Scientific Computing Workstation Build

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Ricardo_20

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Jul 15, 2016
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Hello!

So there have been several questions on scientific PC builds.. However, for my scenario, they're either all outdated, or the budgets are far off.

Bambiboom has given some excellent advice, and I'm hoping he/she responds to this thread!

My budget is about $3000, and I'm looking for a PC that can perform extensive FEA simulations (such as COMSOL) and high quality CAD rendering. I have a build I made from PC part picker, and I'd be nice to have it reviewed by someone with great experience in this area.

http://pcpartpicker.com/list/Qczjyf

The most expensive part is obviously the processor. We may upgrade up to 128 GB RAM in the future, so I hope the processor+motherboard combination allows for such an upgrade. Thanks in advance!

PS: To satisfy the budget, I'm willing to sacrifice the monitor & keyboard/mouse for pricier components related to performance
 
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bambiboom
Ricardo_20,

In my view, the applications are so calculation intensive, problems using FEA and rendering potentially long-running, that the double precision should be as high as possible and as COMSOL can integrate fully multi-threaded applications such as Matlab, a dual Xeon / ECC RAM / Quadro or Firepro is the general solution.

A useful performance level is somewhat difficult in the budget, but to open the conversation:

OPTION 1: Upgrade Used Workstation:

HP Z620 - 1 x E5-2690 - 8GB - 1 x 1TB 7.2K - Standard Video > $1,100

To this add:

128GB DDR3-1600 ECC registered RAM: about $400
Used Quadro K4200 (4GB): about $500 (This is chosen to allow adding a Tesla coprocessor with a Fermi-series...
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If CAD rendering is a significant requirement, you may want to consider a Nvidia Quadro or AMD FirePro GPU, vice the gaming oriented GTX 970.

Also, you should consult the manual for the chosen motherboard to see what kind of memory is required to support more than 32GB of memory.

Good luck building your number crunching beast.
 
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Thanks for the input! Really appreciate it.
What do you mean by " to see what kind of memory is required to support more than 32GB of memory." ?



 
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Oh ok I see, thanks.
Also, what difference does it make between a gaming oriented GPU and the GPUs you specified for CAD rendering?
 
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Ricardo_20,

In my view, the applications are so calculation intensive, problems using FEA and rendering potentially long-running, that the double precision should be as high as possible and as COMSOL can integrate fully multi-threaded applications such as Matlab, a dual Xeon / ECC RAM / Quadro or Firepro is the general solution.

A useful performance level is somewhat difficult in the budget, but to open the conversation:

OPTION 1: Upgrade Used Workstation:

HP Z620 - 1 x E5-2690 - 8GB - 1 x 1TB 7.2K - Standard Video > $1,100

To this add:

128GB DDR3-1600 ECC registered RAM: about $400
Used Quadro K4200 (4GB): about $500 (This is chosen to allow adding a Tesla coprocessor with a Fermi-series processor)
Samsung SM951 512GB AHCI M.2 SSD > $290 (This will contain the OS/ Programs and active projects and libraries
M.2 to PCIe adapter card > about $30
Used LSI 9260-8i SAS/SATA RAID controller : about $130
2X Seagate Constellation ES.3 3TB drives (RAID 1) : $320

_______________________

TOTAL: about $2700

The idea is to start with a single CPU system and add the second processor later if needed. This would be an outstanding system for the use: 8-cores /16 threads @ 2.9 / 3.8GHz with a single threaded performance of 1889, 128GB of ECC registered RAM, an excellent 4GB Quadro, one of the fastest SSD's today and a solid storage disk subsystem.

A good feature of this approach is that in the future:

z620 2nd CPU riser : about $180
2nd Xeon E5-2690: about $200
Used Tesla K20 GPU coprocessor > About $900

Gives the system 16-cores /32 threads and the Tesla K20 coprocessor. would have tremendous calculation power, rendering capability, and the single threaded applications will run well. Visualization- 3D CAD modeling would be quite good with a 3.8GHz clock speed, though comparatively, the single-threaded performance of the i7-6900 is one of the best -single CPU's don't have to synch the other processor and typically have a speed advantage. For example, a Xeon W3690 and X5690 are both 6-cores with 3.47 / 3.73GHz clock speeds, but the single-only W3690 has a Passmark average of 9519 (single-threaded = 1571), and the X5690 numbers are 9211 and 1523. So there is some sense in having a single CPU system if there is a heavy priority of use on single-threaded applications, but unless the work is almost entirely 3D CAD modeling, more cores will be advantageous.

