[独立平台] [生命科学类] Folding@Home

vmzy

Happy 15th Birthday, Folding@home!
September 30, 2015 by Vijay Pande ·
I’m happy to announce that October 1, 2015 is Folding@home’s 15th birthday.  It’s amazing for me to look back at all we’ve done together, all we’ve built, and all that’s come out of it.  From CPUs to GPUs to PS3 to NaCl to Mobile.  And today we’re in the midst of an update of the FAH web site, rollout of new mobile and other (yet unannounced) clients, as well as new projects in cancer and Alzheimer’s.

And we look forward to celebrating the changes to come over the next 15 years!
大意：
FAH 15岁了。接下来我们将升级网站，手机客户端以及新版（暂时保密）客户端，还要出新的癌症及阿兹海默症子项目。

译注：v7很久没更新了，卡包bug实在无法忍受。难道官方要出v8了？希望能直接上boinc平台，劲大好使！

vmzy

Issues with FahCore21
November 20, 2015 by Vijay Pande ·
We’ve discovered that the new FahCore_21 is producing more errors than we consider acceptable for some clients.  The error rate seems to depend on several factors but most noticeable is that it doesn’t work well with second generation Maxwell GPUs.  A few projects have made their way through Advanced testing have been distributed to everyone under the default “FAH” client-type setting.  To allow donors to limit this exposure, those projects have been reclassified as “Advanced” which is appropriate for a FahCore that is still under development.

As has always been the case, the “Advanced” setting will give you access to newer projects which may have a higher error rate.  It is our intention to provide only the safest assignments with the default setting or you can choose to configure your system to run these advanced projects depending on how frequently you encounter these errors.

These conditions are expected to improve as new projects, new versions of that FahCore, or new versions of the drivers incorporate whatever fixes are required.  In the meantime, Work Units which are completed successfully allow scientific research to progress toward even more challenging projects than we’ve done so far.
大意：
我们发现FahCore21兼容性不太好，尤其是Maxwell二代。所以我们把FahCore21的任务类型改为Advanced了，以免普通用户收到他们。

zhouxiaobo

FAH’s achievements in 2015, with a glimpse into 2016

1) FAH Infrastructure

• New clients.  We will look to expand the mobile clients more broadly.  (Sorry for not saying more here, but like many of our rollouts, we do combined announcements with our partners.)
• New Gromacs core.  The Gromacs core continues to be a workhorse core for CPU clients and we are working on releasing an updated core with more broad hardware support, including support for AVX, which will give some donors an automatic performance boost.
• WS to do more advanced science.  In conjunction with new methods below, we will be rolling out new WS features, such as high frequency adaptive sampling (see below).
• More advanced analytics.  We’ve been working on this area for a while and it’s often pushed behind other priorities, but this is becoming a greater and greater need for us to monitor FAH in a much improved way.
• New stats system.  Given all of the other infrastructure work, this is possibly the least likely to happen in 2016, but we recognize this as a key need.  This is the last part of FAH which is very old and has not been recently updated.
  

2) New methods

• MSM advances.  We’re continuing to push advances in MSMs, especially in connection with modern machine learning advances.  This will also give us a big boost in our ability to understand the deeper meaning in FAH results.
• Adaptive sampling.  Adaptive sampling has played a key role in many FAH calculations, but it’s been done with a great deal of manual work by the WS project managers.  In conjunction with new infrastructure, this will be now automatic.
• OpenMM.  OpenMM’s development will continue to push into greater speed and functionality, with a particular push into much improved speed for the advanced accuracy AMOEBA force field and support for AMOEBA in Folding@home.  Both will come with OpenMM 7.0 which will roll into a new core (likely Core22).
  

3) More accurate models
Development of force fields more broadly.  Going beyond water, we expect to revamp force fields across the board, with broad impact in our calculations for FAH.  FAH will also play a key role in quantitatively understanding the improvements these force fields bring.

4) Disease targets
As discussed above, we will continue push to bigger and more sophisticated systems, hopefully with channels becoming much easier as kinases did.  Also, I have been working on ways we can partner with other groups, including groups from pharma, for “open source” science in this space, making results fully available to improve the whole community’s ability to impact disease.  Sorry that this is more brief here – like major software announcements, we hold back details on future targets until we’re ready to roll them out.

Summary.  I’d like to thank all of our donors for their contributions to Folding@home.  It’s exciting to me to be discussing these amazing results and 15 years ago would not have imagined that we’ve been able to do what we do now and I’m excited in terms of how our vision and plans for the future will be able to push us even farther.


