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GPUGRID
  • 2018-12-24: Season's Greetings from Gpugrid!

    We hope that the cold of the winter is at least a bit relieved by WUs crunching... to you all crunchers we wish a Merry Christmas and a happy New Year!



  • 2018-11-30: WU: IAP

    Dears,

    I am sending a new experiment on the short queue targeting inhibitor of apoptosis proteins.

    Inhibitor of apoptosis proteins (IAPs) constitute a family of conserved protein in the apoptotic pathway. In other words, they prevent the "programmed death" of cells; therefore, their over-expression enhances survival and resistance to anticancer agents. Small molecules (smac mimetics, SM), similar to the natural antagonist of IAPs, are a first generation of drugs which have been developed to sensitize cells to apoptosis. Although they are currently used in cancer therapy, there are some cases in which the SM-mediated degradation brings to the non canonical activation of NFkb and so to the expression of CIAP2 gene, suppressing TNF-alpha killing; in other words, resistance may arise to SM. In this set of simulations we are testing some mechanisms with which apoptosis in resistant cancer cells may be restored.

    The WUs are tagged "*IAP*".

    Thanks!



  • 2018-07-27: Windows apps restored

    We restored the windows applications.

    If you get errors such as "197 (0xc5) EXIT_TIME_LIMIT_EXCEEDED", please try these:

    - R?e?r?u?n? ?b?e?n?c?h?m?a?r?k?s?
    - Reset the project
    - Wait the problem out

    If nothing works and you want to fix right away, there is a more complex workaround editing client_state.xml

    The problem is somewhat explained here.



  • 2018-07-17: Windows GPU Applications broken

    Currently we have the windows applications broken. We are looking into it.

    Linux and CPU jobs work fine



  • 2018-07-03: More CPU jobs

    ...with a new and improved application (Linux only). The current version should eliminate dependencies on gcc and devel libraries.



  • 2018-06-06: More CPU jobs

    Please remember that to run QMML jobs (linux only) you will need to install both the gcc and libc6-dev or glibc-devel (the latter depends on your distribution) packages.



  • 2018-06-06: Attempting a fix for multiple CPU jobs starting at the same time

    Application QC version 319 uploaded as an attempt to fix the problem.



  • 2018-03-22: Phd position, please share it

    http://www.multiscalelab.org/jobs/phd-machine-learning-computational-chemistry/



  • 2018-03-01: New publication: Molecular Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors

    Hello everyone!

    I just wanted to announce that our work on the chemokine CXCL12 has just been published (https://www.ncbi.nlm.nih.gov/pubmed/29481075) and badges have been distributed accordingly. I have updated the science page (http://gpugrid.net/science.php?topic=methods) and you should now be able to check your contribution to the work.

    Thanks again your contribution and for making this project awesome!

    Gerard M.



  • 2018-02-20: The experimental QC for W10 is now called QC_beta

    Another attempt... instructions here



  • 2018-02-18: Experimental QC app for Windows 10

    Dears,

    have a test QC app for Windows 10. QC relies on the PSI4 software which does not have a Windows version. Therefore, we'll rely on WSL (Windows Subsystem Linux - a nice lightweight Linux-like environment to run native apps inside Windows), provided by Microsoft in the recent version of Windows 10.

    Unfortunately I don't think there is a way to prevent the distribution to non-W10 and non-WSL hosts.

    Therefore, to run QC tasks, the first time only you will have to prepare the environment as follows...

    Enable WSL. The procedure unfortunately varied over time, the most current being here Install the Ubuntu distribution via the App store (it is free of course). Launch the newly-installed Ubuntu command line via its icon.
    It will request a password for a new user being created. Provide one. Now you have a working Ubuntu environment. As for the native ones, manual installation of the gcc package is required. So, in the Ubuntu bash prompt, execute the following commands (the prompt reads like "(your_chosen_user)@MACHINENAME:path")

    sudo apt update
    sudo apt install gcc


    (Of course, if you already have WSL installed, you will just need step 4.)

    Technical details: In addition to the normal Boinc project and slot directories, the app will use space in the /tmp/gpugrid_miniconda directory inside your WSL installation (not directly accessible from Windows). Unlike the Linux app, the space is not automatically cleaned up when you uninstall BOINC or reset the project. To clear it, either uninstall Ubuntu, or remove it from the Ubuntu prompt.



  • 2018-02-05: CPU jobs on Linux

    Hi, we need more CPUs on Linux to run QM simulations. Anybody can help?



  • 2018-02-05: Linux app failing

    We will need to upload a new linux app soon to solve the expired current executable.

    gdf



  • 2018-01-04: New Student and QMML Project

    Hello everyone and happy new year!

    My name is Dominik and I am a masters student from Germany. I studied biochemistry in the city of Bayreuth, but I always focused my work more towards biophysics and bioinformatics. I'm in the group since October, where we have since then started to initiate a quantum chemical machine learning project.
    We soon came to the conclusion that we need a quantum chemical database in order to drive research forward in this field.

    This is where we need your help!

    Some of you have already seen that I released a small amount of 50.000 WUs yesterday evening and there is even more. The WUs contain a certain amount of small molecules for which quantum chemical simulations will be performed. Depending on the size of the molecule the simulation (and the WU) will take longer. We did initial benchmarks to estimate how to design the WUs, but everything turned out a bit different with the very long WUs I prepared for Toni which you were fighting with over the last month. Thanks to everyone who was helping and sticking through this! I will try to adjust the WUs as best as I can, but for now the current DOMINIK WUs that are already on the server are fixed.
    Regarding the windows based QM tasks I cannot give a clear answer about this yet, but it's definitely one of our goals.

    It is a long term goal of ours to keep running the quantum chemistry tasks on GPUGRID and I try my best to ensure that there are always tasks available.

    So thanks again to everyone who is participating and helping out. I really appreciate it very much.

