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ArcGIS for Desktop has native 32-bit data processing limitations, which is somewhat offset by 64-bit background processing capabilities. Additionally, multiprocessing and parallel processing capabilities are limited on ArcGIS for desktop.

Given these software limitations, what are the pros and cons of using a workstation over a desktop computer for geoprocessing with ArcGIS for Desktop? For example, how do vector and raster based processing speed tests compare between these classes of computers? Is the additional expense of a workstation worth the cost of the software bottleneck?

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It may be helpful to define what you mean by workstation vs. desktop, as they can mean very different things to different people. For example, I consider a workstation computer as having more than 4 cores (and sometimes more than one processor), having high-speed storage (such as SSDs or 10-15K RPM HDDs in a striped RAID configuration), and having a workstation-class graphics card (e.g. NVIDIA Quadro/Tesla, AMD FirePro). This can get very expensive (case in point) and is probably overkill for most ArcGIS applications.

You should also state what your budget is, describe what you intend to do and what size and kinds of data you'll be working with. Will you be doing multiprocessing, with e.g. Python or .NET? Do you need to do real-time 3D visualizations? Are there other processor, memory, or graphics-intensive applications that you will be using other than ArcGIS?

That said, nowadays, in general, I think your choice is whether you want a quad-core processor or one with more cores, and whether to get an SSD or not (I would definitely suggest getting one and putting your OS and applications, including ArcGIS, on it though).

See also these related questions:

Update: Regarding your edit, the links are specifications for barebones computers, e.g. no RAM, storage, processor or graphics card is included. So it basically comes down to what kind of case, motherboard and power supply you are getting. I don't think this is an appropriate forum for discussing the differences between these various components, suffice to say, the workstation barebones would able to take greater amounts of RAM (with ECC) and more powerful graphics cards. I personally would have a hard time justifying it just for ArcGIS.

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