How to Build a Powerful Data-Crunching Computer, Part 2: Putting Together the Pieces

If you haven’t already seen it, check out my post on how to choose computer parts. Now I’m going to show you how to put the pieces together! I recommend watching newegg’s tutorial video if you want a bit more guidance and/or would like to see a video in addition to my photos. (Note: these instructions are for an Intel CPU build)

The first thing to do is take everything out of the boxes they shipped in and organize all of the parts.

All of my computer parts

All of my computer parts

Once you’re done admiring all of your components, clear off a workspace to start your build. Also, read the manuals for all of your components, especially the motherboard, because every one has slightly different instructions.

1. Installing the CPU on the motherboard

Take your motherboard out of the box and place it on a non-conductive surface. THIS IS IMPORTANT!! Static electricity can destroy your motherboard so be careful. I put mine on top of the box it came in (but not on top of the protective covering it shipped in).

My motherboard

Next, open up the cover for the CPU location by squeezing the levers and hinging open the cover.

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Then line up the arrow in the corner of the CPU with the arrow in the corner of the CPU slot and gently place the CPU, holding it by the edges, onto the CPU slot.

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Close the cover and gently close the latches. The plastic cover will pop off when this happens (though ‘pop’ is not always the best term–on mine I had to nudge and pick up the plastic piece, but it came off with minimal force).

2. Install the memory

Next, consult your motherboards instructions for where to install the memory. My motherboard has 8 memory slots, but I only had four memory units to install. If you don’t install them in the proper configuration, the computer may not recognize your memory (which would be problematic!). To install the memory, open up the little latch on either end (they may only be on one side) and line up the memory. The memory has two sections on it and one of them is longer than the other. Line up the short section on the memory piece and the short section on the memory slot. Then apply some pressure and push the memory into place. You’ll know they’re in properly when the latch snaps closed again.

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At this point my build differs from the traditionally suggested steps!

Most instructions, especially those for beginner builders, suggest doing an out-of-the-case build to test the parts. That’s because sometimes the pieces are defective and it’s easier to find that out before you’ve installed the motherboard into the case. However, because I didn’t have any thermal paste remover or isopropanol on hand, I didn’t want to install my CPU fan twice. So I skipped the out-of-the-case build and installed the motherboard into the case.

3. Install the motherboard in the case

The first step is to remove the side panels. Set them aside somewhere safe, and lay the case on its side, so that the main body of the computer is facing you. Then pop the motherboard backplate in the case at the back. This just pops in and takes a bit of pressure.

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Then gently slide in the motherboard, lining up the external ports with the backplate. The motherboard will sort of click into place and the motherboard’s screw holes will line up with the  holes in the case.OLYMPUS DIGITAL CAMERA

Then secure the motherboard in place with the nine screws. So as not to place excessive pressure on any one side of the motherboard, I started with the center one and then did the corners in a diagonal pattern, then finished off the remaining screws.

4. Install the CPU cooler

Every CPU cooler is different so follow the instructions! I had to remove the fans on the sides of the cooler itself, then install the special screws to lift the cooler above the CPU and then install the brackets. OLYMPUS DIGITAL CAMERA OLYMPUS DIGITAL CAMERA

Before installing the main CPU unit, apply a pea-sized blob of thermal paste in the center of the CPU. My CPU cooler came with thermal paste, which is what I used, but you can also buy fancy thermal paste separately. Some people spread the thermal paste all over the CPU, but the paste will spread when you place the CPU cooler on top, especially once the CPU heats up, so it’s not necessary to spread it out.

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Place the CPU cooler on top of the brackets and screw it into place. Then I placed the fans back onto the cooling unit. It is important to keep in mind air flow! I made sure both fans were positioned to blow the air out of the case through the back, using the arrows on the fans to determine which direction the air is flowing.

OLYMPUS DIGITAL CAMERAPlug the fans into the motherboard in the appropriate CPU fan plugins (and feel free to plug in any built-in case fans at this point too!)

5. Install the Graphics Card

The graphics card is best placed in the PCI slot closest to the CPU. To do so, remove the plates on the back of the case that align with the PCI slot. Then open the latch on the PCI slot and slide the graphics card into place, pushing gently to secure it in place. Then secure the graphics card in place with the screws that were removed with the back plates.OLYMPUS DIGITAL CAMERA

6. Install the power supply unit (PSU)

The PSU fits in at the bottom of the case below the motherboard. There is one fan on the PSU an dyou can face it up, towards the inside of the case, or down, towards the outside. It doesn’t make a huge difference, and what may be more important is lining up the screw holes on the PSU with the screw holes on the case. I installed my PSU with the fan facing up, towards the inside of the case, because it was best aligned that way, and because my computer will be positioned on the floor on top of carpet so it wouldn’t pull in much air from the bottom anyway.OLYMPUS DIGITAL CAMERA