    Have a great start into 2018!



  • 2017-12-19: Experimental QMML WUs

    We are experimenting with CPU workunits. Right now they are Linux only. Please note that you may need to install "gcc" in your machine for them to work. More details in the Multicore forum!



  • 2017-11-10: New multicore app and WUs

    Dears,

    we would like to test our new CPU multicore application for quantum chemistry tasks ("QC"). Since it?s the first time we have a CPU app out, I?ll test the behavior of GPUGRID with a relatively large batch that you will see soon. Workunits are named "*QC309big*".

    Here?s some features of the app, in short (subject to change):

    * Platform: Linux only for now, generic x64.
    * Threads: as many as Boinc decides. I guess it depends on your machine, your preferences, and other running tasks in ways which are obscure to me?
    * Run time: about 1 CPU hour per WU (so, shorter if multithreading)
    * Credit: computed with the default algorithm (tasks are short, don?t expect much). Bonus mechanism for fast turnaround is still on.
    * Known bugs: restarts and checkpoints. This should be mitigated with the ?keep in memory when suspended? option. Sorry about that, it?s outside of our control.
    * Network behavior: the first time you get a WU of this kind it downloads a Python interpreter (miniconda) and then some open-source packages, and installs them in the project directory. The installation is reused whenever possible.
    * Disk usage: could go around 1 GB, perhaps more when tasks are running. Resetting the project should remove everything.
    * Memory usage: should be around 1 GB when running.

    Depending on the results of this test, we?ll start thinking about other platforms.

    Thanks and nice crunching!

    Toni



  • 2017-08-09: New publication: High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD

    Dears, we added badges for a recent methodological publication, High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD.

    We describe a procedure to automatically set-up membrane simulations, and show it working en masse on all membrane structures published in the OPM database (hence the WU names you may have seen in the past).

    Membrane proteins are quite interesting because they are involved in extra-cellular signalling, not to mention how many of them are drug targets; simulations are especially time-consuming to set-up, and we tried to develop tools to make the process less error-prone.

    Thanks to all contributors!



  • 2017-06-12: New publication: Complete protein?protein association kinetics!

    Hey all,
    some astute members might have noticed we got a new publication out? https://goo.gl/MoIi0d

    You remember these BARNA/BNBS workunits? Well, we finally made it :)

    Frank and Nuria did an incredible work with our simulations and got the paper published in Nature Chemistry which is a top-top journal in our field!

    To thank you all for this incredible contribution we will be handing out badges soon and you have my (and our group's) heartfelt thanks to all of you!

    ps. A layman news piece on the article https://www.upf.edu/home/-/asset_publisher/UI8Z8VAxU47P/content/id/8788860/maximized



  • 2017-06-12: Complete protein?protein association kinetics

    Hey all,
    some astute members might have noticed we got a new publication out? https://goo.gl/MoIi0d

    You remember these BARNA/BNBS workunits? Well, we finally made it :)

    Frank and Nuria did an increeedible work with our simulations and got the paper published in Nature Chemistry which is a top-top(-top?) journal in our field!

    To thank you all for this incredible contribution we will be handing out badges soon and you have my (and our group's) heartfelt thanks to all of you!

    ps. A layman news piece on the article https://www.upf.edu/home/-/asset_publisher/UI8Z8VAxU47P/content/id/8788860/maximized



  • 2017-04-17: An important note for Windows XP users

    Dear all,

    GPUGRID will stop supporting Windows XP in April 2018

    Every version of the science application we have to maintain costs us time and effort, and it's important that we focus our resources where they can give us the best return.

    Building and testing Windows XP versions our applications is increasingly difficult now the OS is unsupported by both Microsoft and NVIDIA.
    There are now fewer than 20 Windows XP machines crunching on GPUGrid, out of a total of over 2500, and it's difficult to justify on-going engineering effort for a small fraction of our capacity.

    Sadly, this means that it's time for us to stop supporting Windows XP. The recent update to the application will be the last, and will cease to work one year from now. After that time work will only be issued to hosts running Windows 7+ or Linux.

    If this affects you, please accept my apologies. Your contribution has been greatly appreciated, and I hope that you'll continue to support us.

    Matt



  • 2017-04-17: App update 17 April 2017

    Dear All,

    If you've been following other threads on the forums, you'll know that the Windows versions of the science application have recently been updated. There are now two versions, 849 (CUDA 6.5) and 918 (CUDA 8.0), which will be assigned to hosts as follows:

    * 849
    - Windows XP (32 or 64 bit) and any GPU >= sm 3.0
    - Any 64bit Windows with a Kepler 3.0 device

    * 918
    - Any 64bit Windows, Vista or later with any GPU > sm 3.0 and driver >= 370.0

    The peculiar exception for sm 3.0 devices is due to a compiler problem with CUDA 80 that affects only that hardware version. When that's fixed, hosts with a non-XP Windows will get 918.

    If you see any behaviour that deviates from this, please report it here.

    If you think you should be getting work, but aren't please check that your system complies with the above, in particular the driver revision and that the OS is 64 bit.



  • 2017-04-07: New acemdlong app

    Windows Version 915 is now unified for Kepler, Maxwell and Pascal.

    No problems expected, bit report anything unusual here..

    MJH



  • 2016-12-23: Download problems. Can you help?

    After some tests the only thing that we are sure is that downloads of large files stall when the operating is CentOS7. If we use CentOS6 they do work. Can anybody reproduce it?

    the way we test it on gpugrid is:
    wget --no-cache --delete-after http://www.gpugrid.net/download/libcufft.so.8.0

    We don't know if it is a combination of CentOS7 and our network or it's a problem of CentOS7.

