38.17 Dell Precision T3500 Workstation (Nyx)

38.17.1 Nyx Usage

Nyx is a 64bit workstation and server for web server, desktop, and data mining.

38.17.2 Nyx Hardware

The workstation has an Intel Quad Core Xeon 64bit CPU, 6GB of RAM, two 1TB hard drives, nVidia NVS 295 video chip, a DVD\(\pm\)RW dual layer burner, and 22inch screen. An additional 19inch screen was added.

38.17.3 Nyx Specifications

From the dmidecode, lspci and lshw commands and /proc/cpuinfo:

Spec Details
Machine: Dell Precision T3500 (dmidecode)
CPU: Intel Quad Core Xeon CPU W3520 @ 2.67GHz (cpuinfo)
Bogomips: 5333 [140112] (cpuinfo)
Memory: 6GB DIMM DDR3 3x2GB using 3 of 6 slots 3x1066MHz (lshw)
            & 6GB DIMM DDR3 3x2GB using 3 of 6 slots 3x1333MHz (lshw)\\
Network: | Broadcom NetXtreme BCM5761 Gigabit Ethernet eth0 tg3 (lshw)|
Disk: | 1TB 931GiB Samsung HD103UJ /dev/sda (lshw)|
                | 1TB 931GiB Samsung HD103UJ /dev/sdb (lshw)|
                | 1500GB 1397GiB Seagate ST31500341AS SATA external /dev/sdc (lshw)|
                | 2TB 1862GiB WD My Book 1140 SCSI USB /dev/sdd (lshw)|
DVD: | Optiarc DVD+/-RW AD-7203S (lshw) |
Video: | Nvidia G98 [Quadro NVS 295] (nouvea) |
Audio: | Intell HD Audio Controller snd_hda_intel (lshw) |
Boot: | Grub |
Kernel: | 2.6.28-15-generic |
                | 3.11.0-12-generic [140112]|

38.17.4 Nyx Operating System

The machine came with MS/Windows Vista Business pre-installed and this was first set up on booting the machine. Ubuntu 13.10 was initially upgraded to from 13.04 but there were stability issues with the kernel version and nouvea video driver. A clean install of Ubuntu 13.10 was undertaken [140113]. Video driver issues continue with Unity and so GNOME Shell is used and is stable. Upgrade to 14.04 went smoothly [140419].

38.17.5 Nyx Install Log

38.17.5.1 27 August 2009

Download ubuntu-9.04-desktop-amd64.iso from ftp://ftp.iinet.net.au/pub/ubuntu-releases/9.04/. This was burnt to CD and following an F12 on boot was used to boot Nyx.

Standard Ubuntu install. The options chosen: Language: English; Location: Sydney; Keyboard: USA. Partition: described below; Who are you?: Enter the details; Migrate documents and settings: Select nothing; Install; Restart.

Partition (MS/Vista was already installed on /dev/sda1 and /dev/sda2):\ | Spec | Details | |:–|:–| | MS | 73M & sda1 not touched| | MS | 10G & sda2 not touched| | MS | 50G & sda3 Orig 989G| | / | 928G & sda5 ext3| | swap | 10G & sda6| | /home | 1TG & sdb1 ext3|

On starting, the Update Manager kicked in as well as the Hardware Drivers application to indicate that there are restricted drivers available. Starting the Hardware Drivers application indicates the NVIDIA accelerated graphics driver (version 180) is available. Click on Activate to have it installed. On the next restart the screen looks just great and the nvidia-settings application is activated when trying to set the Display options. Also Install Updates using the Update Manager.

Some applications installed include: most emacs-snapshot ess auctex libglade2-dev r-recommended ggobi r-cran-rgtk2 r-cran-cairodevice r-cran-rggobi ssh nfs-server ubuntu-restricted-extras

Add in the Medibuntu (Multimedia, Entertainment and Distractions In Ubuntu) repository for Skype and DVDs. See https://help.ubuntu.com/community/Medibuntu. Installed: skype.

Install rattle.

38.17.5.2 12 January 2014

Download the Ubuntu 13.10 image for 64bit install and burn to DVD on Kyral. Reboot and choose F12 to boot from DVD. Then choose Try Ubuntu to run the live version from DVD. Test Ubuntu to ensure dual monitors work just fine and network connected. Looks great though screen saver puts the main monitor to sleep whilst the second monitor is just blanked (under kernel 3.8.0 with Ubuntu 13.04 both monitors go to sleep).

Whilst running the live version do backups:

$ sudo mkdir /a1
$ sudo mount /dev/sda1 /a1
$ sudo rsync -av /a1/etc/ /media/ubuntu/sabrina/nyx.etc.140112/
$ sudo rsync -av /a1/var/ /media/ubuntu/sabrina/nyx.var.140112/
$ sudo rsync -av /a1/usr/local/ /media/ubuntu/sabrina/nyx.local.140112/

Clean install of Ubuntu 13.10 from DVD using dash icon. Choose English. Choose to download updates while installing. Choose to install third-party software. Clicking on Continue and then cursor turned busy bit there was no further activity for quite some time. Eventually a popup notes that we had /dev/sda mounted and asked if it should be unmounted. It is reported that the delay is not an issue on a clean drive.