Another positive in this approach is that the system may be prepared for use in only hours, in place of days total in researching, ordering, assembling. wiring, configuring a system from parts. and, then there is a support structure for the system in updating BIOS and drives, parts and etc.

If it's necessary to use all new components- well ,a used GPU, there are of course very good possibilities, with a single CPU system or a dual motherboard starting with a single 8-core:

OPTION 2: New Workstation:

BambiBoom PixelCannon COMSOListicRenderMathematicaSimulucious iWork TurboSignature Extreme CalcuBlast 9800 ®©$$™®£™©™_7.16.16

CPU: Intel Xeon E5-2630 v3 Eight-Core Haswell Processor 2.4 /3.2 GHz 8.0GT/s 20MB LGA 2011-3 CPU, OEM > $600

Xeon E5-2630 v3

CPU Cooler: Noctua NH-U9B SE2 CPU Cooler >$59.99

Motherboard: Supermicro X10DAI-O Dual LGA2011/ Intel C612/ DDR4/ SATA3&USB3.0/ A&2GbE/ EATX Server Motherboard> $363

RAM: 32GB (4X 8GB) Samsung DDR4-2133 8GB/1Gx72 ECC CL15 Server Memory > $228 ($57 each)

GPU: Used Quadro K4200 (4GB) this is so as to be able to add a used Tesla co-processor in future (matching Kepler series) > about $500

Drive 1: Samsung 950 PRO Series 512GB M.2 PCIe 3.0 x4 Solid State Drive, Retail (V-NAND) > $318 (OS and Programs)

M.2 to PCIe X4 adapter: Lycom DT-120 M.2 PCIe to PCIe 3.0 x4 Adapter >$22.85

Drive 3: Seagate Constellation ES.3 2TB 7200 RPM 128MB Cache SATA Internal Hard Drive > $127.70 (Storage)

Power Supply : Seasonic SS-1050XM2 ATX 1050 Power Supply > $197.00

Case: Lian-Li Case Full Twer Chassis Aluminum USB3.0 Black Retail PC-A76 > $242.02

OS: Operating System: Microsoft Windows 7 Professional SP1 64-bit English (1-Pack), OEM > $139.

_______________________________________

TOTAL= about $2,800

This has a slower CPU and fewer features such as the RAID, but this has a more modern Xeon- 2600 v3, allows adding a second CPU, up to 512GB of RAM, a motherboard that can use an NVMe SSD, and having three PCIe x16 slots- two GPU coprocessors. The 32GB is done to accommodate the budget but the system should really start with 64GB.

So, a couple of alternatives to start with.

OPTION 3

Would be a single CPU system possibly:

Intel Xeon E5-1660 v3 Eight-Core Haswell Processor 3.0 / 3.5GHz 0GT/s 20MB LGA 2011-3 CPU, OEM > $1,075

___http://ark.intel.com/products/82766

OR>

E5-1660 v4 8-core @ 3.2/3.8GHz > about $1,300 at the moment.

The motherboards for Xeon E5 v4 are in a state of flux, and the CPU's not available everywhere, but possibly:

ASUS X99-PRO/USB3.1 X99-RPO USB3.1 X99 22NM CPU > $351

X99 gets a lot of performance from the CPU and the disk system is fast, fast.

And the other parts are similar to above and about $3,200-$3,500 as the CPU is expensive. To me, a single CPU system is limiting the upgrade potential of a dual CPU system but without a substantial cost savings- a dual CPU motherboard may cost only $50-$100 more than a single. OF course, two CPU's can cost more than a single, but a pair of E5-2630 v3's at $6o0 each is less costly than a single E5-1660 v4 and for the same price there are 16-cores instead of 8. The clock speed of the E5-2630 v3 is lower, but the system calculation density is far higher.

What kind of projects are you doing?