Once you’ve screwed in the PSU, start connecting the PSU to the motherboard and graphics card. My PSU came with a bunch of labeled cables, which fit exactly into the PSU in labeled slots. The motherboard’s instruction manual will help you find where to plug in the power cables. OLYMPUS DIGITAL CAMERA OLYMPUS DIGITAL CAMERA OLYMPUS DIGITAL CAMERA OLYMPUS DIGITAL CAMERA

7. Plug in the case components

The case has power and LED connectors that must be plugged into the motherboard for the front panel power button and USB plugs to work, and this is a good time to plug them in.

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The piece labeled 1394 is a firewire connector, which my motherboard doesn’t support, so I tucked it in the back where it would be out of the way.

8. Check the build!

This is a perfect time to test the build, if you hadn’t already tested it out of the case. Plug in the PSU and if you so choose plug in your monitor. Then turn on the computer by pushing the power button on the case (since you’ve connected the case’s power button to the motherboard already!). The motherboard has an LED display to show error messages, so you don’t necessarily need the monitor. If you do use the monitor, the BIOS screen will pop up. Check to make sure the computer recognizes your CPU and memory, and that there are no error messages. If there are no warnings or errors, well done! It worked!

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9. Install PCI Express components, such as the WiFi card

Similarly to how you installed the graphics card, remove the back place that lines up with the appropriate PCI express slot, and gently place the WiFi card into the slot. Secure it in place with a screw.

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10. Install the hard drives

The hard drives fit snugly and precisely into the hard drive slots. Then plug the SATA power cables into the PSU and the hard drives, and plug SATA cables into the hard drives and into the motherboard. OLYMPUS DIGITAL CAMERA OLYMPUS DIGITAL CAMERA OLYMPUS DIGITAL CAMERA OLYMPUS DIGITAL CAMERA

11. Install the optical drive, if applicable

The optical drive (a.k.a. DVD/CD drive) pops cleanly into one of the drive slots. The front cover piece on my case had a pinching mechanism to remove it, and then the optical drive slid easily into the slot. Then connect it to the PSU with a SATA power cable and to the motherboard with a SATA cable. OLYMPUS DIGITAL CAMERA

12. Cable management

Finally, before replacing the side panels on the case, organize the cables so that they take up the least amount of space possible inside the case and in the small amount of space in the back (behind the panel holding the motherboard. There is no ‘right’ way to do this, but you want as much air flow as possible inside the case, so as many cables as possible should be secured in the back. They can be held together and organized with zip ties, twist ties, and/or velcro ties. I used whatever I had on hand. Then replace the side panels on the case and hook up the monitor, keyboard, and mouse. Turn on the computer and check out the BIOS. Verify again that everything looks OK, and if it does, then you’re done! OLYMPUS DIGITAL CAMERA

I stored all of my extra parts, pieces, and manuals–plus the UPC codes from the boxes–in the motherboard box. Also keep track of the CDs that came with your components–you’ll need them in Part 3 to install all of the drivers you’ll need for your computer.

Next up is installing an operating system and setting up the computer. I’ll post a tutorial about installing Windows 7 and setting up the computer in a week or so, so keep an eye out for Part 3!

 

 

How to Build a Powerful Data-Crunching Computer, Part 1: Choosing the Parts

Most of my research hinges on the analysis of ‘big data’. I have terabytes of DNA and RNA sequence data that I am analyzing, and the analysis of that much data requires a powerful computer with a whole lot of RAM. Many people use supercomputers, which are like many powerful computers hooked up together, but there is often a long queue to use the computing resources, meaning that you may have to wait a while for everyone else to finish up using the supercomputer before your data can be run. Supercomputers are also a bit more complicated to use because you have to submit a job and you can’t just run your programs like you would on your own computer.

Since so much of my research requires these sophisticated computers, I’ve decided to build myself a computer! I thought it might be useful to some other scientists if I share my experiences choosing computer parts and then putting them together to make a sophisticated data-crunching machine!

The first step to building a computer is of course choosing the parts.

1. RAM

The first thing to decide is how much random-access memory (RAM) you want. RAM is what programs use to store data not saved in files, such as temporary information. In DNA analysis, how much RAM you have is very important because often you need to compare many sequences to find matches, and all of the potential matches are stored using RAM. The most RAM you can get before having to upgrade to a server instead of a desktop is 64 GB (which is a lot). For my lab computer, I went with 64 GB, but for my own personal computer I chose 32 GB, but left room to upgrade if I wanted to (i.e. I chose 4 x 8GB RAM, leaving an additional 4 slots available if I want them).