Next option is to Erase Ubuntu 13.10 and reinstall. There is an option to Reinstall Ubuntu 13.10 which keeps currently installed software where possible, but my aim here is a clean installation. By default choose to use the entire disk /dev/sda for Ubuntu, deleting the 2 current partitions overwrite empty disk space.

Ubuntu will use a default partition of the drive. From a previous installation /dev/sda1 is a 900GB partition formatted as ext4 mounted on / and /dev/sda5 is 100GB of swap. To retain this partition choose the choose advanced partitioning tool.

Choose location. Choose English (US) keyboard. Enter your name, computer name, username, and password. Log into Ubuntu One.

The system is then installed onto the chosen partition. Once completed we are asked to reboot the computer. Both screens are functional and at the highest resolutions (1680x1050 for the 22" and 1280x1024 for the 19") on reboot. From System Settings I rotate my second screen anti-clockwise.

Test this configuration out for a while before mounting my home drive (from /dev/sdb1). It will use a new empty home drive for now (on /dv/sda).

After reboot, the Software Updater (an icon in the Dash on the left hand edge of the screen) notices that 153.8MB of updates are available and provides an option to Install Now. Do so and then if requested, restart the computer.

Open a Terminal and install wajig to ensure everything is up to date and to install my usual suite of applications:

$ sudo apt-get install wajig
$ wajig update
$ wajig dist-upgrade
$ wajig install ssh meld most
$ wajig install emacs ess auctex bzr
$ wajig install nfs-server
$ wajig install keepassxc
$ wajig install transfig xfig gsfonts-x11
$ wajig install r-recommended r-cran-* r-bioc-*

Tasks:

  • Set up /etc/fstab:

    • List UUIDs using sudo blkid
    • Create mount points /media/sabrina, /media/lactans, /var/www/access, /var/www/repository
    • Mount /home, /media/sabrina, /media/lactans, /home/cpwil, /var/www/access, /var/www/repository
    • Do sudo mount -a to ensure all mounting succeeds.
    • Reboot and ensure all mounts worked.
  • Using my old home folder resulted in a locked up session on reboot! Clean out the old home folder and start fresh.

  • Had to write a script using various xrandr commands to get both displays going.

38.17.6 Troubleshooting

38.17.6.1 13.10 Screen Saver Issue [140112]

After a fresh install of Ubuntu 13.10, the second screen is no longer being put to sleep, and only blanking.

38.17.6.2 12.04 Upgrade Issues [120429]

Serious Issues:

  • Sound is now choppy—changed settings to headphone only out and was okay again.
  • Using Unity 3D results in all cores 100% CPU on some unity or window manager processes at times. So back to Unity 2D for now. Seems to happen when I click to close a tab in Chromium. gtk-window-decorator and unity-panel-service are running 100% CPU. As of 11 May 2012 it has not happened for a while.
  • Revelation has lost its menus in the global menu?
  • File Open dialogs take forever to open up: revelation, keepassx. Fixed after an upgrade [120411].
  • wallch is now all in Arabic. That was a bug in wallch. Had to edit to set language=4.
  • Inserting a USB thumb drive did not mount it? I installed usbmount and that seemed to mount it though it does not show a desktop icon. Fixed after an upgrade [120411].

38.17.6.3 10.10 Upgrade Failed to Boot [101206]

On upgrading to 10.10 I could not boot with the new kernel (2.6.35-22-generic). This is a known kernel bug but won’t be fixed for Ubuntu 10.10 apparently. The older kernel will boot (which I was doing until eventually I installed a new version of VirtualBox and that could not compile with the old kernel because the kernel header package is no longer available for that version). The temporary patch is to add pci=nocrs to the kernel line in /boot/grub/menu/list. This will probably be overwritten next time update-grub is run.

38.17.6.4 Not Automounting [090918]

For some reason (probably because after a reboot it takes a few seconds too long for the USB drive to settle'') some of my drives that used to automount in older systems (presumably because they took longer to boot, thus giving time for the drive thesettle’’) no longer get mounted at boot time. Yet, when I run the command to mount all the automount drives after booting, they all get mounted:

$ sudo mount -a

I notice that in /etc/init.d/mountall.sh ext3 is not listed to be mounted. I tried adding the following to /etc/rc.local but that did not work either?

mount -a -t ext3

The relevant /etc/fstab entry is:

UUID=... /mnt/lactans ext3 defaults 0 0

38.17.6.5 Partitioning Options [090827]

On first attempt when the partition option was presented it claimed This computer has no operating system on it.'' (seems to be referring to /dev/sdb1) and offers toInstall side by side, choosing between them each startup’’ (presumably noticing Vista on /dev/sda). It mentions that with the Use the entire disk'' optionThis will delete Windows Vista (loader) and install Ubuntu 9.04.’’ This then ends up installing Ubuntu in a 2.5GB partition on /dev/sdb5!

So reinstall, and choose to ``Specify partitions manually (advanced)’’, setting up the desired structure.



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