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TPU's WCG/BOINC Team

Norton

Moderator & WCG-TPU Captain
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Motherboard X370 Taichi/ ASUS R3E/Asus P8P67 Pro/P9X79 Pro/EVGA X58 SLI 3/SuperMicro 4P
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Video Card(s) RX 580/HD 4670/HD 7770/HD 7770/HD 7770/onboard/HD 7770/onboard
Storage WD 500GB SSD/Seagate 2TB SSHD, everything else is Western Digital (mostly)
Display(s) Dell U2414H & 2409W / Dell 2208WFP (shared)
Case Silverstone FT01B/Source 530/Corsair 230T/Define XL R2/Silverstone FT05/Define R4/custom
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Power Supply Corsair HX850/TX650/CS650M/X Gold 750/EVGA P2 850/X Gold 1050/HX650
Mouse Logitech G300s
Keyboard Thermaltake Challenger Prime (Great for $30!!!)
Software Win 7 Home 64 (Win 10 Pro 64)/Win Pro 64 or Ubuntu 12.04 LTS/14.04 LTS/17.04
Benchmark Scores Why sit on the Bench when you can get in the game and Crunch!!!
Joined
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Cooling Corsair H55 ][ Stock
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Case Antec Nine Hundred ][ it's a server blade, lol
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Benchmark Scores 65970 BogoMIPS. Ha. Ha. Ha. >=|
Joined
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After messing around with this case a bit, it is really cool. Really well designed.
 

manofthem

WCG-TPU Team All-Star!
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@james888 looks awesome. It's a Fractal case right? They are terrific! :)
 

t_ski

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Taking the 14.04 update.... :twitch:
 
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manofthem

WCG-TPU Team All-Star!
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Video Card(s) 2x R9 290's | 980 SC ACX2.0 | n/a
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Power Supply Corsair AX1200 | XFX 550Pro | SeaSonic 660XP2
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Another update on the FAAH project. Great to see that we are putting forth so much data for them! Let's keep up the awesome work! :D


Improved efficiency and processing capabilities for FightAIDS@Home


By: The FightAIDS@Home research team

16 Jul 2014

SummaryNew methods and processes help the research team process World Community Grid data more efficiently and provide more accurate docking techniques.



As the volume of data generated by World Community Grid volunteers for ourFightAIDS@Home (FAAH) project has increased, so has our need to optimize how we handle and store that data. In this project update, we discuss new improvements in how we process the extremely high result data rate you generate, which is allowing us to focus more resources toward the analysis of FAAH data. Further, improved docking techniques are being created and applied from the results of deeper analysis coupled with ongoing experimental data from our collaborators.


Example of repositioned side-chain, histidine, by Vina cycling through the original space-filling representation, original stick representation (orange), and new position compared to old position (dotted black lines).
Processing your results faster

Managing the very large data throughput generated by World Community Grid volunteers for FAAH is a great challenge. Beside the scientific results we have achieved over the years, we also have developed novel software and protocols to process, analyze and store the results you generate quickly and efficiently.

Recently, we exploited the parallel computational resources available at Scripps. In the last few months, we have shifted our processing of the incoming World Community Grid data to our local High Performance Computing cluster, Garibaldi. Since the implementation of the AutoDock Vina software for FAAH last year, you have generated several terabytes of compressed docking results each month, which was putting a strain on our storage system. Until recently, most of our work and resources have been focused on processing this data to make it suitable for deeper analysis. We had to devote most of our local computational power to this processing. With our new methods, we have increased the processing rate by several orders of magnitude with the use of multiple processors and the optimization of processing scripts. Processing a batch that used to take between 30 minutes to few hours now takes just a few minutes. Streamlined scripts and parallel processing has yielded 180,000 processed batches in two weeks.

We have created new analysis programs using structural and statistical methods to mine more information from the results you generate. Statistical analysis tools will first be used to reduce over 5 million docked compounds to a few thousand top-ranking candidates. Structural information will then be used to cull the list further by filtering for key intermolecular interactions and against unfavorable interactions. A new database structure that will incorporate these programs is being developed to handle this large and fast-growing flood of results. Once optimized, the whole processing and analysis workflow will be fully automated.

