install the Sun SDK package ahead of time:
#> yum install java-1.6.0-sun-devel
…after this, install whatever openoffice package you need!

Our automatic package setup script (which installs the packages and apps used on all default astronet machines) at /etc/secret/clientconfig/install-programs/install_packages.sh has been updated to reflect this problem by specifying the sun package explicitly. Only machines where packages are being installed by hand should need to worry about this.

–James