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  1. Posté(e) · Signaler la réponse

    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. 

     

     

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  2. Posté(e) · Signaler la réponse

    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

     

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  4. Posté(e) · Signaler la réponse

    We have had some issues with the GPU assignment server (AS) migration to new hardware.  Several issues have been resolved, including 

     

    - issues with ATI GPU client work assignments- some work servers without work

    But there are two remaining issues which we have filed tickets with Stanford IT, including- port 80 forwarding for the GPU AS- allowing assignments to 171.64.122.70

    Of these remaining issues, the port 80 issue is a big issue for those who have port 8080 blocked and we've been pushing IT to get this resolved ASAP.  The second issue (going to 171.64.122.70) is less time critical (that server can still receive completed WUs from clients), but we would like to get more GPU work servers on line in general.

     

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  5. Posté(e) · Signaler la réponse

    We hit a few snags with bringing back one of the servers, so we've left the stats update down until we could resolve the problem.  It looks like we have a reasonable fix for now, so we're going to turn the stats update back on.  This means the stats will likely take a while to update due to the backlog, but all the points from the last 10 hours or so should be coming in.

     

     

    We will likely take the stats update off line again tomorrow morning so we can make a longer term fix to the issue at hand that slowed us down today.

    However, in general, the outage went ok, especially considering it included a major migration of hardware.  The new hardware should be much more reliable (0.5 year old vs 5 years old) and also much more versatile and sophisticated.

    Almost all of the migration is done, but the last main bit of infrastructure that needs to be migrated is the stats system, which we're waiting for a new server to come in.

     

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  6. Posté(e) · Signaler la réponse

    Our planned shutdown today is going onward as planned.  We hope to have the main systems migrated, except for the stats db (which will be down) and the stats web pages.  The main web pages, work servers, and AS's should be up (although the AS's may have issues if the migration isn't working correctly).

     

     

    We are monitoring the situation very closely.  Thanks for your patience here!

     

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  7. Posté(e) · Signaler la réponse

    There is going to be some major maintenance at Stanford on Monday May 18 in the morning (Pacific time).  Most of FAH will be up, but right now, the stats web site looks like it will be down.  Also, it is possible that the GPU AS and PS3 AS will be down, although we are working on migrating those this week to avoid downtime.  The data servers (work servers) should all be up.  Stats updates will be suspended briefly during this period as well, but will start back up (with no WUs lost) after we're done.

     

     

    I'll post more as we have more to say.  At its worst, those servers should only be down for about 3 hours, assuming all goes well with the infrastructure work being done.

     

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  10. Posté(e) · Signaler la réponse

    In order to speed the stats updates, we've suspended the updates for the project WU counts.  This does not affect WU counts or points, just the stats pages which tells donors how many WUs they have contributed to each project.

     

     

    We have polled donors in the past regarding this issue, and there was overwhelming support for this change, especially if it could significantly increase stats updates speeds.  After doing some in house tests, we expect that this will greatly enhance stats updates speeds, so we have rolled this out.

    Even if this is the main culprit for the slow stats updates, we may put this back in time, once we work out a better scheme for how to update this information and/or get hardware better suited for it.  The main issue here is that this is a lot of information, with data going back many, many years, and it has become unwieldy.

    For now, this should lead to a pretty dramatic difference in stats update times.  It looks like we can now get it done in about 20 minutes, rather than the ~2 hours it was taking previously, for 3 hours worth of stats accumulated.  

    If this looks good, we will likely switch stats updates to occur more frequently in the future, starting with every 2 hours.

     

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  11. Posté(e) · Signaler la réponse

    There has been much interest in our stats page (osstats) detailing different OS's and the FLOPS they produce:

     

     

    http://fah-web.stanford.edu/cgi-bin/main.py?qtype=osstats

     

    We've been trying to come up with a way to standardize these numbers so that they can be more easily compared to each other.  That has resulted in a new FAQ:

    http://folding.stanford.edu/English/FAQ-flops

     

    We also plan on updating the osstats page to include both the Native FLOPS (which is on there now) and the more common x86 FLOPS, which allows for a more "apples to apples" comparison of FLOPS.

     

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  12. Posté(e) · Signaler la réponse

    We're happy to announce a new paper (#63 at http://folding.stanford.edu/English/Papers).  This paper describes the code behind the Folding@home GPU clients, detailing how they work, how we achieved such a significant speed up on GPUs, and other implementation details.  

     

    For those curious about the technical details, I've pasted our technical abstract below:

    ABSTRACT.
     We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core.
     

     

    Also, this software is now available for general use (for scientific research outside of FAH).  Please go to  http://simtk.org/home/openmm for more details.