Importantly, what we have learned and are learning from these refined methods to handle big data will be made available in the AutoDockTools suite, which is utilized by many research labs worldwide.

Improved protein-ligand binding modeling capabilities

Proteins are typically large molecules and often can bend or flex in various ways at various points and at normal temperatures they rapidly bend to many or all of the possible configurations (bent shapes). When searching for ligands that might attach to a protein target, the ligand might not match the shape of the protein in one of its configurations, but might match in another configuration of the protein. By considering more configurations of the protein, it is more likely that a ligand can be found which matches one of the protein's configurations. Since February 2014, we have been running flexible receptor side-chain Vina jobs on FAAH, which we expect to enhance our docking results. While our typical docking methods hold the protein structure rigid, the flexibility feature in AutoDock Vina allows selected residue side chain conformations to be sampled along with the flexible ligand molecule. This enables the protein pocket to adopt alternate shapes to better model protein-ligand binding and the so-called “induced fit”, minimizing the bias of using a rigid target structure. Currently, we are testing this approach on several sites (LEFGF, FBP, and Y3) in HIV integrase.

The downside of performing flexible receptor calculations is that the search complexity increases, and computing run-times are therefore 5 to 10 times longer. The World Community Grid staff has been adjusting their methods to account for the different Flexible Vina work unit. Once these dockings have finished and the analyses performed, we will be able to optimize our application of Flexible Vina on World Community Grid and extend it to other targets.

Another way to minimize rigid-protein bias in traditional docking is to dock to an ensemble of protein structures. Two ways to generate these ensembles, both used in FAAH dockings, are molecular dynamics (MD) simulations and simply using multiple available structures for a given protein receptor. The last hundred experiments have included ensembles ranging from tens to sometimes hundreds of receptor structures. Ensembles add another layer of analysis with the goal of achieving a more accurate ranking of compounds from several sources of data.

Further experimentation

Despite the encouraging results on the first hits previously reported, we are encountering experimental issues that are making the process of identifying hits very challenging. As often happens in science (and particularly in HIV-related experiments!), it is hard to achieve robust and consistent statistics from biological assays.

Experiment 30 Compounds (October-December 2009), Target: HIV Protease, Exo/1F1 Sites:
Five out of ten compounds had promising results from a differential scanning fluorimetry (DSF) assay, performed by the Torbett Lab. Unfortunately. X-ray crystallography by the Stout Lab gave inconclusive data; crystals had formed but diffracted poorly, so no binding sites were confirmed. The compounds were sent to our collaborators at Scripps, Florida, but complications with producing enough HIV Protease delayed these efforts. This obstacle was recently resolved with the help of the Elder Lab, and nuclear magnetic resonance (NMR) experiments are soon to be performed.

Experiment 33 (June-December 2010), Target: HIV Integrase, Active Site of the Catalytic Core Domain (CCD):
Preliminary results were mixed. The Kvaratskhelia Lab (OSU) recently reported promising results for 2 out of 10 compounds, but these compounds were considered poor candidates due to poor chemical properties that indicated poor specificity, meaning that although they may bind to HIV Integrase, they will probably bind just as easily to other proteins reducing their effectiveness.

We anticipate identifying many more hit compounds for all 3 proteins and their various sites by the end of the year and we’re grateful for World Community Grid volunteers for giving us the opportunity to learn more about HIV and its interactions.


Taken from here
 
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Hi! I'm from the Internet
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Norton

Moderator & WCG-TPU Captain
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Video Card(s) RX 580/HD 4670/HD 7770/HD 7770/HD 7770/onboard/HD 7770/onboard
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Benchmark Scores 6.9 processes per second!/ cruncher's!!
Ok, weird. I thought TPU had a way to do this. Had no reason not to believe that. So, what happened to BOK's site? Did he kill more SSD's? Do we need to start a fundraiser for him? I was able to send him a paltry amount last time he was having issues.