    There could also be other problems but this is one.

    gdf



  • 2016-12-21: WU: BNBS

    In case anyone is wondering what these WUs are, we are running some extra simulations on the Barnase Barstar system (previously called BARNA: http://gpugrid.net/forum_thread.php?id=3709#36142 ) to answer some questions of the reviewers. If the results get us through the review process this will be a major publication :)



  • 2016-11-30: New server is running

    Post here any problem please



  • 2016-11-30: New server is running!

    Post here any problem please



  • 2016-11-30: Server going down for upgrade

    Please be patient.



  • 2016-11-17: Major server upgrade!

    Dear cruchers!

    the GPUGRID server you know and (I guess?) love has done a huge service to science. Thanks to your support, the experiments we have being running grew in size and scope... AND we have enough ideas for the future to keep this trend.

    So, we decided to significantly upgrade the capabilities of our server - and a new is almost in place. Likely next Monday, we'll stop the server for some hours, then perform the transition. We now need your patience, because the switch-over will require some down time (and hiccups, possibly).

    But we are definitely looking forwards for the new expanded experimental capacity! We'll keep you informed!



  • 2016-10-27: PASCAL App Testing

    Hello Crunchers,

    I have just put out application version 900 for owners of Pascal GPUs. To test this you need:

    * A Geforce 10-series or Tesla P-series GPU
    * 64 bit Windows 7 or later
    * NVIDIA Driver 360+
    * Accept beta work, and WUs from the acemdbeta and acemdshort applications

    Please report all problems in this thread.



  • 2016-10-25: I'm a postdoc! AMA

    Hey! I guess I forgot to tell you guys, but better late than never :P
    I successfully defended my Ph.D. on the 16th of September!
    Now I'm continuing for a while as a postdoc in your good-ole well-known lab.

    I would like to thank you all for making this possible! Without you* I would never have done all this cool research, publications and completed my thesis.

    Many, many thanks and to further awesome research!


    * and your awesome GPUs :D



  • 2016-10-25: I'm a postdoc!

    Hey! I guess I forgot to tell you guys, but better late than never :P
    I successfully defended my Ph.D. on the 16th of September!
    Now I'm continuing for a while as a postdoc in your good-ole well-known lab.

    I would like to thank you all for making this possible! Without you* I would never have done all this cool research, publications and completed my thesis.

    Many, many thanks and to further awesome research!


    * and your awesome GPUs :D



  • 2016-10-20: New badges!

    Dear all!

    We added badges for two great papers which came out this year. Both appeared in Scientific Reports, a highly-regarded open-access journal.

    I don't think I can do better justice to the works than the author's own words, so I am copying here their abstracts, which hopefully convey the gist of the respective impact:

    Noelia's study of ions binding to the myo-inositol monophosphatase enzyme:

    Molecular recognition is rarely a two-body protein-ligand problem, as it often involves the dynamic interplay of multiple molecules that together control the binding process. Myo-inositol monophosphatase (IMPase), a drug target for bipolar disorder, depends on 3 Mg2+ ions as cofactor for its catalytic activity. Although the crystallographic pose of the pre-catalytic complex is well characterized, the binding process by which substrate, cofactor and protein cooperate is essentially unknown. Here, we have characterized cofactor and substrate cooperative binding by means of large-scale molecular dynamics. Our study showed the first and second Mg2+ ions identify the binding pocket with fast kinetics whereas the third ion presents a much higher energy barrier. Substrate binding can occur in cooperation with cofactor, or alone to a binary or ternary cofactor-IMPase complex, although the last scenario occurs several orders of magnitude faster. Our atomic description of the three-body mechanism offers a particularly challenging example of pathway reconstruction, and may prove particularly useful in realistic contexts where water, ions, cofactors or other entities cooperate and modulate the binding process.
    Nathan's study of S1PR1 receptor:

    The binding process through the membrane bilayer of lipid-like ligands to a protein target is an important but poorly explored recognition process at the atomic level. In this work we succeeded in resolving the binding of the lipid inhibitor ML056 to the sphingosine-1-phosphate receptor 1 (S1P1R) using unbiased molecular dynamics simulations with an aggregate sampling of over 800??s. The binding pathway is a multi-stage process consisting of the ligand diffusing in the bilayer leaflet to contact a ?membrane vestibule? at the top of TM 7, subsequently moving from this lipid-facing vestibule to the orthosteric binding cavity through a channel formed by TMs 1 and 7 and the N-terminal of the receptor. Unfolding of the N-terminal alpha-helix increases the volume of the channel upon ligand entry, helping to reach the crystallographic pose that also corresponds to the predicted favorable pose. The relaxation timescales of the binding process show that the binding of the ligand to the ?membrane vestibule? is the rate-limiting step in the multi microseconds timescale. We comment on the significance and parallels of the binding process in the context of other binding studies.



    Edit: The Science page does not contain the new papars yet, but you will find them in your profile page. WU names were respectively like 1mgx1, 1mgx2, 3mgx1, 3mgx2, 5MG, 20MG, 20MG2, INSP, INS1P (Noelia's) and RPS1 (Nate's).



  • 2016-10-13: WU: CASP

    Hey all. The next weeks I will be sending out some simulations starting with the CASP name. It will consist of a total of 3600 simulations running at any time (meaning that once some of them complete, new ones are sent to reach again 3600) probably for a month or so.
    It will probably be my most thorough and organized method test so far so it should be fun :D

    The simulations have their length written in their name (1ns, 5ns, 20ns and 50ns). Some will end up in the short queue and some in the long queue. Longest simulation time I measured on a 780 was 8 hours for one of the proteins at 50ns and shortest at 0.1 hour.

    Right now I sent out the first protein called NTL9 to test if everything works as expected (so no 3600 simulations yet) but the next week I will probably send out another 4 proteins. So there should be lots to crunch in the coming days :)



  • 2016-10-04: Disk full (solved)

    One of the disks of the server is full, and the project is down. Apologizes for the problem! We are trying to fix it.