大意：
回眸2015，展望2016
2016年，FAH将会在基建（客户端、服务端、运算核心等）、算法、分子模型的准确性、疾病的确切目标上继续前行，不辜负大家的多年期盼以及项目整整15年的努力。

coju

不知何时能支持中文界面，E文不好。

湘西匪首

New paper on non-native salt-bridge effects on folding

在F@H上的非原生盐桥效应的新研究

Salt−bridges are electrostatic interactions between positively charged residue side chains (like arginine or lysine) and negatively-charged side chains (like aspartic and glutamic acids).  They play an important role in stabilizing many protein structures, and have been shown to be designable features for protein design.
这一段简介了盐桥这个货是氨基酸链间的静电作用。然后，它对于蛋白质结构稳定和蛋白质结构的构成有重要作用。（感觉就是传说中的键的一种）

In this work, we study the effects of non-native salt bridges on the folding of a soluble alanine-based peptide helix (Fs peptide) using extensive all-atom molecular dynamics simulations performed on the Folding@home distributed computing platform. Using Markov State Models, we show how non-native salt-bridges affect the folding kinetics of Fs peptide by perturbing specific conformational states. Furthermore, we present methods for the automatic detection and analysis of such states.
这里一大堆说了也不懂的专业名词，大意就是，这个是研究非原生盐桥对肽折叠的影响巴拉巴拉，然后他们提供了一种能自动探测和分析这种影响状态的方法。（在F@H上大家一起跑跑跑）

Why are these results important to our understanding of protein folding? It used to be thought that protein unfolded states resembled a “random coil” with few structural features.  We now know that salt-bridges forming in unfolded states can significantly affect folding stability and dynamics. Our work shows that we can quantitatively predict these effects.  Eventually, we hope to be able to use such knowledge to engineer the folding properties of proteins.
最后就是搞这个的重要性：以前大家都认为蛋白质折叠状态是随机的，现在晓得了盐桥对折叠的重要作用，而且，这种作用看起来可以被定量的预测。最后，他们希望能够用这些新知识来改变蛋白质的折叠特性。

vmzy

Planned server outage 2/28
February 24, 2016 by Vijay Pande ·
The Stanford networking team will be upgrading some infrastructure this coming Sunday, February 28, 2016, from 12AM – 4AM. This work will be partially  disruptive to where some key FAH content is served from.  Our site will experience some downtime during this window. We cannot pinpoint per-site when the downtime will occur, however it will last approximately 5-10 consecutive minutes sometime during this window.
大意：
本周末2016/2/28,斯坦福将对网络进行维护，届时网络会不稳定，大概会出现5-10分钟断网。

金鹏

Filed Under: Uncategorized ·

Closing in on 100 Petaflops
May 11, 2016 by Vijay Pande ·

It’s been a while since we updated the FLOP per GPU report (since Tue, 26 Feb 2013 in fact).  A lot of progress has been made in 3+ years in GPU-land.  Over the last 3 years, FAH has seen a few trends, especially consolidation into people to GPUs and the increase in power from those GPUs.  The upshot is that today, FAH is running off the power of about 40,000 GPUs.  While that’s not a ton of donors, due to the power of GPUs, this is an immense amount of compute power.  In terms of FLOPs, we’re getting close to 100 Petaflops, which would be a major milestone in computing.  In terms of our ability to tackle complex systems, we’re simulating considerably bigger, more complex systems for longer timescales than ever before, which perhaps is the most important part of this beyond just the numbers.

Thanks to everyone who has helped make this possible.  And we’ll do a better job of more frequent updating of this page so these big jumps don’t catch people by surprise.

金鹏

Where can I see more detail about what’s going on in FAH?
May 12, 2016 by Vijay Pande ·

For those new to FAH, here’s a reminder for where the nitty gritty details can be found if people are interested to learn more than what’s on our web site.

In terms of new projects and more detailed (less high level) announcements, they’re here on the FCF: https://foldingforum.org/viewforum.php?f=24

For code updates, our science code development is done in the open on github, open source:  https://github.com/pandegroup/openmm and our other mature projects are on github.

For updates on Pande Group papers, here’s a good link that’s automatically kept up to date:  http://www.ncbi.nlm.nih.gov/pubmed/?term=pande++vs .  And for a sense of the most important works, this one is useful: https://scholar.google.com/citations?user=cWe_xpUAAAAJ&hl=en

As you can see from those links, there’s a ton of activity going on behind the scenes.  Feel free to drop by the FCF or follow us on Github if you’re curious to learn more.

金鹏

Out with the old psummary, reminder of the new
June 28, 2016 by Vijay Pande ·

Our projects page is a key way for donors to see the most up to date information about what is running on Folding@home.

About a year and a half ago we updated our project summary page.  We posted about it here: https://folding.stanford.edu/home/new-psummary-page/ As promised in that post, we are now deprecating the old psummary.  For most people this change will be transparent.  However, if any 3rd party tools are still using the old psummary they will have to update their code.

The new psummary can now be found in the following places: http://fah-web.stanford.edu/psummary.html    and  http://fah-web.stanford.edu/new/psummary.html

You can also access this data in JSON format:   http://fah-web.stanford.edu/psummary.json

vmzy

New FAH software client: V7.4.15 in open beta testing
August 23, 2016 by Vijay Pande ·
I am happy to announce we have a new client ready for beta testing. This client makes some important improvements over the v7.4.4 release. In addition to a number of bug fixes, this release adds better support for matching the number of CPUs available on a system to the number of CPUs projects can actually handle. This will get some Folding@home clients, which are currently not getting work, folding again.

