FAH vijesti

Esh · Jun 19, 2009

MD Workshop

Next week, we will be having a Molecular Dynamics (MD) workshop (see http://simbios.stanford.edu/calendar.htm for details) for three main pieces of Folding@home-related software, namely OpenMM (the GPU acceleration code behind the FAH GPU client), MSMbuilder (the software used to parallelize calculations over all of Folding@home, i.e. how to make all the individual donors' calculations work together) and OpenMM/Zephyr (a tool intended to make molecular dynamics simulation easier for non-experts, built from the accelerated OpenMM codebase).

We're very excited about not just making the key software pieces that drive FAH available to other researchers, and moreover, we're working hard to teach others how they work and how to use them efficiently.

You can learn more about these projects at their simtk.org web pages as well:

OpenMM: http://simtk.org/home/openmm

MSMBuilder: https://simtk.org/home/msmbuilder

Zephyr: https://simtk.org/home/zephyr

Esh · Jun 19, 2009

GPU server issues

We've had a rough night with GPU servers. One has been down hard over the day yesterday (it crashed hard and now can't find its / partition -- the admins are attempting a rescue disk fsck this morning). Two more went down last night (PST) due to the heavy load, but those were easy to get back up (they are up now).

We are stretched a bit thin as we are implementing the new server infrastructure in parallel with the old one. The upshot is that once the new one has been deployed, we will have much more functional collection servers (CS's) and also get work servers (WS's) that should not need to be restarted nearly as frequently when under heavy load.

We are beginning the roll out of the new WS (v5) code this week onto GPU servers, although these issues have slowed us down a bit.

Esh · Jun 19, 2009

How does FAH code development and sysadmin get done?

One of the more common question I get asked is how we do our client/server/core programming and backend system administration. Also, others were curious about updates on various core projects. So, I thought it made sense to answer both in one post, since the answers are related. This will be a bit of a long answer to several short questions, but hopefully it will help give some insight into how we do what we do.

...

As the GPU2 code base matured in functionality, GPU2 core development has been mainly bug fixes, which is a good thing. SMP2 has been testing in house for a while and I expect it will still take a few weeks. The main issue is trying to make sure we get good scalability with threads based solutions, removing bottlenecks, etc. The SMP2 initiative lead to two different cores, one for the Desmond code from DE Shaw Research and another for a Gromacs variant (a variant of the A4 core). We having been testing both in single cpu-core format (the A4 Gromacs core is a single core version of what will become SMP2) and we hope to release in a week or two a set of single core Desmond jobs. If those look good, multiple-core versions via threads (not MPI) will follow thereafter.

The v5 system roll out is continuing, with the plan to have a parallel v5 infrastructure (set up by the new sysadmins) with our current one, and have the science team migrate new projects to the new infrastructure. The v5 code has been running for a while in a few tests and we expect one of the GPU servers to migrate this week, with one or two servers migrating every week as time goes on. The new code does not crash/hang the way the v3/v4 code does (it hung under high load and needed the process to be killed) and so we expect much more robust behavior from it. Also, Joe Coffland has been great regarding responding to code changes and bug fixes.
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Kompletan tekst: http://folding.typepad.com/news/2009/06 ... -done.html

Esh · Jul 6, 2009

Updated Windows SMP client

For those running the windows SMP client, I just wanted to remind donors that the previous client expires today and that an update has been available for a few days. Please see the "Drop-in binary for current Windows SMP console client (6.24) Expires July 4, 2010" on our High Performance Client page (at the bottom of the page):

http://folding.stanford.edu/English/DownloadWinOther

You can also go directly to the update at this link:

[email protected]

Note that this is a "drop in replacement" which means that you would copy this binary on top of the existing binary.

For new installations, please use the previous package and install the replacement on top of it.

Esh · Jul 18, 2009

A new type of work unit

We are preparing for the public release of a new work unit category: extra-large advanced methods work units. Some background information is provided below; we'll update this thread with more details as they emerge.

