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[独立平台] [生命科学类] Folding@Home

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 楼主| 发表于 2011-4-1 09:50:49 | 显示全部楼层
March 31, 2011
Core 16 for ATI released; also note on NVIDIA GPU support for older boards

In a previous post, I mentioned our plans for supporting ATI GPUs.  I'm happy to announce that with the release of v7 into open beta, we have now released ATI core 16 GPU3 WUs into advanced methods for Folding@home.  Please see Dr. Lin's forum post for details.
We are doing a gradual rollout of these WUs, for a couple of reasons.  First, while this has gone through beta testing, it is still pretty new, so we want to be cautious with its rollout.  Second, I would like to add some more servers to help the load.  These servers are being delivered today and will likley be on line in a week or two.  Depending on the load on the ATI core 16 Work server, we may wait for a full release until the new hardware is on line.
Just a reminder from the previous post that there are some limitations in our ability to support ATI boards.  In particular, we're limited to those which support OpenCL 1.1 in order to get any sort of reasonable performance out of the hardware.  This means that only 5xxx ATI GPU boards or later will work with the new core 16 (the series 3xxx are not supported and the series 4xxx does not have sufficient OpenCL support).  However, we will keep core 11 support going hopefully at least until Sept 1, 2011 in order to support the older hardware.
Also, we are looking at support of older NVIDIA GPUs as well.  In particular, there have been reported issues with some 8xxx series boards.  We may have to limit their support as well due to analogous hardware compatibility issues.
We're excited to be able to release OpenCL support for ATI GPUs.  However, I want to stress that it is still pretty early days for this code, but we're excited about where this is going.
大意:
ATI Core 16开始公测。需要v7客户端,并且客户端类型为advanced。
因为ATI新服务器没有到位,再者任务确实很少,所以可发放的任务不多。
由于core 16需要OpenCL 1.1的支持,所以只有5xxx以上(包含)才能使用core16。3xxx、4xxx显卡将继续使用core11,直至2011-9-1。
由于NVIDIA 8xxx有问题,我们打算放弃对他们的支持。
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发表于 2011-4-1 09:57:17 | 显示全部楼层
难道说V7是A卡独占的?
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 楼主| 发表于 2011-4-6 11:10:53 | 显示全部楼层
本帖最后由 vmzy 于 2011-4-14 16:13 编辑

April 05, 2011
Change to the stats system
There are some changes to the stats system which are needed for consistency between the web site stats (eg http://fah-web.stanford.edu/cgi-bin/main.py?qtype=userstats) and the flat files (eg http://fah-web.stanford.edu/daily_user_summary.txt.bz2).  The main issue is how we handle passkeys and their impact on donor rankings.  I want to stress that this will not change point values or anything other than how we list the ordering of donors in our ranking.

Passkeys are a relatively recent addition to Folding@home.  The passkey, a new feature beginning with the v6.0 FAH client, is a unique identifier that ties your contributions directly to you (not just those with your donorname). The use of a passkey prevents others from cheating using your name.

In order to have the stats flat files match the web site in terms of donor ranking, we need to change both the flat files and the web site. The issue is how we handle passkeys. The web site ignores accounts with passkeys right now (needed to do a fast SQL count(*)), whereas the flat files aggregates all passkey accounts into the same donor name and then orders by the aggregate points for that donorname.

Our proposal to fix this is to treat each donorname+passkey combo as a unique donor in terms of ranking in the flat files and web site. This would let the two be consistent. We've batted around alternatives and nothing else would fit the goals of being fast for the web site and consistent between the two.  We will not of course give out the passkey in the file, although we are planning on distinguishing passkeys by revealing the last 2 digits.  This should be enough to identify different accounts without giving away any critical information.

In the next few days, we will release flat files with the additional donorname + passkey info.  After May 1, we will transition the FAH web stats to use the same method.  This lag between the two is intended to give 3rd party stats a chance to update their scripts, if they choose.  

I want to stress that 3rd party stats could choose to aggregate in the old way or the new way.  We are making this change mainly so that the stats we present are consistent.
大意:
统计系统变更:以前是按照用户名进行统计,现在准备按用户名+passkey进行统计,几天后统计文本将更新,5月1日起统计网站也将切换,望第三方统计网站能尽快修改。

More transparency in testing
For 10 years, we have rolled out Folding@home work units (WUs), Cores, and client software using a Quality Assurance (QA) protocol that involves several steps, including internal testing (int), closed beta testing (bet), open beta testing (adv), and full release (fah). The goal of this gradual rollout is to try to keep problematic WUs and software from getting released and to allow donors to have some choice in terms of how bleeding edge they’d like to be.