  • 2016-08-30: New beta application

    Hi Crunchers,

    The eagle-eyed amongst you might have noticed the recent appearance of "Python Runtime" as the latest addition to our stable of applications.

    * what is it? This app deploys a Python runtime environment based on the Conda python distribution.

    * why do we need it? Almost all of our application development is now done in Python. This app will give us a way to reliably deploy and execute our software on GPUGRID volunteers' computers by providing a uniform, known Python environment

    * how will it be used? If all works well, we'll be able to quickly test and deploy whole new applications, including replacements for the quantum chemistry and CPU MD applications we have previously experimented with. Being able to rapidly deploy new applications will markedly improve the rate at which our research group can innovate.

    For the moment the app is Linux only but we hope to roll it out to Windows once it proves reliable.

    Matt



  • 2016-07-22: Geforce 10 / Pascal app coming soon

    hi Crunchers

    Just to let you know that there'll be a new app coming to support the ascal GPUs just as soon as Nvidia make a public release of CUDA 8.

    Matt



  • 2016-05-27: WU: OPM995 simulations

    Here we go again :) This time with 33% more credits + corrected runtimes which means an additional 2x credit for WUs which take more than 18 hours on a 780 and only WUs which take up to a max of 24 hours on a 780. I hope I don't seriously overshoot on credits this time but it's really a bit hit & miss.



  • 2016-05-03: WU: OPM simulations

    Hi everyone.
    Once again after a few years I have decided to simulate ;)

    This is for a new project where I try to automatically build and simulate hundreds of membrane proteins from the OPM database http://opm.phar.umich.edu/ as a proof of concept.
    But I will also keep an eye out to see if something fancy happens in those simulations which I am quite sure it will.

    Membrane proteins are very interesting in general as they are involved in many diseases and are simulated quite often. So building a protocol to simplify this process would help lots of biologists.

    For the moment I sent out just 100 simulations as a quick test, but in the next few days I will send out around 3000 equilibrations.

    Beware! The simulations are very very different, so there is no point in comparing them to each other. I have some systems which run on the short queue in an hour and some monstrous ones which run on long for 10 hours. The credits are scaled accordingly to simulation complexity so no one will be cheated of his hard earned credits :)

    Also keep in mind that the first batch will be minimization/equilibration simulations, which start the minimization by using the CPU for maybe 1 minute and then should switch to GPU for the equilibration.

    I might post here some pictures of the systems as well because some of these proteins are just gorgeous!

    Edit: I made some gifs for you here ;)
    http://imgur.com/a/YbjOd



  • 2016-04-28: New PhD student starting in June

    Hi,
    we finally have a new PhD student starting in June and another one by the end of the year.
    So our usage of GPUGRID will raise again after June.

    thanks.
    gdf



  • 2016-03-17: Noelia's PhD defence and departure

    Dear all,

    I have defended my doctoral thesis very recently, on March 4th, and it would have been impossible without your support. My thesis focused on the understanding of ligand-receptor interactions on a different set of systems, in all cases by running simulations in GPUGRID.

    The thesis itself will be publicly available after an embargo period (here is the link in any case: http://hdl.handle.net/10803/363212) due to the still-unpublished works it contains. In summary, with the support of GPUGRID we have produced works on seven systems, three are already published, two under review and the two left will be submitted very soon (so expect new badges soon!!).

    I must also say that I will be no longer working in GPUGRID. I have already moved to Boston where I will apply the methods that I have learned working on here to drug discovery programs.

    Many thanks again,
    Noelia



  • 2016-03-01: New SSL certificates

    I've just moved the project over to using Let's Encrypt certificates. Please post here if there are any connectivity problems

    Matt



  • 2016-02-28: *CXCL12_chalcone_umbrella* batch

    Hi everyone,

    yesterday we launched a bit more than 13,000 short WUs called *CXCL12_chalcone_umbrella*. They are pretty small WU, of 8ns (compared to a normal long WU ~40ns) and we hope they are easy and fun for you to crunch. Please post any problem you may encounter.

    Scientists have been using a technique called Umbrella Sampling for some time now, with relative success in determining what we call binding free energy (which indicates how strongly a drug can bind its protein target). It is a pretty straightforward and much less expensive technique compared to the one we regularly use in our lab (adaptive sampling). However, it is particularly error-prone if the assumptions we take are wrong.

    We are particularly excited about these WU, because while most scientific effort have been focused on reproducing free energies for single particular models or (most of the time) very simple toy models, it is the first time to our knowledge that, thanks to the fantastic community we have built together in GPUGRID, we can use this technique in a real case to screen potential drugs binding to CXCL12, a chemokine related to cancer metastasis.

    Thanks to everyone for your contribution and I will be happy to assist you if you find any problem on the way. :)



  • 2016-01-14: Linux app live again

    I've just put out a fixed Linux app, version 847. Please report any problems here.

    Matt



  • 2015-12-16: do you have any experience with running a VM based application in BOINC?

    There are projects giving out VMs instead of normal applications. We are considering it. How is it? Does it work?

    thanks.

    gdf



  • 2015-12-16: Badges ready for the last paper!

    Hello guys!

    We recently published a paper which used a considerable amount of GPUgrid simulations. It would not have been possible without your contributions.

    The paper is:

    N. Ferruz, M. J. Harvey, J. Mestres and G. De Fabritiis, Insights from Fragment Hit Binding Assays by Molecular Simulations, J. Chem. Inf. Model., 2015, 55, pp 2200-2205

    You can also browse ranking positions ;) :

    https://www.gpugrid.net/science.php?topic=methods

    Thanks to all!
    Noelia



  • 2015-12-15: Running low on WUs at GPUGRID

    Hi,
    somebody might have noticed that we recently running low in WUs.

