WCG News: GPU application is coming!

[Dirk Broer]

13 Mar 2012



The Help Conquer Cancer Project Publishes Paper in Journal of Physics

Category: Help Conquer Cancer
Tags: Project Update , Research Papers

Summary
The Help Conquer Cancer (HCC) project researchers have published a paper describing their efforts in re-implementing their algorithms to take advantage of Graphics Processing Unit (GPU) hardware present in many of today's computer's. If the algorithms lend themselves to use a GPU implementation, this can dramatically increase their performance. Their work has led to the testing of a beta release of HCC using GPU hardware on World Community Grid. This paper discusses their experiences.



Paper Title:

"High-throughput protein crystallization on the World Community Grid and the GPU"

Abstract:

We have developed CPU and GPU versions of an automated image analysis and classification system for protein crystallization trial images from the Hauptman Woodward Institute's High-Throughput Screening lab. The analysis step computes 12,375 numerical features per image. Using these features, we have trained a classifier that distinguishes 11 different crystallization outcomes, recognizing 80% of all crystals, 94% of clear drops, 94% of precipitates. The computing requirements for this analysis system are large. The complete HWI archive of 120 million images is being processed by the donated CPU cycles on World Community Grid, with a GPU phase launching in early 2012. The main computational burden of the analysis is the measure of textural (GLCM) features within the image at multiple neighbourhoods, distances, and at multiple greyscale intensity resolutions. CPU runtime averages 4,092 seconds (single threaded) on an Intel Xeon, but only 65 seconds on an NVIDIA Tesla C2050. We report on the process of adapting the C++ code to OpenCL, optimized for multiple platforms.

Access to Paper:

To view the paper, please click here (http://iopscience.iop.org/1742-6596/341/1/012027/pdf/1742-6596_341_1_012027.pdf).

[Jason1478963]

They ran a batch of beta this week and We will have to wait and see what changes are made and how things went. I received a few work units and 3 of them were not on hardware that could run them currently. The one that did run turned out to be an invalid on my 5850 running in xp64, but it ran 359secs on a work unit that usually takes a hour and a half to two hours. It seems there is much confusion on what hardware will run and what will not.

The following failed to run the work units for me and need to be looked into.

win7 64bit HD6370 mobility need to check CCC
Vista pro 64 HD4850 CCC 11.5
XP 32 HD4850 CCC 12.1

I have run poem on the 5850 before and have it running CCC 12.1 on xp64. The computers that did complete OK on this work unit were both running CCC 11.5 according to the result status. The Beta test run this time was windows only and they did run some on CPU as well.

[Dirk Broer]

I suspect that
A. the HD 6370M just won't cut it as it has no OpenCL support (http://developer.amd.com/sdks/AMDAPPSDK/pages/DriverCompatibility.aspx)
B. Vista (SP2) pro 64 with a HD 4850 has only Beta Level Support for AMD/Ati OpenCL 1.1
C. XP 32 unfortunately is not supported for AMD/Ati OpenCL 1.1

[Jason1478963]

If I look at specs for it at http://www.amd.com/us/products/notebook/graphics/amd-radeon-6000m/amd-radeon-6300m/pages/amd-radeon-6300m.aspx#2 they say the 6300m series will have support later in 2011. It could be delayed I imagine. When I look at http://developer.amd.com/sdks/AMDAPPSDK/pages/DriverCompatibility.aspx they seem to be missing a few drivers on the list which makes me wonder what they support now.

Is there support for xp64 as it seems to attempt to run them. It also runs poem, but not very fast without opening up a core for it. I've been tempted to get another copy of windows 7 to replace xp64 to gain the directX 11 support for gaming. I just hate to waste money on an OS when I could waste it on electricity.

I've not had the best luck with the latest drivers for the 4850 and it makes me concerned about trying the beta versions. I did hear a guy had one attempt to run on a 4350 but wasn't able to finish it. I do look forward to seeing some of these cards able to run these units when they hit production. it would be a shame if we were not able to use the 4xxx series on this project.

[Dirk Broer]

I do indeed hope to use my HD 4770 for WCG, it is doing stellar work on MilkyWay right now (also OpenCL)

[vaughan]

I hope it pays better than their CPU projects. Single reason I stopped running this project was the abysmal return of cobblestones per dollar electricity expended.

[Jason1478963]

My guess is it won't compare to other GPU projects out there. It would be nice if all projects were based on x points a gigaflop. I think I would have quit if I was running for just points as points alone aren't worth electricity to me anymore. Its not like the points can get you a tax credit or a coffee. I try and look at the benefit of the research more then the points and thats why I rarely leave WCG as it would be very hard for me to justify the electric bill. It seems the recent software change did bump the project credits a bit and we may have to wait to see if they return or have increased. http://i137.photobucket.com/albums/q210/Sekerob/WCGProjectPointsPerHour.png You can see a jump in credit/hour when they updated servers but its not easy to see how it will compare yet.

[Dirk Broer]

I hope it pays better than their CPU projects. Single reason I stopped running this project was the abysmal return of cobblestones per dollar electricity expended.
They pay better than LeidenClassic, LHC or Test4Theory at least

[Jason1478963]

It appears they are doing another round of beta and have a list of cards that returned valid results and a list of invalid or errors. they are currently trying to narrow the list to cards returning valid results. For the list of cards and discussion on this test https://secure.worldcommunitygrid.org/forums/wcg/viewthread_thread,32825

It is sad to see the 4xxx series out of the picks for now. It removes a bunch of my cards out of the project and I'm afraid my 5850 will be off to as its running XP64 bit at the moment. stop in the chat channel if you would like to chat more on the beta run and results so far.

[Dirk Broer]

It also runs poem, but not very fast without opening up a core for it.

Poem needs to be beated and battered into good behaviour using an app_info.xml that will free the core for it.

[Jason1478963]

Thanks for the info on POEM. it seems lately it has been hard to get work units from there when you want to test things.

It seems the WCG server update has changed the credit at WCG a bit. It is looking better so far, but I'm not sure how it will compares to other projects.

In the last round of WCG GPU BETA my best luck came on my windows 7 64bit running a 6570 and a 6450 completing 12 of 12 work units with a valid return running CCC 12.12. There was 4 on the 6450 and the rest on the 6570. The XP 64 running 12.2 on a 5850 and 5450 did worse in the last round then the previous beta running CC 12.1 and just the 5850. I was hoping the latest driver would work well for both setups. They windows 7 machine is running BOINC 7.0.8 and the XP 64 is running 7.0.3.

[Dirk Broer]

So there is still hope for my Llano system (HD 6570 + A6-3500 = HD 6690D2)?
I will upgrade to a A8-3870 when money permits, but that will leave my combined card a HD 6690D2 (though more tweakable)

[Dirk Broer]

I'm running a bèta HCC on the HD 6530D of my A6-3500 APU right now...takes about a mere 13 minutes to complete!
The HD 6670 takes a little under 9 minutes to complete a WU. Now waiting for the effect on my WCG beta scores.