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Building a computer for scientific computing

post #1 of 20
Thread Starter 
I am a computational biologist and have been relying on a mix of my own servers and Amazon EC2 for doing scientific computing. I have a new client who doesn't want any data outside of our firewall, so I need to build a one-off compute server for this project. Obviously the less I spend the better, since it's a one-off. The system will run Linux (probably Ubuntu) and I have no need for anything other than integrated graphics.

I was thinking about the following, but I would like to hear suggestions.

2x AMD Opteron 6272 CPU (16 core each)
Tyan S8230 Motherboard
32gb Quad memory 256gb SSD

cooling and case? I have no idea.
post #2 of 20
Quote:
Originally Posted by BrianRunsPhilly View Post

I am a computational biologist and have been relying on a mix of my own servers and Amazon EC2 for doing scientific computing. I have a new client who doesn't want any data outside of our firewall, so I need to build a one-off compute server for this project. Obviously the less I spend the better, since it's a one-off. The system will run Linux (probably Ubuntu) and I have no need for anything other than integrated graphics.
I was thinking about the following, but I would like to hear suggestions.
2x AMD Opteron 6272 CPU (16 core each)
Tyan S8230 Motherboard
32gb Quad memory 256gb SSD
cooling and case? I have no idea.

What kind of computing? Does it allow for GPU acceleration / CUDA?

post #3 of 20
Thread Starter 
Currently the software I'm using doesn't support GPU/CUDA. They're doing whole genome sequencing, so massive amounts of data. The SSD will basically be used for swap and the system will have minimal disk as the actual data lives on a large RAID array. That's next year's problem/expense, I need to put in something like a 750Tb array.
post #4 of 20
Quote:
Originally Posted by BrianRunsPhilly View Post

Currently the software I'm using doesn't support GPU/CUDA. They're doing whole genome sequencing, so massive amounts of data. The SSD will basically be used for swap and the system will have minimal disk as the actual data lives on a large RAID array. That's next year's problem/expense, I need to put in something like a 750Tb array.

750TB holy mother. eek.gif

Anyways, if the software suite you're using is nicely multi-threaded, the race between AMD and Intel is dead even as far as price/performance. If you want to sink $1000 into processors, that money will buy you essentially the same performance from either company in heavily threaded apps.

If you're workload is largely single threaded or multithreaded with some single threaded parts, then AMD doesn't stand a chance against Intel.

I'd go with a dual socket 2011 board and a pair of Xeon E5-2620's. They're both hyperthreaded six core CPU's. That totals out to 24 threads of computing power.
Heisenberg
(10 items)
 
Redemption
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CPUGraphicsRAMHard Drive
Intel Core 2 Extreme @ 2.8GHz (upgrade) Intel GMA 950 2 x 2 DDR2 667MHz (upgrade) 120GB Mushkin ECO2 
Optical DriveOSMonitorPower
Replaced with 42 W/hr aux battery Mint 17.3 1280x800 Dell 65w Dell Adapter 
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Not telling AsRock something Pixel Pusher 2 x 8 GB AMD Radeon RAM @ 1600mhz (All the VM's) 
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Cooler Master Hyper 212 Evo Windows 8.1 Pro x64 Dell U2713HM IBM Model M (CLICKY!!) 
PowerCaseMouseAudio
Antec HCG-900 NZXT Source 210 (it was cheap) Logitech G502 Schiit Modi 
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CPUMotherboardGraphicsRAM
Intel Core i5-4200U Microsoft BGA1168 Intel HD 4400 8 GB LPDDR3 Dual Channel @ 1600mhz 
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Heisenberg
(10 items)
 
Redemption
(18 items)
 