    The main reason for this is that we have very few people at the moment. Practically only Gerard is using it. Noelia is finishing her Phd in February and mainly writing up. Nate finished in July.

    The good news that we are hiring more PhD students and already from January the group should be quite a bit larger with at least two other phD students and possibly one postdoc.

    GDF



  • 2015-12-01: Probable access problems on 9th Dec

    On 9th Dec we are moving the IP of gpugrid to another network. This means changing the DNS. While the dns update is propagating around the world you might experience that the server is unreachable.

    Early next year we are going also to upgrade the server, but this is another story.

    GDF



  • 2015-10-07: PhD position in machine learning at GPUGRID

    http://multiscalelab.org/Jobs/Phd_neural_processing_learning_in_structural_molecular_biology

    Please share in your network.

    gdf



  • 2015-06-27: Update to QC CPU application

    Hello Crunchers!

    Things have been a bit quiet on the GPUGRID development front for a while as we have concentrated on our scientific projects.
    I'm now doing a spot of work on our new CPU quantum chemistry application, with a view to significantly increasing its use in the near future. Expect a flurry of updates (the first, version 101, is live now) - these are aimed at improving the platform support and performance.

    Please note that this app is Linux only. It's unlikely that we'll be able to get a Windows version of this software built.

    Matt



  • 2015-06-18: Urgent PhD position at GPUGRID in Barcelona (please forward)

    hi guys,
    do you know anybody interested in doing a PhD with us. We have a fellowship but we need to find a candidate within a week.

    Please forward it on if you know somebody interested
    http://multiscalelab.org/Jobs/PhD_intrinsically_disordered_proteins_barcelona

    Best,
    gdf



  • 2015-05-12: Server up and working

    Yesterday and tonight we had a powercut. The sysadmin restarted the machine but he did not realize that apache was not running.

    Now it should be all fine.



  • 2015-04-29: Nathaniel Stanley's thesis and departure

    Hello all,

    This past Friday I defended my doctoral thesis, making me the second PhD to be produced thanks to GPUGRID.net. I owe you all a great debt of gratitude for supporting my work. My thesis covered my work on the study of complex binding processes in membrane proteins and disordered peptides. The membrane work was related to the enzyme FAAH and another work we are hoping to publish very soon. The disordered protein work was also a really great surprise for us, and will be continued further. The thesis itself will be published publicly after an embargo period (due to the still-unpublished works it contains). We will post the link as soon as it's available.

    I must also announce that I will be leaving GPUGRID and moving on. I haven't accepted a position yet, but it is looking like I will be moving to a university in California in the next few months. It is a great opportunity and I'm very excited about it. I will continue to push forward biology with the methods and applications that I have learned working on here.

    Thanks again and onward,
    Nate



  • 2015-04-24: donation page

    We are currently fixing with the University admin people the donation page.

    It should not take too long.

    gdf



  • 2015-04-20: Plenty of work

    There is plenty of work now. Thanks for your patience.

    gdf



  • 2015-04-04: No work

    We finished one of the storage filesystems and so new work units cannot run until this is fixed.

    Of course it had to happen today. I am trying to fixing things up but it might take many hours because I am copying a lot of data out.

    gdf



  • 2015-03-21: New application: Quantum Chemsitry

    Hi,

    I've introduced a new application, called "Quantum Chemistry".
    We'll be using this to perform preparatory calculations on the small molecules that we simulate in our molecular dynamics simulations. This will help us to improve the quality of our simulations.

    This app is restricted to Linux hosts with a processor that's SSE4-capable.

    The first few WUs are failing, no need to report anything here just yet. I'm behind the curtain monitoring everything.

    Matt



  • 2015-03-21: New application: Quantum Chemistry

    Hi,

    I've introduced a new application, called "Quantum Chemistry".
    We'll be using this to perform preparatory calculations on the small molecules that we simulate in our molecular dynamics simulations. This will help us to improve the quality of our simulations.

    This app is restricted to Linux hosts with a processor that's SSE4-capable.

    The first few WUs are failing, no need to report anything here just yet. I'm behind the curtain monitoring everything.

    Matt



  • 2015-03-04: Server performance

    Let us know if there are still issues of connecting to the server or downloading/uploading.

    gdf



  • 2015-03-04: Server reboot

    We rebooted the server today (after 1 year) to see if the recent problems are going to get better.

    We are also planning to buy a new server as soon as we get some grant money.

    gdf



  • 2015-03-03: Change to CPU/AMD GPU application

    To better reflect the nature of the application, the AMD GPU application is now called Molecular Dynamics for CPU and AMD GPUs.

    It will be issued to any machine that:

    * accepts CPU work
    * has no NVIDIA GPUs
    * has zero or more AMD GPUs

    The intention is that it will use CPU cores, and be further accelerated by an AMD GPU is one happens to be present.



  • 2015-01-27: New Beta app

    Hi,

    If you've an AMD graphics card, please subscribe to beta applications and see if you get the "amdmd" application. For now, it's just a place-holder, but this'll change soon.

    Matt



  • 2015-01-27: New Beta app for AMD GPUs

    Hi,

    If you've an AMD graphics card, please subscribe to beta applications and see if you get the "amdmd" application. For now, it's just a place-holder, but this'll change soon.

    Matt



  • 2015-01-22: WARNING/CHALLENGE: VERY LONG WU (VERYLONG_CXCL12_confAna)

    We just launched 400 very long WU (they will take about 24h in a 780GTX) named VERYLONG_CXCL12_confAna whose results we need as soon as possible (we are in a hurry). They come with a credit+bonus of 400K. Please, if you don't have a good graphic card, reject them. For the brave ones, take it as a challenge and see you on the performance tab ;)



  • 2015-01-21: A new GPUGRID initiative

    Crunching is a creative and challenging way of learning about the behavior of our computers and improving them while helping the GPUGRID team to understand a bit more the mystery of the world we live in and the diseases that affect not only us, but also the people we love. The GPUGRID team couldn?t be more satisfied and proud of forming part of this noble project, and so we?d like to deeply thank each of the 1000 users that connect to us every day, making us part of their lives and making them part of ours, as a team.

