suggestion for hardware configuration for NGS analysis

[sunsnow86]

We are thinking to buy a new server for running NGS analysis. Actually we have one which is just a few month old, but it broke down recently due to the overheating of CPU, which then damage the hard drive. Even though we are able to recover the data, the operation system won’t be restored. That is a pain for us, since we have to install all the software packages from the very beginning. That is why we are thinking to buy a more stable server system. In often times, it will be just used for running the NGS analysis program, and temporally store some data used by the pipeline ( roughly 2 IIlumina IIX runs’ raw data and output from it) . Also we want to have a mirror image of the operation system in a different hard drive just in case one breaks in the future. Would someone would like to share some opinions with us. You suggestion will be highly appreciated. Thanks.

Here is our old system set up, just for your reference, below that is the new system we are going to buy.


OLD:
ITEM DESCRIPTION QTY UNIT PRICE PRICE
=============== =================================== ===== ========== ==========
MB-340-121 GIGABYTE X58A-UD3R 3WAY CROSSFIRE & S 1 0.00 0.00
CU-197-206 INTEL i7-960 3.20GHZ 8M 1366 RETAIL 1 1280.00 1280.00
FA-WATER-301 NZXT 120MM WATERCOOLER WITH 120MM FAN 1 0.00 0.00
CU-OVERCLOCK-2 EXTREME OVERCLOCK (20% MORE) 1 49.00 49.00
HD-403-302 1TB SATA III 6GB/S 7200RPM 64MB CACHE 2 46.50 93.00
RM-317-501 16GB DDR3 / 1600 MHZ MEMORY 3 0.00 0.00
CD-139-201 BLACK SONY 24X DVDRW 1 3.00 3.00
PS-126-108 XTREMEGEAR 800 WATT POWER SUPPLY 1 0.00 0.00
RAID-1 RAID-1 MIRRORING 1 0.00 0.00
SB-LAN-101 GIGABYTE LIGHTNING GUARDIAN ANGEL LAN 1 18.00 18.00
MN-172-101 SCEPTRE X226W 21.5" 16:9 1920 X 1080 1 159.00 159.00
FA-HD-101 VIGOR ISURF II HARDDRIVE COOLING 2 24.00 48.00
CS-425-101 BLACK AZZA SOLANO 1000 FULL TOWER NO 1 50.00 50.00
MR-104-101 12-IN-ONE INTERNAL CARD READER 1 0.00 0.00
MISC NO SLI/CROSSFIRE 1 0.00 0.00
SERVICE-201 SOUND ABSORBING FOAM ON SIDE, TOP AND 1 29.00 29.00
MISC NO OPERATING SYSTEM 1 0.00 0.00
MISC ONBOARD 7.1 SOUND 1 0.00 0.00
RUSH RUSH ORDER FEE (NEXT BUS. DAY) 1 109.00 109.00
BOX1 SYSTEM BOX AND FOAM 1 0.00 0.00
=============== =================================== ===== ========== ==========
Subtotal 1838.00
Shipping 210.00
Shipping Discount -109.00
E-WASTE Fee 16.00
Tax 9.75% 179.21
Total 2134.21

NEW :





SYSTEM COMPONENTS
PowerEdge R710 Qty 1

Chassis for Up to 8, 2.5-Inch Hard Drives, No Operating System Unit Price $8,855.00



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Catalog Number: 4 BEDWBRD
________________________________________
Module Description Show Details

PowerEdge R710 Chassis for Up to 8, 2.5-Inch Hard Drives
Operating System No Operating System
SHIP PowerEdge R710 Shipping
Memory 48 or 64 GB Memory (4x1GB), 1333MHz Single Ranked UDIMMs for 2 Processors, Advanced ECC
Feature Upgrades for Embedded NIC Ports Dual Two-Port Embedded Broadcom® NetXtreme II 5709 Gigabit Ethernet NIC
Processor Intel® Xeon® X5670, 2.93Ghz, 12M Cache,Turbo, HT, 1333MHz Max Mem
Additional Processor Intel® Xeon® X5670, 2.93Ghz, 12M Cache,Turbo, HT, 1333MHz Max Mem
1st Hard Drive HD Multi-Select
Internal Controller PERC 6/i SAS RAID Controller, 2x4 Connectors, Internal, PCIe,256MB Cache,x8
BIOS Setting Power Saving BIOS Setting
Embedded Management iDRAC6 Express
Internal Optical Drive DVD ROM, SATA, Internal
Bezel Bezel
Riser Card Riser with 2 PCIe x8 + 2 PCIe x4 Slot
System Documentation Electronic System Doc, OpenManage DVD Kit with Dell Management Console
Hard Drive Configuration RAID 5 for H700 or PERC 6/i Controllers
Rails No Rack Rails or Cable Management Arm
Hardware Support Services 3 Year ProSupport 4HR 7x24 Onsite: Non Mission Critical
Installation Services No Installation
Proactive Maintenance Maintenance Declined
Power Supply High Output Power Supply, Redundant, 870W
Power Cords No Additional Power Cords
Power Cords 2x 10 feet (3m) Power Cords, 125 volt 15 AMP NEMA 5-15P to C13 Wall Plug
Hard Drives (4) 73GB 15K RPM Serial-Attach SCSI 6Gbps 2.5in Hotplug Hard Drive

[rpauly]

Hi,
We are looking to purchase an NGS server too.
Did the above configuration work for you?

Any additional suggestions shall be greatly appreciated.

~Thanks,
Rini

[GenoMax]

What kind of data, genome size(s), sample # are you looking at? How many simultaneous jobs and of what kind (RNAseq, assemblies etc) do you expect to run?

[jpummil]

I wonder if we should have a "sticky" for this topic as it comes up quite bit. We'd never get complete consensus among the community, but some solid guidelines look to be needed by many. Sort of an "If this, then that" sort of post? Of course, as computational hardware, sequencing technology, and software all evolve, so must the list of recommendations.
Avoid vendor specifics of course, but general recommendations seem to be sought quite often.