[独立平台] [生命科学类] Folding@Home

shouldbe

不会吧，连买硬盘的钱都没有了？搞分布式存储？这玩笑有点大了。

shouldbe

http://topic.pcpop.com/topic3/TopicWeb/645.aspx

vmzy

September 25, 2009
Update on new FAH cores and clients
We have been pretty busy with new cores for FAH and I wanted to give donors an update.

1) SMP2: Gromacs and Desmond.  Much effort has gone into our "SMP2" project, the codename for the second generation SMP client.  The main goal here was to make it MUCH easier to use.  In order to do that, it meant getting rid of our use of MPI.  We have had two approaches to this.  Both ditch MPI by using threads instead.  One was to switch to a new piece of software for the core.  This has led to the "Desmond" core, based on software from DE Shaw Research.  The second approach was to communicate the MPI issues with the Gromacs developer team and work with them to push for a threads-based Gromacs implementation.  Both of these are coming along well and we are testing cores in house.  You should hopefully see these cores "in the wild" (i.e. running on FAH) in a month or two, assuming that tests go well.

2) Normal Mode Langevin (NML) Dynamics in the Protomol core.  We have been working on another approach to speeding dynamics greatly, based on a new technique called Normal Mode Langevin (NML) dynamics.  This method uses the same style models as normal MD (same force fields, etc) and thus should have the same accuracy, but with a pretty significant speedup due to algorithmic advances.  NML is complementary to our other methods, so we're hoping to add it to everything else (in particular to the GPU core).  To start, we will be testing it in a new core, based on the Protomol software.  Protomol is designed to allow for rapid prototyping of molecular simulations, which is perfect for NML.

3) GPU3:  Next generation GPU core, based on OpenMM.  We have been making major advances in GPU simulation, with the key advances going into OpenMM, our open library for molecular simulation.  OpenMM started with our GPU2 code as a base, but has really flourished since then.  Thus, we have rewritten our GPU core to use OpenMM and we have been testing that recently as well.  It is designed to be completely backward compatible, but should make simulations much more stable on the GPU as well as add new science features.  A key next step for OpenMM is OpenCL support, which should allow much more efficient use of new ATI GPUs and beyond.

I'm very excited about these new advances.  It really should fundamentally improve the key science software behind FAH as well as making the donor experience much more smooth on our more experimental clients (i.e. on GPU and SMP).
大意：
1、smp2大概一个月后开始公测。
2、内核改算法，计算加速
3、GPU3开发中，提高稳定性和兼容性，提供对ATI的opencl的支持

金鹏

opencl下A卡的计算效率应该要比现在提升很大吧？期待。。。

foxhound

十分期待SMP2呀~~~~

另外GPU3现在的开发进度如何？

金鹏

SMP2对硬件要求奇高，至少八线程，就是目前的爱妻开档，8G及以上内存，面向高端和服务器平台的说

foxhound

原帖由 金鹏 于 2009-9-27 23:02 发表
SMP2对硬件要求奇高，至少八线程，就是目前的爱妻开档，8G及以上内存，面向高端和服务器平台的说

那开超BIG包才会接到这种任务 普通任务不会

vmzy

October 13, 2009
New servers coming soon
We've ordered a new class of servers which should make a big impact on FAH server load, and also allow us to release several new big projects with more WUs.  We're very excited about this since we've been limited by server space recently, which has also lead to WU shortages.  The new servers each have 24 x 2TB drives, so we should have plenty of space.

The servers should physically arrive next week, so including set up time, WU testing protocols, etc, it will still take a few weeks to get the new WUs out broadly, but at least the ball is rolling.
大意：
因为服务器硬盘空间不足（所以最近WU比较紧张），而且马上要上马新的大项目（译者注：难道是传说中的SMP2，据说是11月开服），所以我们新购置了一组服务器（每个服务器硬盘空间为24 x 2TB）。
新服务器下周到货，然后我们会开始安装调试。

金鹏

猜想是基于opencl的GPU3先上的说

SMP2局限性太大，估计速度会慢些

vmzy

October 22, 2009
Updates on new cores: Protomol and GPU3 core
There has been a lot of work on updating the Protomol core to bring it in line with the other cores in Folding@home.  I'm happy to say that a lot of progress has been made and it's looking much better.  Joe will continue to test it, but it looks close to be moving to the next levels of QA.

The GPU3 core is also moving along.  It will be called core_15 (the natural next number in the GPU series).  The main changes there have been to incorporate the updated GPU code from OpenMM.  OpenMM was based on our FAH GPU MD code to start, but has had several enhancements and additions.  In particular, it should be much more stable than the previous FAH GPU MD cores.  However, this stability does come at a mild cost in performance.  We will address this at the benchmarking stage, since all core 15 (GPU3) projects will start fresh, not continuing existing projects.
大意：
Protomol（NML）和GPU3新内核进展顺利。
译者注：smp2呢？流产了？

vmzy

November 12, 2009
stats hiccup -- we're on it
There was a problem with the stats server over the night.  We got to it first thing in the morning (around 6:30am pacific time), but it looks like a few stats updates were missed.  The missed data is backed up on another machine and we can re-enter it.  However, we typically take a couple of days to re-enter it, to make sure it is done right.