    Behind each computer, behind each GPU and each WU or forum post, there?s the real protagonist of our story as a community: YOU, the cruncher.

    At GPUGRID, we are considering the possibility of starting a new campaign to thank the users that contribute with our project by sending them little tokens of gratitude, such as proteins/aminoacid molecules printed by our 3D printer or merchandising such as t-shirts or stickers. We still have to establish the contest rules, but most likely each of the user would have a probability of winning based on their contribution. Once in a while we would like to run a story about the winner, explaining why you crunch, what's the setup of your computer, a small description of yourselves or a picture of you and your token.

    We believe that it would be a fun and productive experience but before anything we?d like to know your opinion, your suggestions and whether we have your support for this initiative. Let us know!



  • 2015-01-19: Important: No new work for pre-Fermi GPUs

    Hello,

    From today no new work will be scheduled to old pre-Fermi GPUs. This includes Geforce 8800, GTX200 series and GTX9800.


    Matt



  • 2015-01-13: Recommended driver 343 branch or higher

    Happy New Year Crunchers!

    Per the plans we announced last year year, the CUDA 4.2 application is now terminated leaving the CUDA 6.0 and CUDA 6.5 applications in production.

    Henceforth, the CUDA 6.0 application will become the "compatibility" application, providing support to older systems. It will not receive any feature updates.

    All new feature releases - new GPU support, performance improvements, etc - will be introduced in the CUDA 6.5 application. Baring any unhappy surprises, CUDA 6.5 will be our build platform throughout 2015 and into 2016.

    As you can see from our statistics graph http://www.gpugrid.net/graphs/trend-appver.png , showing the fraction of our results produced by each application version, currently some 20% of our results are produced by the CUDA 6.0 application.

    We'd very much like to reduce that to a minimum, so that as many people as possible are using the better application. To ensure you are getting the CUDA 6.5 application, please ensure that your NVIDIA driver is on branch 343 or higher.

    Matt



  • 2014-12-23: Happy crunchmas! (Gerard CXCL12)

    We have fed GPUGRID with some new WU to keep you guys busy this christmas. This time we are simulating the binding of a small ligand to a protein called CXCL12, member of the family of chemokines. This protein appears to be altered in cancer and other inflammatory diseases. Happy Chrunchmas!



  • 2014-12-23: Happy crunchmas!

    We have fed GPUGRID with some new WU to keep you guys busy this christmas. This time we are simulating the binding of a small ligand to a protein called CXCL12, member of the family of chemokines. This protein appears to be altered in cancer and other inflammatory diseases. Happy Chrunchmas!



  • 2014-12-16: Happy holiday season

    Hopefully, a lot more GPUs and CPUs will join after the holiday presents.

    At GPUGRID we are going away starting next week. The first to come back is Nate by the end of the year, early new year.

    Also still remember that if you want, there is the possibility to make a donation. Donations are used to fund a PhD student which can work on Gpugrid. Last year we have received many donations. Thanks to everybody.

    This year we also did well in terms of scientific publications:

    N. Stanley, S. Esteban and G. De Fabritiis, Kinetic modulation of a disordered protein domain by phosphorylation, Nat. Commun. 5, 5272 (2014). pdf

    G. Lauro, N. Ferruz, S. Fulle, M. J. Harvey, P. W. Finn, and G. De Fabritiis,Reranking Docking Poses Using Molecular Simulations and Approximate Free Energy Methods, J. Chem. Inf. Model., 2014, 54 (8), pp 2185?2189.

    *** S. Doerr and G. De Fabritiis, On-the-fly learning and sampling of ligand binding by high-throughput molecular simulations, J. Chem. Theory Comput. 10 (5), pp 2064?2069(2014).pdf

    P. Bisignano, S. Doerr, M. J. Harvey, A. Favia, A. Cavalli and G. De Fabritiis, Kinetic characterization of fragment binding in AmpC ?-lactamase by high-throughput molecular simulations, J. Chem. Inf. Model., 2014, 54 (2), pp 362?366. pdf

    X. Huang and G. De Fabritiis, Understanding Molecular Recognition by Kinetic Network Models Constructed from Molecular Dynamics Simulations, Adv Exp Med Biol 2014; 797: 107-114. pdf

    ** E. Dainese, G. De Fabritiis, A. Sabatucci, S. Oddi, C. Angelucci, C. Di Pancrazio, T. Giorgino, N. Stanley, B. Cravatt, and M. Maccarrone, Membrane lipids are key-modulators of the endocannabinoid-hydrolase FAAH, Biochem J. 2014 Feb 1;457(3):463-72.

    Almost all of these works have been made with your contribution. From next year we are also trying to have a larger impact in biomedicine, further developing new small molecules which can be used for treatment of disease.

    Best,
    gdf



  • 2014-11-21: Discontinued CUDA 4.2 (update)

    We had to discontinue cuda 4.2 apps because of some time limit in the executable.
    As they were going to be discontinued anyway, we will only reintroduce it if really necessary.

    If you were using cuda4.2, update your driver


    * Discontinued CUDA 4.2
    We need CUDA 6 to properly support the new Maxwell, so I'll be retiring the old CUDA 4.2 build. If you are still receiving version 4.2 WUs, please consider updating your driver to version 343 or above.



