Installing workstations

Workstations in the group are 64-bit (a.k.a. x86_64 or amd64) machines set up to run both Windows 7 and CentOS Linux. When you came into the group, odds are a preconfigured workstation was placed in front of you, ready to rock. But how was it configured, you ask? Read on...

Beginning

It should be fairly obvious that you'll need an assembled PC to work with. Not so obvious is the software you'll need:

• Windows 7 x64
• CentOS 5.5 x86_64 (1 of 2)

Other than operating system discs, you'll need the following Windows software discs:

• Microsoft Office 2010 32-bit
• CorelDRAW Graphics Suite X4
• EndNote X4 Media - Windows (These have machine-specific license keys!)

Finally, you'll need the administrator flash drive. You know the drive of which I speak. Keep it secret. Keep it safe.

Windows

This section details installing the Windows 7 OS and software.

OS

Place the Windows 7 DVD into the drive and reboot the system. This will require the BIOS to be configured to boot optical discs before the hard drive. Once the prompt comes up, choose 'Install now'. Accept the license agreement and choose 'Custom' on the next screen.

You should now arrive at a screen that shows the current partition state of the drive. First, click on 'Drive options (advanced)'. If partitions exist, delete them by selecting the partition in the list and then clicking 'Delete'. Now, click 'New' and enter a partition size (in MB) that equals about half the total drive space. It doesn't have to be exact; the partitioner will round to the nearest sector anyways. The installer will give you some garbage about creating extra special partitions for Windows system files, and that's fine. Once the Windows partition was made, proceed.

All the other options (time zone, language, etc.) will be self-explanatory. For automatic updates, choose 'Use recommended settings'. The installer will at some point ask for a user account and password; make this your cluster username and password, or the cluster username and password of whoever will use the system most.

Updates

Once you've logged into your account, don't think that Windows is installed. It will need at least two hours of babysitting while it installs the largest pile of updates you've ever witnessed. You will repeat the following process until no more updates exist:

1. Click on the Windows icon (for old-timers, that's the 'Start' button)
2. Click on 'Control Panel'
3. Click on 'System and Security'
4. Click on 'Check for Updates' under the 'Windows Update' heading
5. Click on 'Check for Updates' in the left-hand pane
6. Install all available updates
7. Restart the computer after updates install
8. Go back to Step 1.

Patience, grasshopper.

Configuration

You will have to configure a few things in Windows.

Power management

In Control Panel => System and Security => Power Options, select High performance from the list. You may have to click 'Show additional plans' to see this option.

Remote desktop access

In Control Panel => System and Security => System, select Remote settings in the left-hand pane. Under 'Remote Desktop', select Allow connections only from computers running Remote Desktop with Network Level Authentication (more secure).

Software

Typical members of this group need a plentiful plethora of packages installed onto their Windows systems in order to function as researchers. Here's what you'll need to install:

• Google Chrome
• Anti-virus
• Adobe Reader
• Microsoft Office
• EndNote X4
• CorelDRAW X4
• ACD/NMR 12
• Java
• NMRViewJ
• PuTTY
• HP LaserJet drivers
• Dell Color Laser drivers

Chrome

Open Internet Explorer. Click the Stop button about a billion times until IE actually stops loading the page. Navigate to Google. Take Google up on its recommendation to download Chrome. The rest is cake.

Anti-virus

Open Chrome and navigate to is.unl.edu. Under 'Quick Picks', click on 'Anti-virus'. Click on 'DOWNLOAD HERE'. Click on 'WINDOWS 64bit Version'. The rest is cake.

Adobe Reader

Open Chrome and navigate to get.adobe.com/reader. The rest is cake.

Microsoft Office

Insert the Office DVD and select 'Run autorun.exe' when the popup comes up. The rest is cake.

EndNote X4

Make sure any Microsoft Office programs are closed. Insert the EndNote X4 CD and select 'Run autorun.exe' when the popup comes up. The rest is cake. Now, restart Windows and log back in. Then, open Microsoft Word. Click on 'EndNote X4' in the top bar. Then click on 'Go to EndNote'. If you get the message, Invalid Class String, then go here to find the solution.

CorelDRAW X4

Insert the CorelDRAW DVD and follow the steps. The rest is cake.

ACD/NMR 12

ACD Labs offers a free version of their 1D and 2D NMR processor software for academics. Open Chrome and navigate to this address, then click 'Download'. You'll need to set up a user account to download the software. Once you've got the installer downloaded, just run it and follow the steps. Yep, the rest is cake.

Alternatively, you should be able to run nmrproc_academia12.exe from Z:\bworley\admin\software without having to download anything or make any accounts.