     

     

     

     

     

     

     

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  13. Posté(e) · Signaler la réponse

    Based on our FLOP estimate (see http://fah-web.stanford.edu/cgi-bin/main.py?qtype=osstats), Folding@home has passed the 5 petaflop mark recently.  To put it in context, traditional supercomputers have just broken the 1 petaflop mark, and even that level of performance is very challenging to aggregate.  The use of GPU's and Cell processors is has been key to this, and in fact the NVIDIA numbers alone have just passed 2 petaflops.

     

     

    Thanks to all who have contributed and we look forward to the next major milestones to be crossed!

     

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  14. Posté(e) · Signaler la réponse

    The machine which handles the main assignment server (AS) and the stats update is currently down.  We expect that this machine will be back up by 10am pacific time.  Since this has happened previously somewhat recently, we are looking into transferring some duties on this machine to both keep it less loaded and to lessen the severity if it goes down again.

     

     

    This means that the stats update will be down until we get the machine back up, but the back up AS should handle all classic clients, and the PS3 and GPU clients are unaffected (as their AS is on a different machine).

     

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  15. Posté(e) · Signaler la réponse

    It's still early (since this paper was just accepted), but I wanted to give FAH donors a heads up on our work on Huntington's Disease aggregation, which is just about to come out in the Journal of Molecular Biology.  I'll comment on it more in a future post.

     

     

    See our papers page for more details.

     

    Voir l'article complet

  16. Posté(e) · Signaler la réponse

    We've made a code change in the two main assignment servers (assign.stanford.edu & assign2.stanford.edu -- but no the PS3 or GPU AS's) to handle a potential problem people have been having with getting through firewalls.  

     

     

    For those who are very experienced with running FAH (eg are familiar with the logs and how to interpret them):  If you have had problems in the past with your firewall, could you now try again and see if you can get a server assignment?  You likely won't be able to get to the server itself (we've just updated the AS code), but just knowing that this fix helped will let me know what we should update all of the work servers ASAP.

    If everything was working fine, but not it isn't, please make a post in the forum:  http://foldingforum.org

     

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  19. Posté(e) · Signaler la réponse

    We're happy to announce a new Pande Group paper (paper #61 at http://folding.stanford.edu/English/Papers).  This paper describes a new computational screen to identify important mutations in influenza:

     

    Functionally Important Residues in Influenza Hemagglutinin. 

    Peter M. Kasson and Vijay S. Pande. Pacific Symposium on Biocomputing

    14:492-503(2009). 

    Download URL:

     

    The influenza hemagglutinin protein performs several important

    functions, including attaching the virus to cells it will infect and

    releasing the viral genome into the interior of the cell. Most

    protective antibodies against influenza also bind to the hemagglutinin

    protein. We wish to understand how mutations to hemagglutinin affect

    viral function, including what keeps avian influenza ("bird flu") from

    being readily transmissible between humans. In this paper, we have

    applied a technique from information theory known as mutual

    information to genetic sequence data to predict important mutation

    sites on the hemagglutinin protein. In follow-up work, we are

    combining this technique with other methods to refine these

    predictions and test some of them using Folding@Home. 

     

    PS For those curious out in more details, check out the paper (see link above) or the technical abstract:

    Influenza hemagglutinin mediates both cell-surface binding and cell

    entry by the virus. Mutations to hemagglutinin are thus critical in

    determining host species specificity and viral infectivity. Previous

    approaches have primarily considered point mutations and sequence

    conservation; here we develop a complementary approach using mutual

    information to examine concerted mutations. For hemagglutinin,

    several overlapping selective pressures can cause such concerted

    mutations, including the host immune response, ligand recognition and

    host specificity, and functional requirements for pH-induced

    activation and membrane fusion. Using sequence mutual information as

    a metric, we extracted clusters of concerted mutation sites and

    analyzed them in the context of crystallographic data. Comparison of

    influenza isolates from two subtypes—human H3N2 strains and human and

    avian H5N1 strains—yielded substantial differences in spatial

    localization of the clustered residues. We hypothesize that the

    clusters on the globular head of H3N2 hemagglutinin may relate to

    antibody recognition (as many protective antibodies are known to bind

    in that region), while the clusters in common to H3N2 and H5N1

    hemagglutinin may indicate shared functional roles. We propose that

    these shared sites may be particularly fruitful for mutagenesis

    studies in understanding the infectivity of this common human

    pathogen. The combination of sequence mutual information and

    structural analysis thus helps generate novel functional hypotheses

    that would not be apparent via either method alone.

     

     

    Voir l'article complet

  20. Posté(e) · Signaler la réponse

    Jim Clark has been a major donor to Stanford and his great contributions has had a huge impact on my group's work in general and on Folding@home in particular.  Jim Clark was a professor of CS at Stanford, but subsequently was involved in many successful major Silicon Valley companies (see his wikipedia page for all the details).  He also donated over $100M to Stanford to build the Clark Center, a University-wide center for interdisciplinary biology.  