Why a new work unit category?

We have some specific projects where we 1) have large simulation systems and 2) want to get results fast. As multi-core processors get more powerful, we can perform calculations on Folding@Home that previously required supercomputing clusters.

What's different about these work units from the donor perspective?

These work units are special SMP work units that have larger upload and download sizes, shorter deadlines, and require more memory and CPU resources. That's why we've created a new category.

Is there any points incentive for running these work units?

The base value of these work units corresponds roughly to what an SMP work unit using the A2 core would yield on an equivalent calculation. However, because fast completion is a scientific priority for these work units, we are doing a **trial** of a new bonus scheme where faster WU completion yields a points bonus.

What systems can run these work units?

Right now, only Linux and OS/X systems can run these work units, and they require 8 or more cores. We prefer 8+ *physical* cores, although fast Core i7 machines that are dedicated folders have proven sufficient during the testing process. The points incentives are designed to match appropriate resources to points value; if your machine is marginal for the extra-large work units, you're probably better off running standard SMP.

Does this have any relation to the large-points value work units and recent high-scoring users?

Yes. The initial projects are 2681 and 2682, valued at ~25K points base. Although these point values seem high, the work units are correspondingly larger, so the base PPD (points per day) value is roughly comparable to standard SMP. A collaborator has donated a large amount of compute time to this project; those clients were initially running under username Anonymous/team 1. To give proper credit for the donation, we have changed the username to PDC, team 1. During the period of this donation, there are at any time between 100 and 400 8-core clients running under this username (800-3200 cores total).

Please stay tuned for further details regarding the upcoming release.

Moncho · Jul 18, 2009

sada moramo nabaciti nativni linux

Esh · Jul 18, 2009

Ne znam da li se bas isplati. Mozda da sacekamo osam nativnih jezgri

Esh · Aug 21, 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.
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Link: http://folding.typepad.com/news/2009/08 ... grity.html

Esh · Aug 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).
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http://folding.typepad.com/news/2009/08 ... utage.html

Esh · Aug 28, 2009

@vijaypande: power is back up. Life is much better.

Esh · Sep 9, 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.
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Link: http://folding.typepad.com/news/2009/09 ... owman.html

Esh · Sep 20, 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
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Download: http://biomedicalcomputationreview.org/5/4/index.html

Esh · Sep 27, 2009

Update on new FAH cores and clients

Par dobrih informacija koje se ticu razvoja novih FAH GPU i CPU klijenata:

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).
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Link: http://folding.typepad.com/news/2009/09 ... ients.html

kolinsb · Sep 27, 2009

fine vijesti, nema sta. nadam se, da ce zaista biti poboljsanja, bar kad je ATI u pitanju. takodjer, koliko vidim izbacene su 511 wu. bar ja poprilicno dugo nisam dobio takvu.

Esh · Oct 17, 2009

New servers

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.
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Esh · Oct 23, 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.
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X-Factor · Oct 23, 2009

Ajde da i to docekamo vise, jedan client gdje ce i vlasnici ATi kartica moci ravnopravno da foldaju

Esh · Dec 2, 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.
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Esh · Dec 23, 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)!
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http://protomol.sourceforge.net/

Esh · Jan 3, 2010

GPU2 core auto-upgrade planned for Monday Jan 4, 2010

Happy New Year! We're starting out the new year with a planned auto-core upgrade for GPU core 11. This is planned to happen Monday morning Stanford time. This will bring the GPU core to version 1.31, which has many improvements. In particular, this core is very helpful with the new P10101 WUs. If you'd like to upgrade sooner, you can always do a manual core upgrade at any time by deleting your GPU core (or perhaps safer -- renaming the file so you can revert back if you want).

However, such manual core upgrades are just for FAH experts. The FAH client software will do all of this for you if you like, by the auto-upgrade mechanism built-in on Monday.

It's also worth mentioning that we have made good progress with the GPU3 core and that should be rolling out of beta to production early in 2010.

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