However, this does mean that a great deal of work is done in closed testing, which has several disadvantages. First and foremost, all the work that beta testers, Forum Moderators, and the Pande Group does to QA WUs is never seen. This also means the rationale for releasing WUs in their current form is not broadly visible. And while entry to the team of donors working on closed beta testing was always available, that is a large bar to cross just to see what's going on.  On the other hand, there are many upsides to closed testing however, including having a tight knit group of knowledgable donors giving useful feedback for strong QA of WUs.

While there are pros and cons of closed testing, I've decided that it is a good time to push for much more transparency in Folding@home in general, including closed beta testing. So, from now on, closed beta testing (bet) forum will be open for all to see. However, in order to keep strong QA, only beta team members can write in this forum (but as always, membership is open to those who are interested and dedicated to testing WUs).

My hope is that this will show all of the hard work that is done in testing WUs and will help answer questions about specific WUs that often come up. Also in this spirit, we have opened our v7 client bug tracker for read-only access so donors can see our progress with client development.

There's a tremendous amount of activity that goes on behind the scenes and I'm excited to open that up so the hard work that's been going on for a decade can now be much more visible (and hopefully better understood and appreciated).
大意:
向论坛会员开放'预'公测板块访问权限
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 楼主| 发表于 2011-5-17 09:24:51 | 显示全部楼层
May 16, 2011
Best Practices FAQ
Folding@home (FAH) is a major scientific endeavor, but is also a kind of contest for some donors to see who can donate the most points. In order to keep a sense of fair competition, we asked donors to help us establish a list of rules, summarized on this FAQ page: http://folding.stanford.edu/English/FAQ-BestPractices .

These rules are stated below to engender the spirit of competition in a way that is impartial for all donors. We thank everyone for their contributions and hope they will enjoy competing and donating to the project.
大意:
关于公平竞争,我们打算创建新规则,希望大家建言献策。
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 楼主| 发表于 2011-6-16 09:59:40 | 显示全部楼层
June 15, 2011
update on v7 client progress

It's been a little while since our last v7 beta release (v7.1.24) and so I wanted to give donors some sense of what's going on.  We've been working on internal testing of two releases past the current beta release and fixing bugs along the way.  While we could in principle release v7.1.25 to open beta, there are enough todo items that we've decided to hold off a bit until it's a bit cleaner and further along.  However, we're not going to hold off forever of course, just long enough for our developers to make some significant progress, especially since doing a release generates a lot of feedback, which takes developers away from coding.
To give some sense of where we are, here's the internal release notes for two recent builds (v7.1.25 and v7.1.26).  Note that v7.1.26 is still in progress.  Also, the #'s after the comment refer to our bug tracker.  We have opened up the bug tracker, so one can see progress directly there on a daily basis if you're interested.

v7.1.26 (still under development):
  * Failed upload attempt could cause WU to dump before it was expired. #679.
  * Added AMD Radeon HD 6600 Series to GPU white-list.
  * Fix failure to restart FAHControl in OSX when 'start minimized'.  #649.
  * Fixed a socket bug that could cause the loss of the end of a message.
  * Build OSX client in 32-bit mode with Intel compiler.