     

     

    Today, Dr. Clark along with John Hennessy (the President of Stanford University) visited our offices to hear about our recent work.  They both were heavily involved in computer architecture in the past, so they were interested to hear about our work with GPUs and the success we are seeing there (in particular, the significant speed increases).  Also, they are both interested in neuroscience and so I was excited to tell them about our recent Alzheimer's work.

    Anyway, I was excited to give them both an update and some idea of where we're going, and it was great fun for me to tell them all about how much we've done.

     

    Voir l'article complet

  21. Posté(e) · Signaler la réponse

    Jim Clark has been a major donor to Stanford and his great contributions has had a huge impact on my group's work in general and on Folding@home in particular.  Jim Clark was a professor of CS at Stanford, but subsequently was involved in many successful major Silicon Valley companies (see his wikipedia page for all the details).  He also donated over $100M to Stanford to build the Clark Center, a University-wide center for interdisciplinary biology.  

     

     

    Today, Dr. Clark along with John Hennessy (the President of Stanford University) visited our offices to hear about our recent work.  They both were heavily involved in computer architecture in the past, so they were interested to hear about our work with GPUs and the success we are seeing there (in particular, the significant speed increases).  Also, they are both interested in neuroscience and so I was excited to tell them about our recent Alzheimer's work.

    Anyway, I was excited to give them both an update and some idea of where we're going, and it was great fun for me to tell them all about how much we've done.

     

    Voir l'article complet

  22. Posté(e) · Signaler la réponse

    Stanford will be closed for the next two weeks for the Winter Holidays (ending January 5, 2009).  FAH will still be up (FAH is always up), but we will be on a reduced staff.  FAH team members have broken up their vacations so that there will always be someone around, but the main issue is that responses to problems will likely be slower than normal.  However, we have been working to add lots of jobs, clear out lots of HD space on servers, get all the servers up, such that we should hopefully be in good shape even if there are some problems. 

     

     

    We'd like to wish all the FAH donors a happy holiday and thank all of you for all your great help with our project.

     

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  23. Posté(e) · Signaler la réponse

    This is very preliminary news, but something I'm very, very excited about, so I'll give some advance news.  On Tuesday, we presented our results regarding new possible drugs (small molecule leads) to fight Alzheimer's Disease at a recent meeting at Stanford.  This meeting was part of the NIH Roadmap Nanomedicine center (http://proteinfoldingcenter.org/) retreat and was supported by NIH grants to Folding@home.

     

    It's very early (so we are not publicly talking about the details until this has passed peer review), but we are very excited that it looks like we may have multiple small molecules which appear to inhibit toxicity of Abeta, the protein which is the toxic element in Alzheimer's Disease.

    This is exciting in many ways.  It's been a long road for FAH to get to this point, but we are starting to see the possibility of seeing these results published easily before our 10th birthday (October 2010).  Considering all the technology development that had to be done in the first five years, these results have come very quickly (in the last 3 years), which is exciting.  In particular, we are now looking to apply these methods to other protein misfolding diseases (we have pilot projects for Huntington's Disease underway).

    Finally, I should stress that while we're very excited about this, it's still early and a lot can go wrong between where we are and having a drug that doctors can prescribe.  Over the holidays, we will be double checking the experimental data, crossing t's and dotting i's to make sure there is nothing missed before we think about submitting this for peer reviewed publication.  Also, there is still a long way from an interesting possible drug (where we are now) to something which has passed FDA clinical trials (where we'd love to be), and a lot can go wrong in clinical trials in particular.  

    Thus, this is an important milestone for FAH and we are very grateful to all who have contributed.  Happy holidays to all!

     

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  24. Posté(e) · Signaler la réponse

    During the next two weeks (December 20 - January 4), the

    Backbone Networking group plans to schedule a backbone maintenance

    window every morning from 4-8am pacific time to implement improvements in the

    network, as they did last year. In most cases, the changes should not

    affect the connectivity of the networks used by Folding@home. In cases

    where they might, any interruption in service should be under 5 minutes.

     

     

     

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  25. Posté(e) · Signaler la réponse

    We have made several bug fixes and speed improvements wrapped into a new ATI GPU client (version 6.23).  We strongly suggest that everyone upgrade.  While current (and new cores, especially ATI GPU core version 1.22) should work with other clients, we are seeing some possible issues which the new client fixes.  

     

     

    As always, we suggest that one backup their machine before upgrading software, especially in case you would like to go back to the previous version.  You can download the new client at

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

     

    and as always, please post comments in the forum (http://foldingforum.org).

    PS For those with NVIDIA GPUs, you could also consider upgrading to client version 6.23 (from http://folding.stanford.edu/English/DownloadWinOther ) as it also fixes some issues.  However, this is less of a critical at the moment for NVIDIA than ATI.

     

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