So, the bottom line is that the stats system is back up, will we recredit some missing WUs not credited over the night, but this will take a couple of days to complete.  Sorry for the delay on the recredit, but it's good to make sure we do it right, rather than in a rush.
大意：
统计系统挂了，维修中。估计要几天才能恢复正常。

vmzy

November 18, 2009
Changes to psummary files in the works
We will be adding one new field to the psummary web pages (eg, http://fah-web.stanford.edu/psummary.html) to include a new part of FAH stats.  We will give more info soon, but for now, please note the additional column on the far right.  

For third party tools which parse these web pages, we have added the column at the far right in the hopes that this would not break current tools' parsing routines.  Note that we are also looking in developing more systematic ways to interact with third party utilities, although that is still in the works.  For now, we will give heads up to changes here in this blog.
大意：
准备增加新的统计页面。

vmzy

November 23, 2009
Stats recredit in progress
We're running a stats recredit from Nov 12.  Sorry for the delay in getting this going.
大意：
正在给之前漏打分的任务重新打分。

vmzy

December 01, 2009
SMP2 core update
We are excited to announce progress in our testing of new SMP2 cores. These cores use threads-based parallelization instead of MPI and, we hope, should be much more robust than our first-generation SMP cores.

The SMP2 cores are currently in testing; watch for future announcements regarding their release. The first SMP2 core to be released will be a Gromacs-based core with core number A3. In conjunction with this release, we are implementing some updates to our points benchmarking system. In particular, we will use early-completion bonuses, which we have been testing with the bigadv work unit program, more extensively for SMP2 cores.
大意：
SMP2消息
SMP2使用线程并发代替MPI，内核使用A3，等测试完成后我们会正式发布。我们改变了SMP2积分策略，对早算完的任务给予积分奖励。

vmzy

December 22, 2009
Release of new Protomol (Core B4) WUs
As announced some time ago we have been working on a new core (Protomol core B4), and it has been looking good in QA so we have started to release Promol core WUs more broadly.  We have a preliminary Protomol FAQ for those who are curious to get more information.

This new core implements the NML (Normal Mode Langevin) method which accelerates the long-time dynamics of the proteins by a factor that can reach speeds up to a hundred times faster than those of molecular dynamics. This method searches for low frequency directives by using normal mode analysis and projects the motion of the molecule along them while resolving the nearly instantaneous motion. If you want to learn more about this method, you should read this pre-publication: Multiscale Dynamics of Macromolecules Using Normal Mode Langevin.

Based on Protomol 3.1, this core and its associated projects have the following goals:

To validate NML by simulating the folding and dynamics of the Fip35 WW domain.
To understand the role of mutations on folding.
To understand the activation of src Kinase, an enzyme that is involved in the onset of some kinds of cancer.

On the technical side, this core is able to take advantage of most modern CPU optimizations (SSE2, SSE3, SSSE3, SSE4.1 and SSE4.2), however, a few compatibility issues are still present on AMD processors, resulting in the core only using SSE2 on these chips. This should change in the not-too-distant future when the issues have been worked out. If you have a processor that doesn’t have the above mentioned optimizations (Pentium 3, Athlon XP, etc.), please report the behavior and the performance of this core on your machine.

For more information about the Protomol core, you should visit the Protomol official site.

The new projects are distributed by a new server (129.74.85.48) which is located at the University of Notre Dame (Indiana) and have the following characteristics:

p10000 : 544 atoms, 84.48 points, preferred deadline 3.07 days, final deadline 23.04 days. This project uses conventional simulation methods.
p10001 : 544 atoms, 50.56 points, preferred deadline 1.84 days, final deadline 13.79 days. This project uses the NML simulation method.
We will be posting more information as time goes on.   I'm very excited about the new capabilities here, since NML allows us to algorithmically get an amazing speed up, i.e. without any additional CPU power.    That algorithmic speed up multiplied by the vast power of FAH could mean very significant advances shortly, making 2010 an exciting year for FAH (in many ways)!
大意：
发布新Protomol B4内核任务（公测）
新内核使用NML (Normal Mode Langevin)算法，比普通算法快百倍左右。
从技术上来说，新内核，几乎支持所有指令集(SSE2, SSE3, SSSE3, SSE4.1 和 SSE4.2)，但目前AMD的cpu最高只能使用到SSE2指令集，我们会尽快解决这个问题。如果遇到问题麻烦到论坛上报。
译者注：只有加-advmethod标签，参加测试的FAHer才有机会接到这种任务。
FAH的BOSS曾说如果一切顺利将在11月发布SMP2，现在12月都快过完了。万恶的跳票啊！
补充一下：b4内核理论上属于classic单cpu版的任务，不是smp哦。smp任务使用的貌似都是A系列的内核。