Contents
Introduction
A high end workstation can be characterized as follows:
- The computer is always powered on
- It is continuously used for running complex calculations
- The risk of hardware failure should be minimal
- Down-time due to maintenance should be minimal
To reach these goals, enterprise class components should be used and the hardware should have redundancy built into it to cope with hardware failures.
In this guide a selection of enterprise class components is listed, that, when put together, will fullfill these requirements with ease.
For software installation help, please refer to the software tutorial.
Memory
8GB DDR II, buffered, ECC
Considerations:
Most functional MRI analyses will not consume over 1 GB of RAM. Therefore a good rule of thumb is to install 1GB of RAM per CPU core. Should you plan to do DTI group analyses, it would be wise to install 2GB memory per core in 4GB memory modules, summing up to 16 GB of memory.
Choice:
It seemed best to choose 2GB memory modules running at 800Mhz. Not only the maximum speed is obtained, but also 4 out of 8 memory slots of the mainboard used which allows later memory upgrades.
Options:
The mainboard can take a maximum of 64 Gb of memory with a maximum memory module size of 8 GB. Always make sure to choose compatible memory before buying it. Memory vendors often tell you exactly which of their components fit with which maiboard. See the memory selector from Kingston, Infineon, Elpida.
Graphics:
PNY Geforce 8800 GTX
Considerations:
Although most computations in the analysis of neuroimaging data are CPU intense, displaying the results is a key part of this analysis. Marketing departments of graphics companies try to convince buyers that for CAD applications, their professional hardware line delivers best performance. This is partially true, but only when the software application supports the specific hardware features and specially tuned drivers are available to obtain the increased performance. This type of support is not available for most neuroimaging software. Therefore, desktop graphics cards (or gaming cards) which run for about one-third of the price of their professional counterparts seem to be the best choice.
Choice:
The PNY Geforce 8800 GTX with 768MB of graphics memory. Nvidia can be considered market leader and its cards are well supported under linux and by most neuroimaging applications. Some applications, for example FreeSurfer, favor Nvidia hardware over ATI hardware. A single Geforce 8800 GTX allows quite complex visualizations and should GPU (graphics processing unit) computing become mainstream in neuroimaging, this card most probably allows you to do that.
Options:
Although the Geforce 8800 GTX can be installed in pairs using a technology called Scalable Link Interface (SLI), the mainboard hosts only two PCI-Express sockets. The second PCI-Express socket will be used by a RAID card in this configuration.
Chassis:
Supermicro SC743T-645B
Choice:
The Supermicro SC743T-645B offers a durable chassis for of the components. Additionally, it allows you to replace defective harddrives without tools. If combined with the 3ware RAID card, you can even replace a defective hard disk while the machine is running. No downtime, no hassle and its safe.
Monitor:
Samsung 245T
Choice:
The 245T 24" widescreen monitor affords you the ability to be efficient and perform at an optimal level. It is also stylish and feature rich. Starting with it's glossy body style which can be desk or wall mounted and continuing with its ability to have multiple screens visible at one time. With its 6ms response time, clear and vivid images and multi connection capability you are in a position to accomplish all that you need and more.
DVD Drive
Samsung SH-S203B/BEBN
Choice:
Blue ray or HD DVD are not mainstream yet and therefore overly expensive. Since most data can be transferred via the network, or a fast USB disk, there is no need to make a choice for Blue Ray or DVD yet. The Samsung SH-S203B/BEBN is a quality DVD burner and connects to the SATA interface on the mainboard.
Floppy Drive:
Supermicro 1.44Mb Floppy
Choice:
Despite that the floppy era seems over, the absence of a floppy disk can be a nuisance when you install a computer based on components. It is not expensive, so get one.
Keyboard:
Microsoft Natural Ergo Keyboard 4000
Choice:
A nice ergonomic keyboard.
Printer:
HP Color LaserJet 1600
Choice:
Writing a report, printing an article, todays neuroimager needs color printing at the deskside. This HP color Laserjet offers an economical solution combined with professional grade prints.
Processor
2x Intel Core 2 Quad E5472
Considerations:
This Quad core processor is a member of the latest 64 bit Intel Xeon processors, featuring a 1600Mhz front side bus, thereby increasing the bandwidth between the CPU cores and other mainboard components. Each processor features four cores that run at 3 Ghz and 12 MB of level 2 cache.