  • 2014-11-05: WU: UBI

    Hey all,
    I am starting some new simulations whose names begin with ubi. They are relatively few so you might not notice them much around.
    Essentially, after some success in folding the NTL9 protein (see previous WU posts) with a new method I was testing, I wanted to scale it up to a bigger, slower-folding (and more famous) protein and see how my method works on it. So here we go with Ubiquitin.
    If this one is also kind enough to fold fast for me, we might be onto something quite useful :)



  • 2014-10-29: New publication: Our study of a disordered protein and its significance

    Hi everyone,

    We are very pleased to announce the publication of our latest research article, titled "Kinetic modulation of a disordered protein domain by phosphorylation", which was published yesterday in the journal Nature Communications. You can see the official journal page link here. Since we know most of you don't have access to the fancy formatted version from Nature Publishing Group, we have placed the our less-fancy formatted pre-print version of the article here (first PDF link at the top of the page).

    Since I am sure the title and abstract is quite cryptic/confusing to everyone, let me explain what we discovered and why this work was important. The main focus of the paper was a disordered protein domain called KID. Disordered proteins like KID do not have any rigid structures (so no x-ray crystal structures), and are in fact very flexible like polymers. However, despite being flexible they are very important and common in many different aspects of cell biology. They are important in many protein-protein interactions, such as ones that are important in communication inside the cell. They are frequently involved in many diseases like cancer (among many others).

    KID is a protein that has been studied for more than 15 years, and a lot was already known about it. Other proteins in the cell chemically modify KID through a process known as phosphorylation, which then causes it to bind to specific proteins. It binds most famously to a protein known as KIX. The behavior of KID in the phosphorylated and normal state has been studied by a technique known as NMR (a cousin of MRI), and the binding of KID to KIX has also been studied this way. However, what we discovered in our study?and not seen by any other method yet?was that when KID is phosphorylated, it undergoes an a slowdown in its motions and forms a temporary, partially folded state. We believe this state is important in the binding process, and modelling and comparison with previous experiments also suggest this. This work is significant because it is the first time anyone has shown that such chemical modifications could change the behavior of a protein in this way, and also that it could have important consequences for the way proteins interact.

    If you have questions, please ask away. We will assign badges and update the webpage soon.



  • 2014-10-16: GPUGRID statistics graphs

    Following up on the announcement to discontinue support for old hardware and the oldest application, here are two graphs showing the normalised throughput of GPUGRID broken down by compute capability and application version.

    http://www.gpugrid.net/graphs/

    The legends are messed up for some reason - the first graph is cc, {1.3, 2.0, 2.1, 3.0, 3.5, 5.0, 5.2 }, the second app version {42, 60, 65}

    These will update daily.

    Matt



  • 2014-10-12: New CPU work units

    I'm starting testing again on the "cpumd" multi-threaded CPU app. Please post observations here.

    Matt



  • 2014-10-06: Important: hardware and app deprecation for 2015 / ha-ha thread!

    Hi,

    With the arrival of Maxwell, we are now supporting 4 generations of hardware, and 6 separate builds of our application on 2 platforms.

    This is starting to tax our resources, so some rationalisation is required. I therefore propose the following:

    * Remove support for SM1.3
    Geforce 200 series cards contribute rather less than 1% of our capacity and, furthermore, lack hardware features that we want to use in future development work.

    * Discontinue CUDA 4.2
    We need CUDA 6 to properly support the new Maxwell, so I'll be retiring the old CUDA 4.2 build. If you are still receiving version 4.2 WUs, please consider updating your driver to version 343 or above.

    These changes will take effect from January 2015

    Matt



  • 2014-10-06: Important: hardware and app deprecation for 2015

    Hi,

    With the arrival of Maxwell, we are now supporting 4 generations of hardware, and 6 separate builds of our application on 2 platforms.

    This is starting to tax our resources, so some rationalisation is required. I therefore propose the following:

    * Remove support for SM1.3
    Geforce 200 series cards contribute rather less than 1% of our capacity and, furthermore, lack hardware features that we want to use in future development work.

    * Discontinue CUDA 4.2
    We need CUDA 6 to properly support the new Maxwell, so I'll be retiring the old CUDA 4.2 build. If you are still receiving version 4.2 WUs, please consider updating your driver to version 343 or above.

    These changes will take effect from January 2015

    Matt



  • 2014-10-04: CUDA 6.5 app for Linux now available on acemdbeta and acemdshort

    Experiences here, please.



  • 2014-10-02: CUDA 6.5 app now on acemdlong

    Matt



  • 2014-10-02: Important news for GTX980 owners

    If you are crunching with a GTX980 on Windows, please update your driver to 344.16

    I am seeing a very high error rate for 980s with the initial driver release, 344.11

    Matt



  • 2014-09-30: New acemdshort app 846

    I've promoted the CUDA65 app version 846 from beta to short.

    You'll only get this if you have a Kepler or Maxwell card, and have a CUDA 6.5-capable driver, in practice rev 343 or higher.

    Please post any problems or regressions here.

    Matt



  • 2014-09-29: New CUDA65 beta app

    Dear all, please give the new acemdbeta app, ver 845, a work out. This supports all GPUs now.
    It's Windows only - if you don't get WUs, you'll need to update your driver.

    Matt



  • 2014-09-29: Changes to scheduling policy

    Hi all,

    In attempt to rationalise the rules for assigning WUS to crunchers, I've made some changes to the underlying scheduler program. Here are the new rules:



    * If you have driver >= 343.00 and sm >= 2.0 you will get a CUDA 6.5

    * If you have driver >= 334.21 and = 2.0 you will get a CUDA 6.0

    * If you have driver >= 295.30 and= 2.0 and
    * If you have driver >= 295.30 and sm == 1.3 you'll only get CUDA 4.2


    Matt



  • 2014-08-29: gpugrid.net layout upgrade

    Hi fellows!

    The GPUGRID team wishes you are having (or had) good summer vacations!

    For September we are planning to release some changes in the web layout. Among others, extended statistic data will be provided so you can follow the progress of your contribution more closely.