v7.1.25:
  * Hide 'Quit on window close' option in OSX.
  * Fixed some problems with WU assign time and time offset calculations.
  * Detect and ignore invalid assign time from older WS.
  * Log computed WS time offset.
  * Removed warning from Slot configuration about changing threads mid-run.
  * Catch and log error accessing battery info in /sys on Linux
  * Fix grayed out name and IP in client add after viewing local client. #640.
  * Remove 'RS480 PCI-X Root Port' from GPU whitelist. #635
  * Added a few new Radeon HD 6xxx cards.
  * Added Nvidia GTX 590 device ID 0x1088 to whitelist.
  * Increase Radeon HD 5xxxx and 6xxxx GPU type level by one. #653.
  * Don't fail WS connections if all data was recieved even on net error.
  * Print IP Address with 'Uploading' message.
  * Fixes for OSX minimize and quit bugs. #649 & #659.
  * Limit max CPUs per slot to system count. #652.
  * Attempt to fix #654.
  * Release system resources when querying OSX battery status.  #650.
  * Don't send 'auth' command from FAHControl if empty. #658.
  * Fixed 'slot-add' NULL pointer exception. #666.
  * Fixed 'log-updates start' error. #671.
  * Fixed FAHClient script parsing bug. #676.
  * Show 'Remote Access' tab in advanced mode. #648.
  * Don't allow minimizing to sys-tray if it is not there.  #670.
  * Also print core return code numbers in hex. #677.
  * Print times in ISO 8601 format. #664.
  * Expire WUs in sending status.
大意:
说明v7开发进度,7.1.25版正在进入最后内测阶段,如果不出意外,很快将开始公测。
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 楼主| 发表于 2011-7-2 21:07:32 | 显示全部楼层
本帖最后由 vmzy 于 2011-7-3 10:52 编辑

Sat Jul 02, 2011 1:11 am
bigadv points changes
After much discussion, we are adjusting the points bonus for bigadv. Bigadv work units have been given a 50% base points bonus over standard SMP; the rationale for this was to compensate for the increased system load, increased memory requirements, and increased upload/download bandwidth requirements. As judged from the high demand for bigadv work units, this has been very much a success, perhaps a little too much so. We would like to continue to offer a bonus for bigadv to offset the above factors, but we don't want demand for bigadv to overwhelm the rest of the project or imbalance the points system.

We are therefore dropping the bigadv base points bonus from 50% to 20%, effective for all work units issued this time onwards.

We very much appreciate the donors who have volunteered to run bigadv work units; these projects add substantially to our scientific capabilities. We do important science with all classes of work units, however, and we want the points system to reflect that. Based on extensive feedback, we are considering renormalizing other parts of the system but have not finalized decisions in that regard.

Thanks again for folding!

New points values, old points values, and unadjusted base values are given in the table below. Deadlines and k-factors remain unchanged.

"Standard points" is what the project would receive for base points if standard SMP. "Old bigadv" is the old bigadv base points (50% bonus). "New bigadv" is the new bigadv base points (20% bonus).

Project Standard points Old bigadv New bigadv Preferred Final k-factor
2684 8529 12790 10235 4 6 26.4
2685 5970 8955 7164 4 6 26.4
2686 5970 8955 7164 4 6 26.4
2689 5970 8955 7164 4 6 26.4
2692 5970 8955 7164 4 6 26.4
6900 5970 8955 7164 4 6 26.4
6901 5970 8955 7164 4 6 26.4
6903 18923 28385 22708 7.2 12 38.05
6904 26284 39426 31541 10.2 17 37.31
大意:
经过激烈的讨论,我们决定下调bigadv的基础分。之前bigadv比普通smp高50%,但是由于得分过高,打破了积分系统的平衡性,所以我们把基础分改为高20%。到期时间和积分奖励系数,均不改变。

July 02, 2011
Change in the points system for bigadv work units
For new bigadv WUs, we have changed how the points are calculated to bring them back into balance with the rest of the points in Folding@home.  There are more details in this post:

http://foldingforum.org/viewtopic.php?f=24&t=19059

The main jist of the change is that we are decreasing the points associated with bigadv WUs, from 50% over SMP to 20% over SMP.  As with previous points changes, this deals with only new WUs to go out, not with WUs that have be collected, etc.  I want to stress that the bigadv program is still continuing, but that, as we've mentioned before, this is an experimental program and subject to changes.

It's clear that any change to the points system is controversial, but this one has been raised as a very serious problem by many donors.  After investigating the issues raised, we agreed that this was significantly out of balance, and made this change.  Moreover, the feedback we have gotten is that we make a change soon and do so quickly, like "removing a bandaid" rather than drag out the pain. I'm sorry to have to make any changes at all, since any change is disruptive, but we (and many donors) felt very strongly that this change was very important.  

The other change that we have in mind to do is to bring all classic and GPU WUs into the Quick Return Bonus (QRB) system.  This would help further bring all FAH projects into balance.  There may be some issues with GPUs and QRB, so we are looking to see what we can do to minimize problems with that before making a change in the points for GPU WUs.