Java

Open Chrome and navigate to this address. Click on 'Free Java Download' and follow the steps. Cake.

NMRViewJ

This software is now non-free, but we have the last/latest available free version on the cluster. Run nvjinstall8_0_3.exe in Z:\bworley\admin\software\nmrviewj and follow the steps. Cake.

PuTTY

Best for last! Open Chrome and navigate to this address. Click on putty-0.62-installer.exe to download the installer. Run the installer; all the default options are fine.

Once PuTTY is installed, you'll need to insert the administrator flash drive. In the flash drive, go to ssh-rsa\clients\myusername, where myusername is the cluster username that you're setting the computer up for. In that directory, there is an id_rsa.ppk file. Copy that file somewhere that only the current user has read access to, such as C:\Users\myusername. Now, open PuTTY and type myusername@bionmr-c1.unl.edu into both the 'Host Name' and 'Saved Sessions' text boxes. In the left-hand pane, click the plus sign next to 'SSH' and click on 'Auth'. Click 'Browse' and open the id_rsa.ppk file in the location you copied it to. Finally, click back to 'Session' in the left-hand pane and click 'Save' under 'Saved Sessions'.

You're ready to rock. Return the administrator flash drive to its sacred resting place.

HP LaserJet drivers

Open Chrome and enter hp laserjet 1320n in the search bar. The first or second real option will be the HP driver download site. Go there and select Microsoft Windows 7 (64-bit). On that page, download the HP Universal Print Driver for Windows PCL5. Run the installer. You want to set up a traditional printer with the following IP: 129.93.61.205.

Dell Color Laser drivers

FIXME: Information not yet available

Linux

This section details installing and configuring the Linux OS.

OS

Insert the CentOS DVD and reboot the computer. When the CentOS boot prompt comes up, type linux text and hit enter. Most of the options will be self-explanatory until you get to the partitioning. You will select Use custom layout and click next.

The partitioning of linux systems in the group is done as follows:

• 128 MB of ext2 mounted on /boot (made at the beginning of the free space)
• All remaining space allocated as ext3 and mounted on /
• 2048 MB of swap (made at the end of the free space)

Make the partitions in the above order. After making the boot partition, subtract 2048 MB from the remaining free space to get the size of the / partition. Then use the rest of the free space (about 2048 MB, but it will rarely be exact) as swap.

You should now have a partitioning scheme that spans the entire disk that looks something like this:

• sda1: Windows system files (few hundred MB)
• sda2: Windows partition (few hundred GB, about half the drive)
• sda3: Linux boot partition (128 MB)
• sda4: Extended partition
• sda5: Linux root partition (few hundred GB, about half the drive)
• sda6: Linux swap partition (roughly 2048 MB)

Everything else will be much more self-explanatory, and the defaults are A-OK for almost all the other options.

Configuration

You will have to configure the system a bit more to get it talking with the cluster and running properly. Once the system boots up, quit out of any configuration menu that may be open. Then, log in as root and perform the following actions:

Add cluster NFS mount points

install -d -v -m 777 /DATA
install -d -v -m 777 /PROGRAMS
echo 'bionmr-c1:/home/DATA /DATA nfs defaults 0 0' >> /etc/fstab
echo 'bionmr-c1:/home/PROGRAMS /PROGRAMS nfs defaults 0 0' >> /etc/fstab
mount -a

Add sudo access to group members

echo '%bionmr ALL=(ALL) ALL' >> /etc/sudoers

Add user accounts

For this one, you'll have to insert the administrator flash drive first. Give the expertly configured CentOS kernel a few seconds to find the flash drive and then barf all over your terminal about it. Hit enter a few times. For this example, we'll assume the kernel gave the flash drive a device node at /dev/sda1. If that's not true and the mount command below gives you an error, run fdisk -l to see where the drive device node was made. Now do this:

mkdir /mnt/flash
mount -t vfat /dev/sdb1 /mnt/flash
cd /mnt/flash
cd passwd
./update.sh
cd ../ssh-rsa
./update.sh
cd
sync
umount /mnt/flash
rmdir /mnt/flash

For every user that needs to use the computer, you'll need to run the following command:

echo 'source /PROGRAMS/.setnmr' >> /home/username/.cshrc

NVIDIA drivers

install -v -m 755 /DATA/bworley/admin/software/nvidia/NVIDIA-Linux-x86_64-290.10.run ./
./NVIDIA-Linux-x86_64-290.10.run

Select 'Yes' for both the 32-bit compatibility libraries and to run nvidia-xconfig.

Default runlevel

sed -e 's@id:3:initdefault:@id:5:initdefault:@g' -i /etc/inittab