Or, what?

I want my Badge! .... We don't need no stinking badges.... I want my Badge.... We don't need no stinking badges....

I'm kinda on the fence. I know I am a Cruncher.

I am also kinda Proud of my Badge.

:confused:

What am I to do?
:D
 

Norton

Moderator & WCG-TPU Captain
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Motherboard X370 Taichi/ ASUS R3E/Asus P8P67 Pro/P9X79 Pro/EVGA X58 SLI 3/SuperMicro 4P
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Memory 16GB GSkill TridentZ-3200 (1700X), 16GB GSkill FlareX-2400 (1600X),... various...., 4P- 16x1GB
Video Card(s) RX 580/HD 4670/HD 7770/HD 7770/HD 7770/onboard/HD 7770/onboard
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BOK is out of Town atm so he doesn't know what happened to his server- it may not be a major issue but we will need to wait until his return to find out...
 
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Getting some numbers on my Athlon 5350.

Before I took it down for undervolting it was actually approaching 1800 RAC. It's currently sitting at 1637 but still climbing, I think. So a realistic PPD might actually be 1600-1800! :O

Edit: Oh, and with the undervolt I also got it to 2,1 instead of 2,05.
 

Norton

Moderator & WCG-TPU Captain
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Motherboard X370 Taichi/ ASUS R3E/Asus P8P67 Pro/P9X79 Pro/EVGA X58 SLI 3/SuperMicro 4P
Cooling NH-D14/Phanteks/NH-U14S/H70/DeepCool/CM 212+ (x4)/NH-U14S/CM212
Memory 16GB GSkill TridentZ-3200 (1700X), 16GB GSkill FlareX-2400 (1600X),... various...., 4P- 16x1GB
Video Card(s) RX 580/HD 4670/HD 7770/HD 7770/HD 7770/onboard/HD 7770/onboard
Storage WD 500GB SSD/Seagate 2TB SSHD, everything else is Western Digital (mostly)
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Keyboard Thermaltake Challenger Prime (Great for $30!!!)
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FreeDC is back up! :) :rockout:
 
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Hi guys, I need a suggestion.
I have a Phenom II 960T (OC'd 3.5 GHz) in my main Rig.

I was primarily thinking of upgrading to a 8350 and later move to Intel Broadwell in late 2015. But due to HDD failure last month i had to buy a SSD and a HDD and spent the amount i was saving for the processor. Now i am a little low on budget and a little confused.
Do you think i should buy a 8320 now and later move to Intel Broadwell when its available or should i OC the Phenom II 960T to 4GHz+ and move to Broadwell when available.

I just game on this rig and Crunch in the remaining time.


Thanks.
 

Norton

Moderator & WCG-TPU Captain
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System Name My Fortress/Trish (WCG)/Julia (WCG)/Ella (WCG)/Junior(WCG)/Cruncher 1 & 2/Kreij (WCG)
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Motherboard X370 Taichi/ ASUS R3E/Asus P8P67 Pro/P9X79 Pro/EVGA X58 SLI 3/SuperMicro 4P
Cooling NH-D14/Phanteks/NH-U14S/H70/DeepCool/CM 212+ (x4)/NH-U14S/CM212
Memory 16GB GSkill TridentZ-3200 (1700X), 16GB GSkill FlareX-2400 (1600X),... various...., 4P- 16x1GB
Video Card(s) RX 580/HD 4670/HD 7770/HD 7770/HD 7770/onboard/HD 7770/onboard
Storage WD 500GB SSD/Seagate 2TB SSHD, everything else is Western Digital (mostly)
Display(s) Dell U2414H & 2409W / Dell 2208WFP (shared)
Case Silverstone FT01B/Source 530/Corsair 230T/Define XL R2/Silverstone FT05/Define R4/custom
Audio Device(s) on board (All)
Power Supply Corsair HX850/TX650/CS650M/X Gold 750/EVGA P2 850/X Gold 1050/HX650
Mouse Logitech G300s
Keyboard Thermaltake Challenger Prime (Great for $30!!!)
Software Win 7 Home 64 (Win 10 Pro 64)/Win Pro 64 or Ubuntu 12.04 LTS/14.04 LTS/17.04
Benchmark Scores Why sit on the Bench when you can get in the game and Crunch!!!
Hi guys, I need a suggestion.
I have a Phenom II 960T (OC'd 3.5 GHz) in my main Rig.