Finally, I would like to remind all that we do listen to donors and take their input very seriously.  There has been extensive discussions about the problems with the points system with the huge PPD's seen with bigadv (sometimes reaching 500,000PPD) and the lack of QRB for GPUs being major shortcommings.  

Considering the great variety of donor opinions on this matter, it is no surprise that we agree with some donors and disagree with others.  Moreover, with points, there will never be any system which makes everyone happy, but our goal is to try our best to balance the project as a whole, taking donor input seriously, and making hard calls when we feel it is necessary.  This was definitely a hard call, but hopefully in time donors who disgaree now will come to understand the issues raised by the other donors and appreciate their point of view.
大意:
为了稳定积分系统的平衡性(有太多人抱怨bigadv彪分过快,有时可达50万PPD),我们下调了新的bigadv任务的基础积分。详见:http://foldingforum.org/viewtopic.php?f=24&t=19059
下一步,我们将给单核及GPU任务加入积分奖励机制。进一步平衡积分系统。

译者注:看来bigadv的ppd要大降了,大家还是老老实实做GPU党吧。
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 楼主| 发表于 2011-7-26 09:51:58 | 显示全部楼层
July 25, 2011
New serverstats page
We've developed a new serverstat page, which we're now suggesting as a replacement for the old one.  The new one is more asthetically pleasing but also has a lot of changes under the hood to allow for more reliable and faster updates.
We're keeping the old serverstat page link pointing to the old page (i.e. no change) in case there were scripts that were parsing the old page.  However, we've set the new page to update every 10 minutes and the old one to only update every hour.  We will keep the old page up for at least two months to give 3rd party utilities a chance to update their code and to give us feedback (please post feedback to http://foldingforum.org ).
大意:
启用新统计系统。新系统不仅页面更加美观,更新速度也更快了。(老系统每小时更新一次,新系统每10分钟更新一次)
为了给第三方签名网站时间改脚本,老系统将继续运行2个月左右。
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 楼主| 发表于 2011-8-8 10:14:34 | 显示全部楼层
August 05, 2011
Results page updated – new key result published in our work in Alzheimer's Disease
We have made a major update to the Results page on the Folding@home web site.  We now list 95 papers that have directly resulted from Folding@home, although we note that there are 193 papers from the Pande group in general.  There are many new results to talk about, but I will just highlight a few below.
One major result is in the area of Alzheimer's Disease (paper #95).  It is believed that Alzheimer's Disease results from the misfolding of the Abeta peptide. Understanding how Abeta misfolds could give us some key insights into how to cure Alzheimer's Disease. This paper experimentally tests a key prediction made in an earlier paper (paper #58: "Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach" by Nicholas W. Kelley, V. Vishal, Grant A. Krafft, and Vijay S. Pande. J. Chem. Phys. 129, 214707 (2008); DOI:10.1063/1.3010881). In this paper, we show experimentally that there appears to be a beta turn in the Abeta as predicted. This leads to a very stable form of misfolded Abeta which could be used as a starting point for a new Alzheimer's therapy. We are heavily pursuing this research direction at the moment.
Another key result is in the area of methods (paper #93).  We are constantly honing our methods to improve Folding@home's ability to predict the behavior of proteins.  This paper demonstrates the current state of the art in terms of both sampling and analysis.  When compared to detailed TTET experiments, we show that our methods can piece out even fairly detailed aspects of folding.  However, we also see the ways in which our models are not perfect, suggesting how we can improve our methods even further.
We'll highlight other papers as time goes on.  I'm particuarly excited about these results.  In particular, the results from paper #95 were first discovered several years ago, but we carried out several followup studies to verify them, etc.  As always, I'm most excited about what we're doing now and hope to get some of our current key results in theses areas out from peer review soon.
大意:
更新结果页面。重点介绍了有关阿尔茨海默氏症的研究结果,介绍了算法方面的改进。
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 楼主| 发表于 2011-10-12 13:11:10 | 显示全部楼层
October 11, 2011
Update on the v7 client – v7.1.38 is now released
We've released the latest v7 client (7.1.38) in our forum.  I've pasted the update from Joseph Coffland (lead programmer), outlining the progress so far.