Choice:
The High End Workstation hosts two of these processors, amounting to 8 cores to run analyses on, allowing to run up to eight single subject analysis at the same time.
Options:
Check this table of Intel Xeon processors to see which other processors will fit in this system.
Processor Cooling:
Supermicro SNK-P0020A4
Choice:
A quality copper heatsink with a 4-pin Pulse Width Modulated PWM fan for less noise.
Mainboard
Supermicro X7DWA-N
Considerations:
The influence of the mainboard on overall computer performance and stability cannot be overemphasized. However, in out of the box computers, this component is often of unknown source and its quality can therefore not be assessed before buying the machine.
Choice:
The X7DWA-N is a quality component from a brand that has made quite a reputation on the heavy duty market. I own two Supermicro based machines myself and am extremely satisfied with this. The choice for this specific mainboard is because it features a few next generation technologies such as a 1600 Mhz FSB and PCI – Xpress 2. This allows for the installation of the faster 1600Mhz processors and also the number of graphics cards can be expanded up to two at full bus speed (x16).
Intelligent Platform Management Interface (IPMI):
Supermicro AOC-SIMLP-B(+)
Choice:
With IPMI, administrators can view the hardware status remotely, receive an alarm automatically if a failure occurs, and power cycle a system that is non-responsive. This is useful for people who like to access the workstation remotely.
Raid:
3ware 9650SE-8LPML
Considerations:
Neuroimaging data consumes a lot of disk space. For a typical neuroimaging study, one should reserve about 4 - 6 GB of data space per subject. This allows the safekeeping of original and processed files. Depending on the number of users that you have for your system and the number of studies that need to be stored on the system, my choice may be provide you with too much space, or too little. Try to make an estimation of how much data you want to house on your system and simply choose larger or smaller disks to solve this problem.
Another issue with vast amounts of data is that it is difficult to create backups. Safety of data can be achieved by introducing RAID level 5, 50 or 6 into your system, at the cost of some disk capacity. You can use the RAID Calculator at the bottom of this page, to see how the RAID level influences the total data capacity in the machine.
Although the Supermicro mainboard comes with a standard RAID controller, in this setup extra performance and safety are chosen by adding a seperate RAID controller.
Choice:
The 8 port 3ware 9650SE-8LPML is an excellent RAID card. It has good linux support.
Options:
Alternatively you can choose the 3ware 9690SA-8I
Raid Battery Backup:
3WARE BBU-MODULE-04
Choice:
A Backup Battery Unit enhances the RAID adapter card with the following features:
- Maximum reliability with cached write data protection.
- Safeguards data against power interrupts during system resumption.
- Eliminates silent data loss by retaining unwritten data until user intervention.
- Uses and protects drive write cache for unmatched data protection and maximum performance.
Disks:
500 GB Seagate Barracuda 7200.11
Considerations:
Seagate offers quality harddisks in which the company believes itself. Therefore a 5 year warranty is provided on these disks.
In the current configuration, if scaled in RAID level 6, two drives can break at the same time without risking data loss. Since this workstation is expected to be always powered on, assume that at least one disk will malfunction within the first three years. If this is within the warranty, they will be replaced by Seagate without additional charge.
A 500GB disk volume is common these days. Should you require more disk space, you can choose either the 750 or 1 TB disks instead. You can calculate how much disk space this would give your preferred raid scheme with the RAID calculator at the bottom of this page.
The computer chassis of this workstation will fit a maximum of 8 drives. Nevertheless it is a good habit to buy at least one spare disk with the exact characteristics as the drives RAID array. This allows you to replace a drive immediately when encountering a disk failure.
Choice:
8 x 500 GB Seagate Barracuda 7200.11 in RAID 6 setup.
Options:
Bigger and smaller, both exist. If you prefer the 3Ware SAS controller instead of the SATAII controller, it is best to buy SAS disks instead of SATA disks to get the benefit of its increased performance and durability. Find a good SAS disk here.
Mouse:
Logitech G5 laser Mouse
Choice:
This mouse features a very high level of precision. Recommended if you are working a lot with a mouse, for example to draw regions of interest or segment structures.
Raid Calculator
Use the RAID calculator to calculate how much disk space a given raid scheme would offer with the disks you selected. Remember, a formatted disk is always somewhat smaller so choose values like 480 GB for a 500 GB disk to get an accurate estimate.