I was primarily thinking of upgrading to a 8350 and later move to Intel Broadwell in late 2015. But due to HDD failure last month i had to buy a SSD and a HDD and spent the amount i was saving for the processor. Now i am a little low on budget and a little confused.
Do you think i should buy a 8320 now and later move to Intel Broadwell when its available or should i OC the Phenom II 960T to 4GHz+ and move to Broadwell when available.

I just game on this rig and Crunch in the remaining time.


Thanks.
Your call on this decision but I have the following for you:
- Game performance should be about the same
- An FX8 will use more power/generate more heat so you need a good cooling solution
- An FX8 can boost your ppd to nearly double of what your 960T does
 
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Memory 8 GB Corsair 2400MHz
Video Card(s) ASUS 1050TI 4 GB
Storage Samsung 960 EVO 250GB + Samsung 850 EVO 120 GB + 2TB Seagate 7200rpm + 500 GB Toshiba 5400rpm
Display(s) 24 Inch LG IPS
Case Deepcool Dukase v3
Audio Device(s) On Board
Power Supply Corsair 600X
Mouse Logitech G300S
Keyboard Logitech K230
Your call on this decision but I have the following for you:
- Game performance should be about the same
- An FX8 will use more power/generate more heat so you need a good cooling solution
- An FX8 can boost your ppd to nearly double of what your 960T does
Then going for an upgrade. buying a 8320 and OC it to 4 GHz.
Thanks.
 

BUCK NASTY

F@H Mod & 4P Enthusiust
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Cooling Coolermaster Hyper 212+
Memory 8GB GSkill DDR3 1600
Video Card(s) ASUS GTX 970 Strix @ 1503Mhz Core
Storage Corsair Force 90gb SSD/ WD Caviar Blue 750gb
Display(s) ASUS 24" IPS
Case Coolermaster Centurion 590
Audio Device(s) Onboard
Power Supply Antec TP750 80+
Software Windows 7 Ultimate 64
Hi guys, I need a suggestion.
I have a Phenom II 960T (OC'd 3.5 GHz) in my main Rig.

I was primarily thinking of upgrading to a 8350 and later move to Intel Broadwell in late 2015. But due to HDD failure last month i had to buy a SSD and a HDD and spent the amount i was saving for the processor. Now i am a little low on budget and a little confused.
Do you think i should buy a 8320 now and later move to Intel Broadwell when its available or should i OC the Phenom II 960T to 4GHz+ and move to Broadwell when available.

I just game on this rig and Crunch in the remaining time.


Thanks.
Have you tried unlocking the 960t to a 6 core? With 6 cores and a nice overclock that rig will perform.
 
Joined
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Processor Ryzen 1700 (3.65 GHz)
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Memory 8 GB Corsair 2400MHz
Video Card(s) ASUS 1050TI 4 GB
Storage Samsung 960 EVO 250GB + Samsung 850 EVO 120 GB + 2TB Seagate 7200rpm + 500 GB Toshiba 5400rpm
Display(s) 24 Inch LG IPS
Case Deepcool Dukase v3
Audio Device(s) On Board
Power Supply Corsair 600X
Mouse Logitech G300S
Keyboard Logitech K230
Have you tried unlocking the 960t to a 6 core? With 6 cores and a nice overclock that rig will perform.
didn't had any luck with that.
 