Once you’ve decide how much RAM you want, you need to decide what type of RAM. Technology is constantly changing, and there is a ‘new’ type of RAM available: DDR4 (as opposed to DDR3). DDR4 is faster but more expensive, so there’s a tradeoff there. I chose to go with DDR4, but DDR3 should work just as well.

Choosing a brand can be confusing, because there are so many companies out there! I went with G.SKILL Ripjaws series RAM because it came well-recommended from more experienced computer builders.

2. CPU

The core processing unit (CPU) is the next component to choose. This is where most of your computer’s power comes from. The type and amount of memory you chose will determine what type of CPU you can get. Intel is generally the CPU brand of choice, and at the moment their cutting-edge CPU model is the Intel i7. To match my desired 64 GB of RAM, I needed a LGA2011-v3 socket type, so that narrowed down my search to three types. Because I’m price-sensitive, I chose the Intel i7 5820k.

3. Motherboard

Once the CPU is picked out, you can choose a motherboard. I did most of my searching for parts on newegg.com, because you can narrow your search results based on the things you want. For instance, since I chose an Intel CPU, I searched “intel motherboard” and then clicked the box for “LGA2011-vs” and under “Maximum Memory Supported” I chose “64GB”. Then I looked through the other specifications I might be interested in (number of ports, expansion slots, etc.) and again asked other people about brands that are good, and I wound up going with the Asus X99 series of motherboards.

Using newegg.com to help narrow down options

Using newegg.com to help narrow down options

One thing to note is that reviews of motherboards are invariably going to be on average middle of the road. This is because there will always be some cases where the hardware is defective, regardless of the company, and those reviews will drag the average rating down.

Once you’ve chosen your RAM, CPU, and motherboard, choosing the rest of your components doesn’t need to happen in any particular order. You just want to make sure everything is compatible. I recommend using pcpartpicker.com to check compatibility of the components you choose.

4. Storage Size and Type

The first major decision you need to make is whether you want to run your operating system off of a solid-state hard drive. Solid state drives don’t have moving pieces like traditional spinning hard drives, but they are quite pricey in comparison. The main benefit is that they allow you to start up your operating system and programs much more quickly and are less prone to mechanical failures. I chose to go without one for my personal computer build, although I’ve got one in my lab computer and love the speed.

Then you need to decide how many other hard drives you want and how much storage space you want. I chose two 4 TB hard drives because my data takes up a lot of storage space, but that becomes a personal decision about how much you need to store and price.

5. Power supply

A necessary component of any computer is the power supply unit (PSU). The EVGA brand was recommended to me, and I chose to go with an 850W PSU because I might need quite a bit of power to run all of my analyses.

6. Graphics card

A graphics card is necessary to run the computer’s display. To choose a graphics card, look at your motherboard’s specifications to see what type(s) and how many PCI slots it has to narrow down your search results. For data analysis you don’t need a particularly fancy graphics card with a bunch of overclocking ability like you would if you were building a gaming computer. The EVGA brand was recommended to me, so I chose based on compatibility, brand, and price.

7. CPU Cooler

This is an important choice. Since I will be working my CPU pretty hard, I chose to go with a dual-fan CPU cooler, the Cooler Master Hpyer D92.

8. Case

The case is important. You want one big enough to fit all of your components and have a bit of breathing room, so I recommend a mid-tower design. I also chose one that came with several built-in fans and a couple of USB slots on the front. These cases can get pretty fancy, so as long as it fits your motherboard and has enough space to keep your computer cool, you can probably choose based on extra features and coolness factor (how many LED-lighted fans do you want?)

9. Wireless adapter

Some motherboards come with on-board wifi, but if yours doesn’t you may want to buy a WiFi adapter.

10. CD/DVD Drive

This is a purely optional component. Having an optical drive will help you install the drivers that come with all of your components, but it is not necessary

11. Accessories: Keyboard, mouse, monitor

I’m pretty happy with a standard wired mouse and keyboard, so I went for the cheap Microsoft set. But I did spring for a nice 27″ monitor. These things, and others (speakers etc) are completely up to your personal preferences.

Important Tip: Shop around!! 

There are many retailers selling computer parts, and some have different promotions going on at different times. newegg.com is usually pretty low-priced, but I recommend also checking TigerDirect.com, Best Buy, ncixus.com, and Amazon. I bought almost all of my components from Newegg, because it was the cheapest, but I did get a couple of items from other vendors.

If you’re having trouble deciding on components, read reviews, watch Youtube videos, and talk to experienced computer-builders. It can be overwhelming but I learned a lot about how computers work just by shopping around for the various components.

For how to put the pieces together, check out Part 2: Putting the Pieces Together!