Documentation
Installation and user guides can be found here:
FAHControl -> The Graphical User Interface (GUI) what controls the Slots.
FAHViewer -> It shows the protein being folded, if applicable.
Pictorial Installation Guide (Windows) -> A detailed pictorial guide on the V7 installation.
Installation Guide (Windows) -> A brief guide on Windows installation.
Installation Guide (Linux) -> A guide for Linux installation.
Installation Guide (OSX) -> A guide for OSX installation that is in progress.
Client Remote Interface -> Documentation for 3rd party developers.
Main Page -> Main page of the V7.

Getting Help
Aside from the documentation the best place to get help is in this forum. If you do have a problem post a message. There are many knowledgeable people ready and willing to help. Keep in mind, we greatly appreciate thorough reports delivered by patient people who can keep a cool head even when things go wrong.

Bugs/Tickets
Open Tickets Ordered by Milestone and Priority
Active Tickets by Change Time
Note: Some tickets may be closed because they are fixed in an upcoming alpha release but are not yet fixed in the beta release.


_______________________________________________________________________________________

Beta Testers,

I've been focusing on addressing the issues which most affect v7 client users and which may help those still running v6 clients to make the decision to upgrade to v7. Your feedback has been very important, not only in finding and solving bugs but in prioritizing development time. One donor had these concerns with using v7.1.33:

Jesse_V wrote:I'd be happy to try out v7.1.33 and its upgrades if I was confident that my participation wouldn't hurt science. I am concerned with a number of bugs in v7, things such as FAHClient taking up way too much CPU time and slowing things down. I also am concerned about v7 not being able to talk to the servers right, especially when errors occur.



Although the issues Jesse_V mentioned only affected a small portion of the v7 users they were legitimate concerns. I made sure these issues were thoroughly addressed in this release. Concerns like this are exactly what we need to hear about.

If you are also concerned about v7 affecting the science of Folding@home I have this to say. v7 is more likely to increase your contribution but if you do have a problem, and you report it, you are potentially helping thousands of users donate computing time to Folding@home so it's more likely a net gain. However, beta testers often have to be satisfied with peer recognition and praise rather than points.

If you've been on the fence about v7 now is a great time to upgrade. Here are some of the other comments we've been getting:

jimerickson wrote:i am running windows 7 ultimate 64bit and windows 8 developer preview release. everything went smoothly. . .keep up the excellent work.

DarkFoss wrote:The upgrade from v7.1.24 to 7.1.33 went flawlessly. . .install took less than a minute and it resumed folding the wu's they finished without issue. . .

OEOTS wrote:Congrats on the new release guys. with V7 you've made it all so much easier.

soya_crack wrote:Wow, that is one of a big advance. That was what F@H just needed. It's awesome. Easy to understand and just kickin' ass, the slot thing is what I was missing from BOINC.

WhiteLion wrote:Awesome! :) The best client i ever use, perfect for newbies, easy setup. . .



There are still several issues that need to be addressed before we go to the front page with the v7 client. Specifically the tickets listed in Milestone Open Beta Phase 2 under ticket report 3. Log filtering (#157), better ETA calculation (#395) and better handling of cores that don't terminate cleanly (#563) are the top three items.

There is more work to do but we are getting ever closer to a front page release of the v7 client. Thanks for all your bug reports and feedback. Keep telling us what issues are most important to you and we will do our best to address them.

Joseph Coffland
Folding@home Developer
Cauldron Development LLC



Documentation
Installation and user guides can be found here:
FAHControl -> The Graphical User Interface (GUI) what controls the Slots.
FAHViewer -> It shows the protein being folded, if applicable.
Pictorial Installation Guide (Windows) -> A detailed pictorial guide on the V7 installation.
Installation Guide (Windows) -> A brief guide on Windows installation.
Installation Guide (Linux) -> A guide for Linux installation.
Installation Guide (OSX) -> A guide for OSX installation that is in progress.
Client Remote Interface -> Documentation for 3rd party developers.
Main Page -> Main page of the V7.

Getting Help
Aside from the documentation the best place to get help is in this forum. If you do have a problem post a message. There are many knowledgeable people ready and willing to help. Keep in mind, we greatly appreciate thorough reports delivered by patient people who can keep a cool head even when things go wrong.

Bugs/Tickets
Open Tickets Ordered by Milestone and Priority
Active Tickets by Change Time
Note: Some tickets may be closed because they are fixed in an upcoming alpha release but are not yet fixed in the beta release.



