[独立平台] [生命科学类] Folding@Home

vmzy

原帖由 sixwords 于 2009-7-20 12:13 发表
通过测算，I7、4G跑2681、2682的PPD值约为9000，并没有GPU2的5倍、10倍之多嘛。

你拿勉强能跑bigAdv的i7和勉强能跑GPU2的N8500比，你就知道我没骗你了。O(∩_∩)O~

foxhound

原帖由 sixwords 于 2009-7-18 11:19 发表
如果八核心CPU、6G内存的PPD可达GPU2的10倍，那么四核心CPU、3G内存的PPD也应该能有GPU2的5倍喽？

如此说来GPU已经没有优势喽？

斯坦福如此易变的PPD政策让人厌恶！不具备起码的实事求是的科学精神。 ...

PPD只不过是一个积分策略，并不代表机器性能

peterz

平时就一直在让机器跑，对于Folding的相关信息没怎么注意，呵呵

vmzy

August 20, 2009
Importance of software and data integrity

The scientific code underlying our research has a lot of dials and switches.  It can be very tempting to play with those switches to optimize the calculations.  However, many of the code settings can impact scientific results in non-obvious ways.  It can also hurt scientific reproducibility.  It is therefore extremely important not to modify the scientific cores or data for Folding@Home calculations. Returning any work results with modified cores or data can taint both your results and the results of any WU's calculated on the basis of those.  Thus even well-meaning optimization can potentially hurt the scientific value of the project substantially.  This is why the EULA specifically prohibits such modifications.

When you donate to Folding@Home, we give you a number of "dials" at the client level that you can use to adjust your contributions.  Many donors find that tuning these "dials" and their machine configuration can optimize their contribution.  Please use only the controls provided by the client and the operating system; do not modify the cores or Folding@Home data in any way.  Doing so is the equivalent of providing a tainted donation.  When we detect such tainted donations, we may remove points awarded, decline further donations by blocking work assignment, or take further action.  We greatly appreciate your contributions to Folding@Home; please don't devalue your collective work by undermining the scientific results.
大意：
劝告大家不要乱修改内核及数据，否则将被屏蔽帐号。这种行为会对科学研究造成很大危害。

注：我朝暂时没有这种败类吧（不过貌似台湾的setier曾经被全球通报批评）？有这精力和技术不如开发我朝自己的分布式项目，好钢要用在刀刃上。

zglloo

难道有人好奇 想逆向！  这样不会封号吧！

vmzy

August 27, 2009
Brief unplanned outage
There was a brief, unplanned network outage.

There was an unintentional network outage caused by maintenance this morning from about 7:30 to 7:50 AM. Ironically, the work we were performing this morning is part of our redesign to prevent things like this from happening.

The good news is that this sort of thing should become much more rare in the future.
大意：
昨天例行维护（升级网络部分代码）网络小断了一下，影响不大。
August 28, 2009
Power outage

I just got news that our main power feed has been damaged by the SIM1 construction crew.  We may be out of power for over 6 hours.  The good news is that most of FAH is immune from this right now.  The bad news is that we may have to stop the stats update and turn off the web server which serves the stats.

Note that the Assignment servers and all of the work servers are separate from this now, so FAH will be running, even if the stats update is put on hold.  Stats would continue to accumulate, just not update on the web site until we turn that back on (if we are forced to bring down those servers).
大意：
今天施工人员不慎把电搞断了，停了6小时电，不过现在除了统计服务器，其它服务器已经全部恢复正常。

金鹏

难怪昨天晚上计算好的WU不能上交

vmzy

September 07, 2009
Meet FAH team member: Greg Bowman
I wanted to continue the series of introducing FAH team members.  Greg Bowman has been a key figure in FAH the last few years, especially in methods and software development and its applications to protein folding (eg see the list of software he's made available on Simtk.org).

Here's a short intro written by Greg to tell his personal story.

Between the second and third grades I lost most of my vision due to a protein misfolding disease called juvenile macular degeneration (JMD).  At the time, I was too young to understand the full implications of my disorder; however, they became abundantly clear during middle school.  I soon learned that JMD is the result of a few point mutations in a key gene I’d inherited from my parents and, therefore, took a keen interest in exciting developments in molecular biology like the cloning of Dolly the sheep as they pointed to a means of curing diseases like my own.

A pressing challenge was then to discover how to make a contribution to molecular biology, given that performing laboratory experiments is extremely challenging with poor vision.  Fortunately, I developed a passion for computer science and mathematical modeling during high school and realized that these skills could be brought to bear on biological problems.  To prepare myself for a career in biological computing, I completed a major in computer science and minors in biomedical engineering and chemistry at Cornell University, where I also began basic research on protein folding.

Now I am performing full-time research on protein folding and misfolding in the Pande lab.  While I have not been able to tackle JMD directly at this point, I have developed methods that will be critical for doing so and begun working on other protein misfolding diseases like Alzheimer’s.
大意：
介绍了项目组成员Greg Bowman。GPU客户端主创人员。
该强淫，小学2、3年级罹患黄斑退化症(JMD)，几乎完全丧失视力。因此投身于基因疾病研究，力图攻克该症。

cicikml

小学2、3年级几乎完全丧失视力
之后的学习和生活肯定特别困难。

Bismarck

vmzy

September 15, 2009
First stage of Storage@home roll out


The first stage of Storage@home is now launching. Storage@home is a sister project to Folding@home.  The goal is to store data on volunteer machines that can then be used and processed in parallel.  You can learn more about this from our previously published paper (paper #48). For this first stage the Storage@home Monitor will collect availability data and some basic statistics on the machines.  We will write up the results in a paper at the end of this month, so we would love to get machines involved.

The installation process is more involved then that of Folding@home, requiring some router, firewall, and command line tinkering, but the system that will result is more capable then existing distributed computing systems.  Also, this first stage is very experimental, testing certain key assumptions needed to see how well Storage@home would work.  Once tested, we will work to move on to the next phases, assuming all looks good.

Please visit the Storage@home forum http://foldingforum.org/viewforum.php?f=56 to read the FAQ and instructions to learn more.  There are many important details there, so I strongly suggest people check out the FAQ to learn about the differences between Storage@home and Folding@home, as well as the nature of this first stage, experimental test.  
The upshot will be that in the future, we should be able to have a much more capable system than what Folding@home can do on its own now, especially in terms of how we handle the massive amounts of data that Folding@home generates, as well as a strategy to help significantly improve server performance and stability.


September 17, 2009
FAH work highlighted in Biomedical Computing Review
Two key parts of FAH technology -- OpenMM (the software that powers FAH on GPUs) and MSMbuilder (the algorithms that FAH uses to stitch together hundreds of thousands of donor simulations to get coherent results) are highlighted in this months Biomedical Computing Review.  You can download a copy here

http://biomedicalcomputationreview.org/5/4/index.html

cicikml

好像是说Storage@home是Folding@home的相关项目，看介绍说它的目的是把数据存在志愿者的电脑上，不需要运算吗？

vmzy

September 18, 2009
Stanford IT has alerted us to a potential problem with our ISP

We're monitoring the situation, but apparently Stanford's ISP is having some sort of issues.  I'll update it here as the day goes on as we learn more.

Bismarck

Storage就带有存储的意思～

莫非要搞分布式存储～

金鹏

满篇E文，围观