brandonwh64

Addicted to Bacon and StarCrunches!!!
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System Name The StarCrunch Defender! | X58 Cruncher!
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Motherboard Gigabyte Z170X-UD5 | Alienware MS-7543 X58
Cooling Corsair A70 Push/Pull | Corsair H50
Memory Crucial Ballistix DDR4 2400 MHz | Pereema 3x2GB DDR3
Video Card(s) Gigabyte Gaming G1 GTX 1070 | Gigabyte 7970 3GB
Storage 2x Samsung Pro 256GB M.2 SSD's in Raid 0 | 4TB Western Digital SATA drive
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Keyboard TESORO Mechanical | ANZO Mechanical
Software Windows 10 Pro on both
Well numbers have been down for the past couple of days while I am battling network gremelins at home and also took a power hit at work last night so my main cruncher was down all night. Got it back up and have a temp setup at home for now but numbers will def be down over the next week since I will be on vacation.

Also anyone have a am2/am2+ cpu I could borrow for testing? I got a board that norton had sold me a while back from a co worker that I helped setup a rig and he has now upgraded and I have this board back. Was thinking of setting up another small cruncher at home to pair with my i3-2100. I may look for a 6 core am3 later but for now just need to test the board properly before diving into a huge CPU.
 
Joined
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Hi! I'm from the Internet
System Name Selene / Yoda
Processor Fx 8350 @ 4.4 / Phenom II x6 1090t @ 3.6
Motherboard Gigabyte 990FXA-UD3 r4.0 / Gigabyte 890XA-UD3
Cooling H100i / Xig Dark Knight
Memory 4x 8gb G.Skill Snipers / 4x 4gb G.Skill Ares
Video Card(s) Gigabyte R9 290x / XfX DD & VisionTek HD6850's C'fired
Storage 256gb ssd, 2x 2tb Wd Blacks & 1x 1tb Wd black / 1x 1tb
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Benchmark Scores What are benchmarks anyway?
Well numbers have been down for the past couple of days while I am battling network gremelins at home and also took a power hit at work last night so my main cruncher was down all night. Got it back up and have a temp setup at home for now but numbers will def be down over the next week since I will be on vacation.

Also anyone have a am2/am2+ cpu I could borrow for testing? I got a board that norton had sold me a while back from a co worker that I helped setup a rig and he has now upgraded and I have this board back. Was thinking of setting up another small cruncher at home to pair with my i3-2100. I may look for a 6 core am3 later but for now just need to test the board properly before diving into a huge CPU.
Pm sent :toast:
 
Joined
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System Name Eternal WIP ][ HP ProLiant server blade
Processor AMD FX-8320 @ 4.4/4.1 GHz ][ 2x Intel Xeon L5520 @ 2.27GHz
Motherboard Asus Crosshair V Formula-Z ][ -
Cooling Corsair H55 ][ Stock
Memory 2x4GB Kingston HyperX Genesis @ 1866MHz ][ 4x4 GiB Hynix @ 1333 MHz; ECC on
Video Card(s) 2x MSI GeForce GTX 770 DirectCU II OC ][ None
Storage 1TB WD Black + 1.5TB WD Green + 750GB Samsung + 64GB OCZ Agility 4 ][ 3x 1 TB Hitachi
Display(s) Asus VG278H + Asus VH226H ][ None
Case Antec Nine Hundred ][ it's a server blade, lol
Audio Device(s) Supreme FX II (Integrated); Using optical S/PDIF output ][ none
Power Supply Corsair AX1200i ][ [stock]
Software Gentoo Linux ][ Linux Mint 16
Benchmark Scores 65970 BogoMIPS. Ha. Ha. Ha. >=|
I tossed two machines (the dual Xeons and one of the FX-8320) to Kreij earlier today.
You're welcome, BTW.
 