Cheers,

BambiBoom

1. HP z420 (2015) > Xeon E5-1660 v2 (6-core @ 3.7 / 4.0GHz) > 32GB DDR3 1866 ECC RAM > Quadro K4200 (4GB) > Samsung SM951 M.2 256GB AHCI / Intel 730 480GB (9SSDSC2BP480G4R5) / Western Digital Black WD1003FZEX 1TB> M-Audio 192 sound card > 600W PSU> > Windows 7 Professional 64-bit > Logitech z2300 speakers > 2X Dell Ultrasharp U2715H (2560 X 1440)>
[ Passmark Rating = 5581 > CPU= 14046 / 2D= 838 / 3D= 4694 / Mem= 2777 / Disk= 11559] [6.12.16]

2. Dell Precision T5500 (2011) (Revised) > 2X Xeon X5680 (6-core @ 3.33 / 3.6GHz), 48GB DDR3 1333 ECC Reg. > Quadro K2200 (4GB ) > PERC H310 / Samsung 840 250GB / WD RE4 Enterprise 1TB > M-Audio 192 sound card > Logitech z313 > 875W PSU > Windows 7 Professional 64> HP 2711x (27", 1920 X 1080)
[ Passmark system rating = 3844 > CPU = 15047 / 2D= 662 / 3D= 3550 / Mem= 1785 / Disk= 2649] (12.30.15)












 
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Quick question.. If I settle with Option 2, and buy 2 CPUs instead of 1, how do I cool both CPUs? Will two Noctua NH-U9B fit in the tower?

Thanks!
 
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Ricardo_20,

Yes, the full tower case can accommodate the pair of large CPU coolers. A bit of research can confirm it.

Another option, if the 2nd CPU is installed sooner and that could greatly simply the project:

Supermicro SuperWorkstation 7038A-

Supermicro SuperWorkstation SYS-7038A-I Dual LGA2011 900W Mid-Tower Workstation Barebone System (Black) > $649 + $13.00 shipping

The Supermicro SuperWorkstation SYS-7038A-I provides the same Supermicro X10 DAi sual Xeon E5-2600 v3 and v4 motherboard recommended earlier, mounted in a case, wired to a 900W server quality power supply and it provides 2X CPU coolers- guaranteed to fit and cool up to 150W CPU's. So many choices have been made and so much assembly, wiring configuration completed, this means that upon receipt, the user need only mount the CPU's, the CPU coolers, RAM, GPU(s), and drives. That saves researching components for performance and compatibility, ordering, assembling, wiring,configuration, and testing. Supermicro are server specialists, so this should be a path to high performance, extreme reliability, and long service. The case is supposed to be very quiet.

There are other versions which may be of interest with hot swap drive bays and another that uses a motherboard with 4X PCIe x16 double-height GPU slots: GPU SuperWorkstation 7048GR-TR this is expensive, but can accommodate up to 2TB of RAM, and four GPU's which would comprise a Quadro and 3X Tesla co-processors- a personal supercomputer These are used for extreme calculation-intensive work. Looking for oil from space- developing a millisecond stock trader, simulating air crashes, starting a weather service? - there's the platform. The particle research facility I visited recently has eleven of those motherboards in rackmount server form in a cluster, running particle experimental simulations on dual 14-core Xeons and 4X Tesla K20X each.

Recalculating for 2X CPU's and Supermicro Superworkstation:

BambiBoom PixelCannon COMSOListicRenderMathematicaSimulucious iWork TurboSignature Extreme CalcuBlast 9800 ®©$$™®£™©™_Revised 7.19.16

CPU: 2X Intel Xeon E5-2630 v3 Eight-Core Haswell Processor 2.4 /3.2 GHz 8.0GT/s 20MB LGA 2011-3 CPU, OEM > $1,200 ($600 each)

Xeon E5-2630 v3

Supermicro SuperWorkstation SYS-7038A-I Dual LGA2011 900W Mid-Tower Workstation Barebone System (Black) > $649 + $13.00 shipping

RAM: 64GB (8X 8GB) Samsung DDR4-2133 8GB/1Gx72 ECC CL15 Server Memory > $456 ($57 each)

GPU: Used Quadro K4200 (4GB) this is so as to be able to add a used Tesla co-processor in future (matching Kepler series) > about $500 Top Passmark 2D = 1280 / Top 3D= 4895

___GPU ALT 1: If the visualizations are restricted to 3D graphs, charts and etc.,and the budget is under pressure, or all new components are required, AND the Tesla K-series co-processor is considered, a lower specification GPU is possible, but should still be a K-series Quadro for example:

PNY Quadro K1200 VCQK1200DP-PB 4GB 128-bit GDDR5 PCI Express 2.0 ATX or SFF Workstation Video Card for DisplayPort > $270 (Top Passmark 2D = 1099 Top 3D =3072

___GPU ALT 2: If the Tesla co-processor is NOT to be considered, and all parts must be new, the suggested GPU is:

PNY Quadro M2000 VCQM2000-PB 4GB 128-bit GDDR5 PCI Express 3.0 x16 Workstation Video Card > $430 (Top 2D rating = 1246 and 3D=4671.