Here are the change logs:

v7.1.38:
  • Fixed network connection dropping.


v7.1.37:
  • Added missing wraplabel.py file to FAHControl.
  • Changed socket error message verbosity.
  • Fail WU on UNSTABLE_MACHINE immediately & return for partial credit. #615


v7.1.36:
  • Fixed a potential socket connection bug. Maybe related to #734.
  • Added several NVidia cards to GPUs.txt. #737.
  • Improved Linux on battery detection. #738.
  • Print WU error state on WU status line.
  • Emit correct exception on FAH transaction failure. #615.
  • Fixed debian package install core permissions problem. #732.
  • Removed core byte order warning. #602.
  • Added GPL link to FAHControl about. #736.
  • Ask user, team, passkey and mode during .deb package install. #739.


v7.1.35:
  • Added 'Enchanter' theme. #731
  • Renamed 'Wimp' to 'Windows-Default'. #731
  • Unminimize FAHControl window on unhide. #567
  • Better core download failure message. #161
  • Cleaned up project descriptions using html2text.py.
  • Store project data in client DB.
  • Use system default font size. #733
  • Added project info to viewer. #575.
  • Added clickable buttons to viewer.
  • Fixed FAHViewer crash introduced in v7.1.34.
  • Fixed mouse wheel scrolling in FAHControl. #463.
  • Fixed color difference for text boxes. #698.
  • Changed FAHControl window name. #711.


v7.1.34:
  • Fixed CPU consumption in client connections. #702
  • Really fixed "Wrong architecture" bug on 32-bit Ubuntu. #599
  • Only warn on config errors. #722
  • Log error and continue of command server fails to initialize.
  • Fixed Slot configuration text. #717
  • Use -1 or 0 for CPUs default to be consistent with GPU options. #717
  • Disabled no longer supported AMD X1300 - 1900 GPUs.
  • Added "OpenGL Render" to info in FAHViewer. (For blacklisting)
  • Added 'override-blacklist' option to FAHViewer. (Nothing black listed yet)
  • 'OK' -> 'Save' in FAHViewer preferences window. #724
  • Fixed NVIDIA_DEV.1244.01 = "NVIDIA GeForce GTX 550 Ti" detection.
  • Added the 'Wimp' theme and win32 theme engines. #723
  • Made 'Wimp' theme the default in Windows. #713
  • Added heartbeat to viewer<->client connection to timeouts dead connections.
  • Stop trying FAILED, FAULTY and DUMP reports if WS connection was made. #728
  • Check WS server versions for unreasonable values. #728.


Here are the highlights and some of the technical details of the changes in this open-beta:

Improved network handling:
A number of networking related issues were solved. The run away CPU usage problem was caused by incorrectly handling dropped connections. Periodic connection loss on Windows machines was caused by not correctly handing a quirk in the Windows sockets API which was the cause of the greyed out FAHControl that some people were experiencing. Also, dropped connections are now being cleared out of the client much more quickly. This keeps dead connections from accumulating which caused problems in a few cases.

Improved communication with older WS:
Several problems with communication with older WS were fixed. This version does a better job of detecting older WS and aborts the error loops that the previous client got into when incorrectly trying to upload DUMP reports to the old servers. This was the cause of the repeated upload errors many people saw in their logs. Also, a bug was fixed in the handling of UNSTABLE_MACHINE core return code which was the start of many of these DUMP communication loops.

GPU detection:
More cards were added to the whitelist and some older, no longer supported, GPUs were removed.

Debian package improvements:
A permissions problem was fixed that was causing WU loss after reinstall. The installer also now asks for user, team and passkey if /etc/fahclient/config.xml does not already exist. RPMs and OSX packages still need this feature.

Added a native Windows theme (Wimp):
The Wimp (Windows Implementation) theme was added to FAHControl. This theme gives a true native look on all Windows platforms because the theme engine actually uses the Windows system to render the GUI components. This is now the default theme for Windows platforms. Still need something like this for OSX.
大意:
V7客户端升级至7.1.38版。修正了大量的问题。建议v7粉更新使用,如果发现问题请及时向官方反馈。
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 楼主| 发表于 2011-10-14 12:57:02 | 显示全部楼层
本帖最后由 vmzy 于 2011-10-14 13:01 编辑