Joined
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Kaunas, Lithuania
System Name Eternal WIP ][ HP ProLiant server blade
Processor AMD FX-8320 @ 4.4/4.1 GHz ][ 2x Intel Xeon L5520 @ 2.27GHz
Motherboard Asus Crosshair V Formula-Z ][ -
Cooling Corsair H55 ][ Stock
Memory 2x4GB Kingston HyperX Genesis @ 1866MHz ][ 4x4 GiB Hynix @ 1333 MHz; ECC on
Video Card(s) 2x MSI GeForce GTX 770 DirectCU II OC ][ None
Storage 1TB WD Black + 1.5TB WD Green + 750GB Samsung + 64GB OCZ Agility 4 ][ 3x 1 TB Hitachi
Display(s) Asus VG278H + Asus VH226H ][ None
Case Antec Nine Hundred ][ it's a server blade, lol
Audio Device(s) Supreme FX II (Integrated); Using optical S/PDIF output ][ none
Power Supply Corsair AX1200i ][ [stock]
Software Gentoo Linux ][ Linux Mint 16
Benchmark Scores 65970 BogoMIPS. Ha. Ha. Ha. >=|
TFW crunching FAAH + MCM gives me at least 5°C higher CPU temps than crunching CEP2 exclusively
 
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System Name My Rig | Kids Rig
Processor Core i5 3570K @ 4.0 ghz 1.15 vcore | FX 8350 @4 ghz
Motherboard EVGA Z77 FTW 1.21 BIOS |Gigabyte 990FXA UDH (rev 4.0)
Cooling CM Hyper 212 EVO R2-push/pull with 2x 120mm PWM | CM Hyper 212
Memory Mushkin Blackline 4GB x 2 1600mhz XMP profile |G. Skill 4GB x 2 DDR3 1866mhz
Video Card(s) Sapphire RX 480 8gb | Asus Strix R9 390X 8GB
Storage Kingston SSDNOW V300 120/240 GB OS & Games / 1000 GB Data | 320GB OS / 500GB Data & Games
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Case NZXT 810 Switch |Thermaltake Soprano Snow Edition
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Mouse Razer Diamondback Chroma | Tt Level 10M
Keyboard Razer Ornata Chroma w/ meka-membrane keys | MadCatz S.T.R.I.K.E. TE w/ Kailh brown
Software Windows 10 Pro | Windows 10 Pro
Benchmark Scores Thanks to Norton/Lt_JWS/Guitar for the 2nd pc parts :)
IMMMMMMMMM BAAAAAAACKKK :D :D :D

had a rough time the last 8 months, but im mentally refreshed and ready to contribute again :D
 

Norton

Moderator & WCG-TPU Captain
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System Name My Fortress/Trish (WCG)/Julia (WCG)/Ella (WCG)/Junior(WCG)/Cruncher 1 & 2/Kreij (WCG)
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Motherboard X370 Taichi/ ASUS R3E/Asus P8P67 Pro/P9X79 Pro/EVGA X58 SLI 3/SuperMicro 4P
Cooling NH-D14/Phanteks/NH-U14S/H70/DeepCool/CM 212+ (x4)/NH-U14S/CM212
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Video Card(s) RX 580/HD 4670/HD 7770/HD 7770/HD 7770/onboard/HD 7770/onboard
Storage WD 500GB SSD/Seagate 2TB SSHD, everything else is Western Digital (mostly)
Display(s) Dell U2414H & 2409W / Dell 2208WFP (shared)
Case Silverstone FT01B/Source 530/Corsair 230T/Define XL R2/Silverstone FT05/Define R4/custom
Audio Device(s) on board (All)
Power Supply Corsair HX850/TX650/CS650M/X Gold 750/EVGA P2 850/X Gold 1050/HX650
Mouse Logitech G300s
Keyboard Thermaltake Challenger Prime (Great for $30!!!)
Software Win 7 Home 64 (Win 10 Pro 64)/Win Pro 64 or Ubuntu 12.04 LTS/14.04 LTS/17.04
Benchmark Scores Why sit on the Bench when you can get in the game and Crunch!!!
IMMMMMMMMM BAAAAAAACKKK :D :D :D

had a rough time the last 8 months, but im mentally refreshed and ready to contribute again :D
Welcome back! :toast: