Folding@home

main web page issues

We're seeing some issues with the main http://folding.stanford.edu web page.  We have some ideas, but it's late here (11pm pacific time), so we'll have to wait for IT to get in to work in the morning to get a fix implemented.

For now, if you see "Access Denied", please try to reload the page: that should yield a working page.

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.

Stats recredit in progress

We're running a stats recredit from Nov 12.  Sorry for the delay in getting this going.

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.

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.

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.

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.

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).

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.

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