Notes about open source software, computers, other stuff.
After an upgrade of one of my Ubuntu server that runs Nagios, I ran into the following error message (again…) when I tried to issue a command from the web interface:
Error: Could not stat() command file ‘/var/lib/nagios3/rw/nagios.cmd’!
This post by Barry O’Donovan shows very nicely how this problem can/should be fixed in Ubuntu. Much cleaner than chmod/chown-ing the directories myself. Thanks Barry!
Sun Grid Engine (SGE) is a bath queue system that can be used to distribute computation intensive tasks across one or more servers/CPUs. SGE has a graphical configuration utility called qmon, but when you start it on a remote machine (using SSH), you may end up with errors like this:
Warning: Cannot convert string "-adobe-courier-medium-r-*--14-*-*-*-m-*-*-*" to type FontStruct Warning: Cannot convert string "-adobe-courier-bold-r-*--14-*-*-*-m-*-*-*" to type FontStruct Warning: Cannot convert string "-adobe-courier-medium-r-*--12-*-*-*-m-*-*-*" to type FontStruct X Error of failed request: BadName (named color or font does not exist) Major opcode of failed request: 45 (X_OpenFont) Serial number of failed request: 329 Current serial number in output stream: 340
The warnings are not really a problem, but the error is. It can be solved by running the following on the client (i.e. your local) machine (assuming it runs Debian or Ubuntu):
sudo apt-get install xfonts-75dpi xset +fp /usr/share/fonts/X11/75dpi xset fp rehash |
I’m currently teaching at the Summmer School in Statistical Omics in Split, Croatia. A great experience!
Because of the computations involved in the project work, we have access to a server. However, since the machine is part of a university cluster, I haven’t been given full root permissions (in fact, I’m only allowed to use sudo to install packages).
Now, the problem I had to solve was that I needed to distribute a certain file (.Renviron) to each student’s home directory. Normally I’d use sudo to do that, but the admin hadn’t allowed me to use cp via sudo. Furtunately, I had a list of user names and passwords for the students (because I had to distribute those), so I thought I’d use su - to change to each student’s account and copy the file, something along the lines of
echo PASSWORD | su - |
and then loop over each account. Unfortunately, while testing the script I found out it wouldn’t work since su complained:
su: must be run from a terminal |
Then I remembered the expect tool, which executes commands based on what it ‘sees’ on the command line. In this case I wanted it to enter the password at su‘s prompt. This is the expect script I came up with, it accepts two command line arguments, the user name and the password:
#!/usr/bin/expect -f set user [lindex $argv 0] set pass [lindex $argv 1] spawn su - $user expect "Password: " send "$pass\r" expect "$ " send "cp -i /common/WORK/school/lennart/.Renviron .\r" expect "$ " send "ls -l .Renviron\r" expect "$ " send "exit\r" |
The script was wrapped in the Bash script that I had already written:
#!/bin/bash # # This script is used to copy files from this directory to the # home directories of the users listed in $USERFILE. USERFILE=accounts.txt SRCFILE=/common/WORK/school/lennart/.Renviron while read user passw; do ./copy_file_to_users.expect $user $passw done < $USERFILE |
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