 
CPUGraphicsRAMHard Drive
Intel Core 2 Extreme @ 2.8GHz (upgrade) Intel GMA 950 2 x 2 DDR2 667MHz (upgrade) 120GB Mushkin ECO2 
Optical DriveOSMonitorPower
Replaced with 42 W/hr aux battery Mint 17.3 1280x800 Dell 65w Dell Adapter 
CaseOther
Latitude D630 Chassis Intel 7260-802.11ac 2x2 
CPUMotherboardGraphicsRAM
Not telling AsRock something Pixel Pusher 2 x 8 GB AMD Radeon RAM @ 1600mhz (All the VM's) 
Hard DriveHard DriveHard DriveOptical Drive
Crucial M4 128GB (8 second boot) Western Digital RE4 1TB Western Digital RE4 2TB Pioneer Blu-Ray Reader/Writer 
CoolingOSMonitorKeyboard
Cooler Master Hyper 212 Evo Windows 8.1 Pro x64 Dell U2713HM IBM Model M (CLICKY!!) 
PowerCaseMouseAudio
Antec HCG-900 NZXT Source 210 (it was cheap) Logitech G502 Schiit Modi 
AudioAudio
Sennheiser HD 598 M-Audio AV40's 
CPUMotherboardGraphicsRAM
Intel Core i5-4200U Microsoft BGA1168 Intel HD 4400 8 GB LPDDR3 Dual Channel @ 1600mhz 
Hard DriveOSMonitorKeyboard
SK Hynix 256GB SSD Windows 8.1 Professional 1920 x 1080p IPS Display Microsoft Touch Cover 2 
Power
48w PSU 
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post #5 of 20

Well if it's just a one-off thing, assuming everything will be running at stock, just stick with stock heatsinks and a cheap case. No need to get fancy.

post #6 of 20
Thread Starter 
Did I really misspell "building?" I'm ready for vacation!

Here's the thing. If it works extremely well, I can use the system for other purposes. I said 'one-off' because right now it's for a specific purpose for one client, and I hate to sink a ton of money into hardware for a single contract. But I do a lot of high-end computational work, so it's unlikely it would ever just sit idle.

To give you an idea of how computationally intensive some of this stuff can be, I've spooled up 774 Amazon EC2 instances at one time to get a job done. I'm not trying to impress, this is what I do for a living. So I'm always after the best bang for the buck.

Would 24 Intel cores outperform 32 AMD cores?
post #7 of 20
Quote:
Originally Posted by BrianRunsPhilly View Post

Did I really misspell "building?" I'm ready for vacation!
Here's the thing. If it works extremely well, I can use the system for other purposes. I said 'one-off' because right now it's for a specific purpose for one client, and I hate to sink a ton of money into hardware for a single contract. But I do a lot of high-end computational work, so it's unlikely it would ever just sit idle.
To give you an idea of how computationally intensive some of this stuff can be, I've spooled up 774 Amazon EC2 instances at one time to get a job done. I'm not trying to impress, this is what I do for a living. So I'm always after the best bang for the buck.
Would 24 Intel cores outperform 32 AMD cores?


That's a good question. Keep in mind that is 24 threads, not 24 cores. It's actually 12 physical cores.

post #8 of 20
Quote:
Originally Posted by BrianRunsPhilly View Post

Did I really misspell "building?" I'm ready for vacation!
Here's the thing. If it works extremely well, I can use the system for other purposes. I said 'one-off' because right now it's for a specific purpose for one client, and I hate to sink a ton of money into hardware for a single contract. But I do a lot of high-end computational work, so it's unlikely it would ever just sit idle.
To give you an idea of how computationally intensive some of this stuff can be, I've spooled up 774 Amazon EC2 instances at one time to get a job done. I'm not trying to impress, this is what I do for a living. So I'm always after the best bang for the buck.
Would 24 Intel cores outperform 32 AMD cores?

That's not bragging. that's awesome! smile.gif

Anyways, your workload definitely sounds massively threaded so either will be a good choice. The way I see it right now from the five Dell dual-Opty 6272 hosts that we've ordered vs our HP Sandy Bridge based servers, they're dead even in compute performance. We've put them under load and the differences have been +/- 10% on all tests. And we spent about the same for them.

Here's a quick chart I made using data from PassMark's Performance Test which is HEAVILY weighted towards math operations.

Heisenberg
(10 items)
 
Redemption
(18 items)
 