We also have added our first 64-bit release for Windows. Due to the number of Windows clients, we have prioritized the Windows beta test, but the OSX release should be available for testing soon. Finally, we have made improvements to GPU detection but more works remains. We hope to solve the current problems with multi-GPU detection during this open-beta test.

Our internal testing team has worked extensively testing this new release. We believe it is in good shape but it is essential that we testing the code on a broader variety of machines. If you do run in to problems with this beta software please post a message at foldingforum.org with your OS version, the client package you installed, what you expected to happen and what actually happen. Posting log files is also very helpful.

As always, we greatly appreciate the efforts of those who help us test our software. Correctly functioning and efficient software is a huge part of making Folding@home successful and ultimately finding cures for diseases. We look forward to hearing from you in the forums!

More details can be found in the forum: FAHClient V7.4.15 (Open-Beta)

v7.4.15:
Fixed further FAHControl connection dropping issue related to UTF-8 encoding.
Fixed invalid PyON escape sequences in remote interface.
Convert Windows error messages to UTF-8 to avoid parsing problems.
Updated GPUs.txt.
大意：
发布7.4.15新版客户端
改进了多cpu支持，改进了多gpu侦测机制。暂时只放windows版客户端，osx版稍后放出。
更新内容：解决utf-8兼容性问题，以及由此带来的客户端连接异常问题。

vmzy

fah-web down, rebuild in motion
September 6, 2016 by Vijay Pande ·
Our main web server for stats (http://fah-web.stanford.edu) went down over the weekend due to a double failure.  Our sysadmins are working on this today and expect it to be up later this evening.  In the process and due to previous issues, we have also made plans to upgrade the hardware on this machine.
大意：
统计服务器挂了。我们的系统管理员正在处理此事，我们打算正好趁此机会进行他就服务器的硬件升级。

vmzy

Heads up: Scheduled Maintenance
September 13, 2016 by Carlos Hernández ·
A handful of Stanford-hosted FAH servers—including a stats server— will be undergoing scheduled maintenance starting today until Thursday. Assignments and points should not be affected; however, points may not be correctly reported on the website until after maintenance is completed.
大意：
今明两天，一大堆服务器（包括上次挂掉的统计服务器）将进行例行维护。届时任务传输、积分授予都不会收影响，只是积分统计结果可能会无法及时更新。

vmzy

Retiring Core15, OpenMM 7.0 on its way to FAH
October 9, 2016 by Vijay Pande ·
OpenMM is our main GPU code, fully open sourced, that drives FAH.  OpenMM has its roots in the original FAH GPU code, the first GPU code for molecular dynamics.  Core15 represents that very long history and it’s time for us to move on and retire that Core as its code is old and outdated.  Unfortunately, that means that some older GPUs (that are not supported by OpenMM) will no longer be supported by FAH.

OpenMM 7.0 has just been released and represents several key advances in speed and science.  We’re working to bring this into a new FAH core shortly to continue pushing the envelope of what FAH can do.  Look for that core in more extensive testing shortly.
大意：
淘汰老旧的core15内核（fah将不再支持一些老显卡），准备发布OpenMM 7.0（仍在测试中）

vmzy

Stats system update includes a new feature: monthly leaderboards
October 12, 2016 by Vijay Pande ·
In our regular updating of FAH systems, we’ve done a recent update of the stats website internals to help speed them up and bring them to new infrastructure that should be more reliable.  Along the way, lead FAH Programmer Joseph Coffland added a suggestion from FAH Marketing Relations lead Anton Thynell to include a new sort of competition: a monthly leaderboard.

This monthly leaderboard will naturally give the top donor and top team for each month and we will collect the top leaders for each month for recognition over the year.  Our intent was to give new donors a way to more directly see their contribution immediately and to in general encourage more friendly competition that helps us push forward our science even faster.

The updated page is found here:

http://folding.stanford.edu/stats/
大意：
统计系统加入月度排名功能。

vmzy

Core 21 (OpenMM GPU) issues with new Windows NVIDIA drivers 375.57 and 375.63
October 27, 2016 by john Chodera ·
Core 21 (OpenMM GPU) issues with new Windows NVIDIA drivers 375.57 (released 10/20) and 375.63 (released 10/23)

We have received a number of reports that the recent release of Windows NVIDIA drivers 375.57 (released 10/20) and 375.63 (released 10/23) is causing many core 21 (OpenMM) projects to fail. We don’t yet know the cause of this problem, but are actively investigating it.

In the meantime, we strongly encourage you to stick with or downgrade to the last known working Windows NVIDIA driver (372.70) if you would like to continue folding core 21 (OpenMM) GPU projects.

If you have already upgraded to 375.57 or 375.63 and are experiencing issues, we encourage you to report your issues to the NVIDIA Driver Team:

http://surveys.nvidia.com/index. ... 41fa8f07694a40f8ac6

Thanks for bearing with us, and we hope to have a solution soon.

~ The Folding@home core 21 team.
大意：
N家最新驱动有问题，计算结果有误。请暂时不要升级至372.70（不包括）以上最新版驱动。