October 13, 2011
Comparison between FAH and Anton's approaches
Right now, the two most powerful supercomputers for studying protein folding are Folding@home and a very impressive special purpose computer from DE Shaw Researched, called ANTON.  We're often been asked "how do they compare?"  The approaches are very different, so comparisons aren't completely straightforward.  ANTON takes the traditional approach to studying protein folding, where one performs a few (often 1 or 2) long trajectories to study the process.  Folding@home takes a statistical approach, which has two primary benefits:  1) it can access folding on dramatically longer timescales (milliseconds, instead of microsecond folding events over a single long trajectory) and 2) it can give statistically significant results on those long timescales.
The main concern about the method in FAH is that since it is such a radically new approach, does it work reliably?  Previous tests of FAH have been to experiment, which is the gold standard test, but also brings in other issues, such as how good are our models of reality.  Thus, while FAH's approach has done well compared to experiment, it is useful to compare FAH and ANTON directly, since they use the same models, etc.  Comparison of our statistical approach (using Markov State Models, aka MSMs) directly with data from ANTON would go a long way to showing that the MSM approach works for even non-trivial systems (they have been previously tested for long dynamics on small systems).
In a recently published paper, we make this comparison.  By applying MSMs to data from ANTON, we find that FAH's approach (MSMs) can reproduce the long timescales in ANTON data very well.  Moreover, we also find that the MSM approach can find important new features missing in the more traditional analysis approach originally applied to the ANTON data, relevant for understanding folding and function.  
For us, this is exciting since it shows the capabilities of the MSM method.  However, I want to stress that perhaps the most exciting part is how ANTON and FAH could be used together.  A run on ANTON followed by more thorough sampling in Folding@home could be the best of both worlds.

PS Here's the abstract for our paper (http://pubs.acs.org/doi/abs/10.1021/ja207470h?prevSearch=lane%2Bpande&searchHistoryKey=):

Two strategies have been recently employed to push molecular simulation to long, biologically relevant timescales: projection-based analysis of results from specialized hardware producing a small number of ultra-long trajectories and  the statistical interpretation of massive parallel sampling performed with Markov state models (MSMs). Here, we assess the MSM as an analysis method by constructing a Markov model from ultra-long trajectories, specifically two previously reported 100  s trajectories of the FiP35 WW domain (Shaw et. al. (2010) Science, 330: 341-346). We find that the MSM approach yields novel insights. It discovers new statistically significant folding pathways, in which either beta-hairpin of the WW domain can form first. The rates of this process approach experimental values in a direct quantitative comparison (timescales of 5.0 s and 100 ns), within a factor of ~2. Finally, the hub-like topology of the MSM and identification of a  holo conformation predicts how WW domains may function through a conformational selection mechanism

大意:
FAH和Anton的对比
当前最常用的2个研究蛋白质折叠的工具就是FAH和Anton。首先,他们的算法不同,Anton使用的是传统的算法,FAH依照统计学研究做了非常多的优化。其次,同时FAH的模拟时间更长(毫秒级),而Anton短(微秒级)。再次,FAH的模拟结果输出要比Anton多。
尽管FAH做了优化,但计算结果都与实验室结果进行了验证,保证结果的准确性。
最近我们用这2个工具,来了个横向大比拼。
结果,FAH不但找到了许多Anton没找到的新的折叠路径(这对科研有很大用处),而且完了5秒级的模拟。而Anton仅完成了100纳秒的模拟(5千万倍的差距啊)。
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 楼主| 发表于 2011-11-9 09:40:32 | 显示全部楼层
November 08, 2011
Not getting SMP WUs? Here's a fix.
We've been getting reports that donors can't get SMP WU's.  There are plenty of SMP WUs, but they require client v6.34 (or later).  The servers that can handle the older SMP client (v6.29 or later) are running low on WUs, but there are plenty of WUs for the newer clients.

If you're not getting WUs, please consider upgrading your client.  You can download it here:

http://folding.stanford.edu/English/DownloadWinOther
大意:
老smp客户端任务匮乏,如果你还在使用老smp客户端,请尽快升级至6.34版。
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 楼主| 发表于 2011-11-10 09:52:33 | 显示全部楼层
November 09, 2011
Donor Advisory Board (DAB)
We've been working to make the behind the scenes tasks of Folding@home better communicated with FAH donors. In the last few months, there have been many recent changes, including making the beta team forum open and making our v7 client bug tracker open for all to read. Today, I wanted to talk about another experimental change, the formation of a Donor Advisory Board (DAB). We've in the past gotten lots of feedback from donors on our Forum site (http://foldingforum.org). Based on discussions with many donors, we have been working to expand these discussions to a broader group of donors and have formed a Donor Advisory Board. The DAB is currently comprised of: rjbelans (folding@evga), kendrak ([H]ardOCP), zodac (Overclock.net), hrsetrdr (www.overclockers.com), and Michael McCord (MaximumPC), Bruce Borden (Forum Admin), and myself.