 
CPUGraphicsRAMHard Drive
Intel Core 2 Extreme @ 2.8GHz (upgrade) Intel GMA 950 2 x 2 DDR2 667MHz (upgrade) 120GB Mushkin ECO2 
Optical DriveOSMonitorPower
Replaced with 42 W/hr aux battery Mint 17.3 1280x800 Dell 65w Dell Adapter 
CaseOther
Latitude D630 Chassis Intel 7260-802.11ac 2x2 
CPUMotherboardGraphicsRAM
Not telling AsRock something Pixel Pusher 2 x 8 GB AMD Radeon RAM @ 1600mhz (All the VM's) 
Hard DriveHard DriveHard DriveOptical Drive
Crucial M4 128GB (8 second boot) Western Digital RE4 1TB Western Digital RE4 2TB Pioneer Blu-Ray Reader/Writer 
CoolingOSMonitorKeyboard
Cooler Master Hyper 212 Evo Windows 8.1 Pro x64 Dell U2713HM IBM Model M (CLICKY!!) 
PowerCaseMouseAudio
Antec HCG-900 NZXT Source 210 (it was cheap) Logitech G502 Schiit Modi 
AudioAudio
Sennheiser HD 598 M-Audio AV40's 
CPUMotherboardGraphicsRAM
Intel Core i5-4200U Microsoft BGA1168 Intel HD 4400 8 GB LPDDR3 Dual Channel @ 1600mhz 
Hard DriveOSMonitorKeyboard
SK Hynix 256GB SSD Windows 8.1 Professional 1920 x 1080p IPS Display Microsoft Touch Cover 2 
Power
48w PSU 
  hide details  
Reply
Heisenberg
(10 items)
 
Redemption
(18 items)
 
 
CPUGraphicsRAMHard Drive
Intel Core 2 Extreme @ 2.8GHz (upgrade) Intel GMA 950 2 x 2 DDR2 667MHz (upgrade) 120GB Mushkin ECO2 
Optical DriveOSMonitorPower
Replaced with 42 W/hr aux battery Mint 17.3 1280x800 Dell 65w Dell Adapter 
CaseOther
Latitude D630 Chassis Intel 7260-802.11ac 2x2 
CPUMotherboardGraphicsRAM
Not telling AsRock something Pixel Pusher 2 x 8 GB AMD Radeon RAM @ 1600mhz (All the VM's) 
Hard DriveHard DriveHard DriveOptical Drive
Crucial M4 128GB (8 second boot) Western Digital RE4 1TB Western Digital RE4 2TB Pioneer Blu-Ray Reader/Writer 
CoolingOSMonitorKeyboard
Cooler Master Hyper 212 Evo Windows 8.1 Pro x64 Dell U2713HM IBM Model M (CLICKY!!) 
PowerCaseMouseAudio
Antec HCG-900 NZXT Source 210 (it was cheap) Logitech G502 Schiit Modi 
AudioAudio
Sennheiser HD 598 M-Audio AV40's 
CPUMotherboardGraphicsRAM
Intel Core i5-4200U Microsoft BGA1168 Intel HD 4400 8 GB LPDDR3 Dual Channel @ 1600mhz 
Hard DriveOSMonitorKeyboard
SK Hynix 256GB SSD Windows 8.1 Professional 1920 x 1080p IPS Display Microsoft Touch Cover 2 
Power
48w PSU 
  hide details  
Reply
post #9 of 20
Thread Starter 
That's useful information. The more I read the more I'm getting concerned about the quality of the AMD 6200 series, and I have read that Linux isn't entirely stable on them. Honestly it doesn't do me a bit of good how screaming fast the CPU is when it crashes trying to run a 2-day computation.
post #10 of 20
For big money Intel do 10 core/20 threaded Xeon CPU's, a pair of these would hit $10K.....

dunx
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CPUMotherboardGraphicsGraphics
i7 - 960 Asus P6T7 WS Revolution with MIPS water blocks. XFX HD 7950 + waterblock Powercolour R9 280X 
RAMHard DriveHard DriveOptical Drive
Crucial Ballistics Tracer 6 x 4Gb 2Tb WD caviar green Crucial M4 64 Gb SSD  Sony NEC DVD  
CoolingOSMonitorPower
Apogee Drive + Allphacool 180mm rad W7 Dell 29" 21:9 IPS monitor Coolermaster 1250W PSU 
CaseAudio
Antec P280 Scythe Kama Bay Speaker 
CPUMotherboardRAMHard Drive
i7-4770K Asus Impact VI HyperX beast 2400MHz 2x 8Gb WD 1Tb caviar black x3 
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Intel X-25 SSD 80 Gb Corsair H80 W7 Panasonic 32" HDTV 
KeyboardPowerCaseOther
Keysonic wireless Silverstone 450 W SFX PSU Fractal Design Array R2 Griffin Powermate 
CPUMotherboardGraphicsGraphics
i7 870  Asus Maximus III Formula GTX 480  HD 5870 
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OCZ 4x 2Gb  WD 2TB Green Corsair H70 Dell 17"  
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