Folding@home

Meet new FAH GPU programmer Yutong Zhao

We have had an unfilled spot in our GPU programming team for a few months and I'm happy to announce that we recently made a great new hire: Yutong Zhao.

Yutong completed his undergraduate degree in Math, Chemistry, and Biochemistry from the University of Toronto, and a Masters degree in Computational Chemistry from HKUST, focusing on GPU-powered clustering algorithms. Previously, he has also worked on projects such as FoldIt! Currently, he is the lead developer of the Folding@Home GPU core and aims to extend functionality while increasing maintainability. He also plays a key role on the OpenMM side, he works on devising parallel algorithms to speed up MD simulations. He also maintains a blog detailing some of his algorithms and problems on www.proteneer.com .

GPU update

We've put a new revised AS up and we think this should fix the recent issues. We will of course continue to monitor the situation.

Updates on GPU issues

We've been working to fix two issues with GPU clients in FAH.  Here's an update:

1) There was an issue with NVIDIA clients with G80 GPUs getting stuck in a core_outdated download infinite loop.  This has now been resolved.  This was caused when we stopped older projects which used core_11 (which the G80's were primarily running) and now the G80's are directed to more recent projects.  However, with the ending of the old projects and the start of the new ones, that means G80 GPUs go to core_15, which has much more strict testing for GPU memory errors.  Several donors have reported that these tests are failing with their boards.  We are looking into whether this is an issue with our test or potentially that the boards are not capable of running the latest core.  So, while the core_outdated loop issue appears now to be fixed, there is another unresolved issue which we are continuing to look into.

2) There was a second issue with ATI clients getting directed to servers running NV WU's.  This error is also unresolved at the moment, but we have a handle on what's happening on our end and have a team working on it.  I don't have any news here to report other than we can see the issue cause in our logs, which is the first step to fixing it.

AS patch for GPU assignments

We've been seeing donor reports of WU assignment issues for GPUs (WU's intended only for G80 GPUs going to Fermi and Kepler).  We finished an AS patch yesterday, gave it a day of testing, then rolled it out this morning to address this issue.  We generally don't like to roll out new AS code this quickly, but this time it seemed important to address this issue quickly.  We hope that as of 7:30am pacific time, this issue is now addressed, but we'll be keeping an eye out during the day to see. 

Unified GPU/SMP benchmarking scheme implemented

The  unified GPU/SMP benchmarking scheme will be rolled out today on FAH. All the future GPU projects would now be benchmarked using the new scheme. Most of the existing GPU projects have been re-benchmarked to reflect the changes in the benchmarking scheme. We are still in the process of re-benchmarking some old projects assigned to ATI and G80 GPUs. The uniform benchmarking scheme significantly boosts the base points for all GPU projects. However, Quick Return Bonus for the GPU clients has not been introduced at this stage, but will be introduced once we work out an issue on our side. We would like to thank all the beta testers who participated in testing the unified benchmarking scheme. 

The Protein-Folding Problem, 50 Years On

Guest post from Dr. Gregory Bowman, UC Berkeley

Ken Dill, a long-standing leader in protein folding, just published a beautiful review article about progress in the field.  The main point is that what began as a specific research question has now evolved into an entire field with numerous research directions.  It’s would be difficult to provide a more eloquent explanation than Ken’s, so here are a few excerpts from the article

    “The protein-folding problem was first posed about one half-century ago. The term refers to three     broad questions: (i) What is the physical code by which an amino acid sequence dictates a protein’s     native structure? (ii) How can proteins fold so fast? (iii) Can we devise a computer algorithm to     predict protein structures from their sequences?...  computer simulations of the physical forces in     chemically detailed models have now achieved the accurate folding of small proteins…  What began as     three questions of basic science one half-century ago has now grown into the full-fledged research     field of protein physical science.”

Insights and achievements from Folding@home are highlighted on a number of occasions throughout the article.  So, congrats to all for helping to establish this ever-growing field.

Also, there's a nice video about this online for those who are interested