The goal of the DAB is to improve communication in both directions and so far I think it's been helpful in improving communication in both directions. Pasted below is the first set of agenda items that we have been working on.

1) Improving communication: What can PG do to help improve communication?
2) Beta testing plan: How to improve transparency without lowering the quality of beta testing.
3) Points consistency: How to make PPD more consistent.

We've made changes in all three areas but none of these can be considered "done".  My hope is that the DAB will help feedback in both directions, giving us broader perspectives of donors concerns and also to better communicate what we're doing to improve FAH and push towards greater scientific achievements.
大意:
为了增加与志愿者的沟通,我们开放了内测组板块和v7 bug追踪系统的访问权限,接下来我们打算创建Donor Advisory Board (DAB志愿者建议板块)。
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 楼主| 发表于 2011-11-15 10:04:27 | 显示全部楼层
November 14, 2011
Planned changes to "Big Advanced" (BA) projects, effective January 16, 2012
Big Advanced (BA) is an experimental type of Folding@home WUs intended for the most powerful machines in FAH. However, as time goes on, technology advances, and the characteristics associated with the most powerful machines changes. Due to these advances in hardware capabilities, we will need to periodically change the BA minimum requirements. Thus, we are shortening the deadlines of the BA projects. As a result, assignments will have a 16 core minimum. To give donors some advance warning, we are announcing this now, but the change will take place in 2 months: no earlier than on Monday January 16, 2012.

We understand that any changes to how FAH works is a disruption for donors, and we have been trying to minimize such changes. For that reason, we are not changing the points system at this time.

However, we want to emphasize that the BA program is experimental and that donors should expect changes in the future, potentially without a lot of notice (although we will try our best to give as much notice as we can). In particular, as hardware evolves, it is expected that we will need to change the nature of the BA WUs again in the future.
大意:
由于技术的改进和高性能计算机的发展,为了保持‘与时俱进’,计划于2012年1月16日起调整bigadv项目,将缩短时限,因此cpu下限将上调至16核。
需要强调的是bigadv是实验性的项目,所以将来还会不断的调整。
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 楼主| 发表于 2011-11-19 10:46:45 | 显示全部楼层
November 18, 2011
Recent video about Folding@home from the Stanford News Service
The Stanford News Service recently came by to do a video for Folding@home.
大意:
斯坦福新闻中心最近做的FAH的视频,会翻墙的可以去看下。

Reports of issue with the Stanford medical school network
Several of the FAH servers are located at Stanford Medical School.  The Stanford School of Medicine Networks have reported outages last night (Thursday, Nov 17, 7:50-9:18 pm, pacific time) and this morning (Friday, Nov 18, 7:47 am, pacific time).  Stanford IT is working with the vendor to diagnose the source of the problems.  We have been warned that the medical school network may possibly be unstable today.

However, note that many of the servers at Stanford are not on this network and moreover we have redundant systems (eg redundant assignments servers) not on this network, so work should go smoothly.  There may be delays in updating stats however.  

Hopefully this is a resolved issue, but we are monitoring the situation in case it isn't.
大意:
斯坦福医学院的网络抽风,网络这几天会不稳定。不过我们有备用的网络和服务器,所以网络不会完全瘫痪。

Reports of issue with the Stanford medical school network: Updated
We just received notice that the School of Medicine has scheduled an emergency network downtime Tonight between 5-6 pm (pacific time).  Network engineers expect end users to experience a single, 30-60 second network disruption as part of their work, but I'm posting this in case there's something more significant.
大意:
网络工程师准备调试网络,所以网络会很不稳定,希望大家注意。
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 楼主| 发表于 2011-12-7 10:44:57 | 显示全部楼层
December 06, 2011
Network issue at Stanford
We have a network issue at Stanford in one of our data centers.  We are working on it now.  

Update:  Everything is back up now.
大意:
斯坦福网络断了一阵儿,现在恢复正常了。
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