Simison's system notes for the CCG Ubuntu server

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Table of Contents

Dec. 5, 2012
Permanently setting users PATH
    The CCG Ubuntu server uses /home/user/.bashrc
    With admin priveledges, edit .bashr lines:

#PATH info export PATH=/opt/openmpi:$PATH export PATH=/opt/:$PATH export PATH=/opt/openmpi/bin:$PATH export LD_LIBRARY_PATH=/opt/openmpi/lib:$LD_LIBRARY_PATH export PATH=/opt/openmpi/etc:$PATH

Dec. 5, 2012
    Set up Galaxy server to autostart on boot.
    Edit the /data/galaxy/galaxy-dist/contrib/galaxy.debian-init sample file to refelct the correct path to Galaxy /data/galaxy/galaxy-dist.
    Copy the file to /etc/init.d/galaxy:

$ sudo cp /data/galaxy/galaxy-dist/contrib/galaxy.debian-init /etc/init.d/galaxy

Configure for start at boot with:

& update-rc.d galaxy defaults

The screen should print:

Adding system startup for /etc/init.d/galaxy ... /etc/rc0.d/K20galaxy -> ../init.d/galaxy /etc/rc1.d/K20galaxy -> ../init.d/galaxy /etc/rc6.d/K20galaxy -> ../init.d/galaxy /etc/rc2.d/S20galaxy -> ../init.d/galaxy /etc/rc3.d/S20galaxy -> ../init.d/galaxy /etc/rc4.d/S20galaxy -> ../init.d/galaxy /etc/rc5.d/S20galaxy -> ../init.d/galaxy

Feb. 23, 2013
    installing Nvidia CUDA driver to enable use of BEAGLE libraries for apps using GPU processing.
    I followed Utkarsh Jaiswal's excellent online instructions.
    The first thing to do is to confirm which Nvidia drivers are installed:

$ lsmod | grep video

If the returns something like:

$ Video 19596 nouvaeu

this means you have the deafault open source Nvidia drivers. If the command returns nothing, try:

$ lsmod | grep nvidia

if you see something similar to:

Nvidia 11270980 38

this means you have the proprietary CUDA drivers installed. I had to install the requisite tools (not sure what these are):

$ sudo apt-get install freeglut3-dev build-essential libx11-dev libxmu-dev libxi-dev libgl1-mesa-glx libglu1-mesa libglu1-mesa-dev

I also had to "blacklist" required modules:

$ sudo vi /etc/modprobe.d/blacklist.conf

and add the following lines at the end of the file:

blacklist amd76x_edac blacklist vga16fb blacklist nouveau blacklist rivafb blacklist nvidiafb blacklist rivatv

To clean up Nvidia files

sudo apt-get remove --purge nvidia*

I then downloaded the LINUX: CUDA 5.0 Production Release version "" for Ubuntu 11.10 (Our current Ubuntu version is 12.04) into ~/Downloads/. I changed permissions of ""

$ cd ~/Downloads $ sudo chmod +x

Then reboot. Do not log into the GUI interface, enter Ctrl+Alt+F1 to use terminal login. The CUDA drivers will not install if the display manager is running (ours is LightDM). So kill this before installinig.

$ sudo service lightdm stop

Now run the cuda file ""

$ sudo

You will be presented with the option to accept a license agreement. And you will be presented with three option of installing the drivers, the toolkit and the samples. install all but samples, we will not need them. Now edit the ~/.bashrc file and add:

export LD_LIBRARY_PATH=/usr/local/cuda/-5.0/lib64:/lib export PATH=/usr/local/cuda-5.0/bin:$PATH

Feb. 25, 2013
    IT purhcased a Drobo backup box for the Ubuntu server (\\\BSimison). It is a self-contained box running a Drobo
    proprietary file format called BeyondRAID.  The system supports CIFS, SMB, and AFP.
    The following is how I mounted the Drobo drive:
    First I made a directory as a mountpoint.

$ mkdir -p /backup/Drobo

then I mounted the networked Drobo box to that mountpoint

$ sudo mount -t cifs // /backup/Drobo -o username=*****,password=*****,rw,uid=*****,gid=*****

The 'username' and 'password' are my credentials assigned to the Drobo box, 'uid' and 'gid' are my user id and group id on the Ubuntu box. I then added this mount to the etc/fstab so that it would automatically mount the Drobo box on reboots. First backed up the fstab file:

$ sudo cp /etc/fstab /ect/fstab.bak

I then edited the fstab with the folllowing lines at the end of the file:

# mounting networked Drobo backup drive to /backup/Drobo /backup/Drobo cifs -o rw,nolock,root 1 2

Mar. 11, 2013
    To back up a specific MySQL database I have only had success with the phpMyAdmin web interface. The command line option of: 

$ mysqldump -u xxxx -p xxxx embiotocid_1_radtags > embiotocid_1_radtags.sq

throws the error:

$ mysqldump: unknown variable 'local-infile=1'

I tried numerous options recommended by various online help forums, but none worked. Including deleting the local-infile=1 line in /usr/local/share/stacks/sql/mysql.cnf and restarting MySQL with:

$ sudo service mysql restart

but got the same error. I was able to log into phpMyAdmin, select the database I wanted to export (backup), select all tables, select the "Export" tab and then selected the "Quick - display only the minimal options" option.

Mar. 28, 2013
     The system froze while "ejecting" a MacOS formatted external drive connected via USB. Upon restarting, the GUI login screen did
     not load; only a terminal login option was presented. The error message inlcuded, among many other things, that the NVIDIA
     drivers did not match. I tried to restore an old /etc/X11/xorg.conf file and rebooted with no success. I then tried to manually start
     an X session with: 

$ sudo startx

This failed to start the X session. I then tried to restart the lightdm service (X display manager) with:

$ sudo service lightdm start

Eventually, I decided to reinstall the NVIDIA drivers (really should be a last resort option). First updating apt-get:

$ sudo apt-get update $ sudo apt-get install nvidia-current

This resolved the problem.

June. 06, 2013
     To install an ssh daemon so users can use the ssh protocol to access the Ubuntu server I simply used the apt-get command:

$ sudo apt-get install openssh-server

This starts the ssh daemon and configures the init.d files such that it starts with boot up.