Drive 1: Samsung 950 PRO Series 512GB M.2 PCIe 3.0 x4 Solid State Drive, Retail (V-NAND) > $318 (OS and Programs)

M.2 to PCIe X4 adapter: Lycom DT-120 M.2 PCIe to PCIe 3.0 x4 Adapter >$22.85

Drive 3: Seagate Constellation ES.3 2TB 7200 RPM 128MB Cache SATA Internal Hard Drive > $127.70 (Storage)

OS: Operating System: Microsoft Windows 7 Professional SP1 64-bit English (1-Pack), OEM > $139.

________________________________

TOTAL = about $3,426

Given the advantages of the 2nd CPU in place, 64GB RAM, and the faster initial system project timing, and saving upgrade timing, this seems a more attractive path, although 11% over budget.

This specification is still incomplete as far as the storage- it should have at least a RAID 1 and better a RAID 5 running on a PCIe controller, but the performance would be very, very good. There is a possibility too, depending on the timing of your project that one of the new E5-2600 v4's would be a consideration- they're popping up every so often currently. The problem has been really that both the v3 and the v4 versions have had important gaps in the specification. The best version in some ways were the v2's for example the Xeon E5-2687w v2 which is 8-core @ 3.4 /4.0 GHz. These are of course used and today selling in the $900-$1,600 range. But, the v3 and v4 seem to leap from low clock speeds - $700- to very expensive- high clock speeds- $2,000+ and there's no middle. Only the E5-1650 has remained as an excellent all-rounder.

__________________________________

[For others contemplating projects for similar uses, but with restricted budgets:

OPTION 1: Some perspective on the project economics: Some high performance E5-2600 version one CPU's are amazingly inexpensive at the moment, the reason for OPTION 1. For 3D modeling /visualization work, I use an HP z420 with a Xeon E5-1660 v2 ( 6-core @ 3.7/4.0GHz) which has a high single-threaded performance (Passmark 2105) and split off the rendering / Mathematica, Matlab ,ArcGIS - calculation functions to a dual CPU system. Currently that system is:

Dell Precision T5500[/b] (2011) (Revised) > 2X Xeon X5680 (6-core @ 3.33 / 3.6GHz), 48GB DDR3 1333 ECC Reg. > Quadro K2200 (4GB ) > PERC H310 / Samsung 840 250GB / WD RE4 Enterprise 1TB > M-Audio 192 sound card > Logitech z313 > 875W PSU > Windows 7 Professional 64> HP 2711x (27", 1920 X 1080)
[ Passmark system rating = 3844 > CPU = 15047 (single threaded= 1465) / 2D= 662 / 3D= 3550 / Mem= 1785 / Disk= 2649] (12.30.15)

To replace this system the current project is and HP z620 which will have 2X E5 2690 8-core @ 2.9 / 3.8GHz, 64GB RAM, Quadro K2200- as visualization speed is not as critical, Intel 730 480GB and a 1TB WD Black. The calculation density of the E5-2690 is as high as the E5-2687w v2 but -300 MHz.

Costs so far: used z620: $270, 2X E5- 2690 : $345, 32GB RAM: $165, Quadro K2200- to be taken from the current dual Xeon system., The Intel 730 480GB and a 1TB WD Black storage drive will be taken from the Xeon E5-1660 v2 system which now has a Samsung SM951 M.2 256GB and will have a new Seagate Constellation ES.3 1TB.

The z620 system currently has a cash outlay of $780 and the total in value when complete- the value including the used parts will be about $1,200.

Perofrmnace should be quite good: A pair of E5-2690's averages 20659 (single threaded= 1883) on Passmark and in this example cost $345, compared to a pair of E5-2630 v3 averaging 18694 (single threaded= 1860) for $1,200. Cost/ performance on used workstation is impossible to better.

Reliability of this hardware is impressive: The MTBF of a Xeon E5-2690 is 170,000 hours, so the average failure is continuous running for 19.4 years.]

______________________________________

Sorry, not a quick answer to your quick question- sorry for the long ramble.

Cheers,

BambiBoom







 
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Thanks again BambiBoom. I think we are going with the following build:

CPU: 2X Intel Xeon E5-2630 v3, $1200
RAM: 64GB (8X 8GB) Samsung DDR4-2133 8GB, $456
Case/PSU/MOBO: Supermicro SuperWorkstation SYS-7038A-I Dual LGA2011 900W Mid-Tower, $662
GPU: PNY Quadro M2000, $430
Drive1: Samsung 950 PRO Series 512GB, $318
Drive2: Seagate Constellation ES.3 2TB, $127
M.2 to PCIe X4 adapter: Lycom DT-120 M.2 PCIe to PCIe 3.0 x4 Adapter, $22.85

TOTAL $3,216.55


Luckily, we have the OS for free through our University.

What do you think?


 
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"Thanks again BambiBoom. I think we are going with the following build:

CPU: 2X Intel Xeon E5-2630 v3, $1200
RAM: 64GB (8X 8GB) Samsung DDR4-2133 8GB, $456
Case/PSU/MOBO: Supermicro SuperWorkstation SYS-7038A-I Dual LGA2011 900W Mid-Tower, $662
GPU: PNY Quadro M2000, $430
Drive1: Samsung 950 PRO Series 512GB, $318
Drive2: Seagate Constellation ES.3 2TB, $127
M.2 to PCIe X4 adapter: Lycom DT-120 M.2 PCIe to PCIe 3.0 x4 Adapter, $22.85

TOTAL $3,216.55

Luckily, we have the OS for free through our University.

What do you think?"

Ricardo_20,

That specification would be my selection as the Quadro M2000 is a fantastic value- the performance of the K4200 at half the price. That will be capable of a high level of precision visualization and 3D modeling / animation, plus 10-bit color correction.

A couple of details:

1. This is probably already in place, but if the system is operated in isolation= not linked to a network server, it would be useful to have in mind a solid backup scheme, either a RAID 1 or an external drive with a scheduled differential backup. An external drive, as it runs only when backup and there isolates the drive from problems- viruses, surge and etc, plus can be moved for protection and duplication. (I use a StarTech Aluminum 3.5" USB 3.0 enclosure as it has a cooling fan.)

2. Also, if this is in a laboratory situation, consider connecting to an isolation transformer power conditioner. This regulates the voltage exactly, restores the waveform for accurate CPS, filters RF, and has the best soft surge shutdown. I use 8-12Amp Powervar and OneAC conditioners.

Any questions along the way, let me know here or by PM.

Cheers,

BambiBoom
 
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Excellent, yes I plan on buying a power line conditioner. What do you think of this one?

https://www.amazon.com/Furman-M-8X2-Outlet-Conditioner-Protector/dp/B003BQ91Y6/ref=sr_1_1?ie=UTF8&qid=1469565279&sr=8-1&keywords=power+line+conditioner
 
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Ricardo_20,

An example of the device I 'm thinking of :

PowerVar ABC1200-11 AC Line Power Conditioner Unit Surge Protector PSU 12 Amps > $200

The Furman conditioner have a good reputation for RF filtering in audio uses- lowering the noise floor and good surge protection. However, my preference is to use the isolation transformer type which include a substantial hand wound transformer that produces very good sine and square waves. These are are used for instrumentation calibration and medical and scientific where there is measurement or where for example phase and waveform need to be accurate.especially in an RF, xray, magnetic rich environment. Got plasma? I think some lasers and industrial controls also use this type- quite a range.

These are better than the Furman in situations where there is a lot current swing; variable loads / modulation. Besides gear with microprocessors, on the other end of the scale I use these with vacuum tube electronics: preamplifiers and especially tube microphone preamplifiers. In audio, it's possible to hear the effect by way of the much lower lower noise floor and motors run accurately.

These are amazingly heavy due to the big transformer. A couple of these cost more in shipping than the device itswlf. But they're quite expensive new. I think the list price for a 12A used to to be about $1,400. The three-phase industrial control ones go well into the five figures-$30-40,000. Still, there are so many that are routinely rotated through hospitals and labs so It's possible to get a good price. Sometimes there are "open box" ones that were purchased and never really used for $300-$500. I've had an Ebay one running non-stop for about 7 years with no problems.

As you can tell, I'm a believer in these.

What kind of projects are you doing?

Cheers,

BambiBoom




 
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Thanks very bambiboom for your contribution to this topic over the years. Could you recommend a build for $7000-8000 range? I'm looking at building a machine for integrated circuit simulation. Very CPU intensive, requires large amount of memory, can benefit from multiple cores, but cannot be GPU accelerated.

Thanks!
 
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Please start a new thread with your requirements. Thank you.
 
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