    We are still under development and we are open to any suggestions to make improve your experience as users. Specifically, we would be happy to hear which statistical data you find the most relevant or interesting and therefore susceptible of being displayed as graphs.

    We thank you for your collaboration!

    Gerard M.



  • 2014-07-21: New app for testing

    Hi,

    There's a new CPU app available for Linux clients. A few WUs are out now, with some more to come after I've received the first results back.

    The app is multithreaded, I think the default behaviour of the BOINC client is to allocate all cores to it.

    Please report any observations here.

    Matt



  • 2014-07-21: New CPU Application for testing

    Hi,

    There's a new CPU app available for Linux clients. A few WUs are out now, with some more to come after I've received the first results back.

    The app is multithreaded, I think the default behaviour of the BOINC client is to allocate all cores to it.

    Please report any observations here.

    Matt



  • 2014-06-19: WU: THROMBIN

    Hi guys!!

    There's a new project in the long queue ( NOELIA_THROMBIN ) . It consists of the binding of 6 different inhibitors to the protease thrombin, a protein in the coagulation cascade. With these, we are trying to demonstrate that molecular simulations can be as useful as X-Ray crystallography predicting binding modes.

    Thanks to all,

    P.D: Report any problems please!

    Noelia



  • 2014-06-11: WU: TRPS1S4

    Dear all,

    Just sent 1000 WUs under the group name TRPS1S4. This is probably the last batch of a project you've been crunching for more than one year now (WUs: FXA, FXArep.. and similar names) for thrombosis disease. This last batch is particularly important, since will allow us to see if these simulations can predict experimental outcomes. Please report any problems.

    Thanks to all and happy crunching!
    Noelia



  • 2014-05-31: WU: CMYBKIX

    Hi all,

    I have submitted a bunch of new workunits to the short queue. This should fix the dry spell we have had there for the past week.

    The workunits are named "NATHAN_CMYBKIX". In these simulations I am investigating the binding of a small disodered protein named cMyb to another protein named KIX. Disordered proteins and disordered domains (as opposed to nicely structured ones like hemoglobin) are very important in protein-protein interactions. Mutations in disordered proteins are very common in cancers, amyloid fibril diseases like alzheimer's and parkinson's, and probably a lot of other disease we don't know about. So, with these simulations we will be taking some first steps towards understanding some key things about these types of interactions. Lessons we learn from this system should help us work on many, many others.

    Nate



  • 2014-05-19: WU: BI_3

    Hi all!

    Just sent a new project to the long queue, around 2500WUs, ~100,000 credits each.
    In particular, this project will help us to understand how antidiabetic drugs block its target, but also to develop a better general method for other targets and drugs involved in different diseases.

    Thanks to all!!



  • 2014-04-23: Important news for Linux crunchers

    Hi all,

    We are having a problem with correctly scheduling work to Linux clients because the BOINC client for that platform does not report the Nvidia driver version to us.

    If you find that you are receiving the cuda60 application version and it is not working for you, the fixes are:

    *) Upgrade to driver 334.21 or later

    *) Try the patched (v7.3.15) client I have made available at:

    http://secure.acellera.com/insecure/boinc/boinc (RedHat etc)
    http://secure.acellera.com/insecure/boinc/boinc_ubuntu (Ubuntu)

    (the patch itself is at http://secure.acellera.com/insecure/boinc/gpu_nvidia.cpp_patch )

    This client reports the driver version and allows a correct scheduling decision to be made.

    Matt



  • 2014-04-22: Badges for two new papers

    Dears, we have updated the badges to reflect two recent publications performed with your help:

    * S. Doerr and G. De Fabritiis, On-the-fly learning and sampling of ligand binding by high-throughput molecular simulations, submitted (2013).

    and

    * P. Bisignano, S. Doerr, M. J. Harvey, A. Favia, A. Cavalli and G. De Fabritiis, Kinetic characterization of fragment binding in AmpC ?-lactamase by high-throughput molecular simulations, J. Chem. Inf. Model., 2014, 54 (2), pp 362?366.

    You should be able to see them in your user profile, as usual.



  • 2014-04-21: Recommended driver versions are 334.21 or later

    Hi all,

    As you may have noticed, we now have a CUDA 6.0 application. This brings with it several benefits over the older 4.2 and 5.5 applications, notably:

    * Support for Maxwell GPUs
    * Slightly improved performance
    * Much lower CPU load

    The minimum driver required for this app is 334.21, but any later version is OK.

    In the longer term, our software development will assume CUDA 6. features, and it would be good to have as many of you as possible able to run it.

    Currently 60% of all the WUs we get back are completed on machines with this driver or later (though many of you have been running the 55 app, because of our server scheduling policy)

    If you have the opportunity, please do consider upgrading your driver!

    Don't worry if you can't: the older applications aren't going away. From now on, though, they will get only maintenance updates.

    Matt



  • 2014-04-07: WU: BARNA

    Hey everyone,
    I am sending out some WUs to the long queue called BARNA (pun intended). The system we are investigating is Barnase/Barstar which are two proteins that interact with each other.
    http://en.wikipedia.org/wiki/Barnase
    http://en.wikipedia.org/wiki/Barstar

    This will be (as far as I know) our first protein-protein interaction study and we are hoping to study some interactions like the ones in the crystallographic model and further develop the corresponding analysis tools.



  • 2014-04-06: New CPU work units: 3HHM-1/ZINC

    Hi gang,

    The testing for the CPU application is over and these are the first production WUs.

    In this project we are studying the PI3Kalpha, a mutation of which is implicated in tumor formation. You can read more about it, and see the structure, here: http://www.rcsb.org/pdb/explore.do?structureId=3HHM

    Over the course of this project we will be testing some 22 million commercially-available drug-like molecules, drawn from the ZINC database http://zinc.docking.org/, to find compounds which are predicted to bind strongly to the protein in a way which will inhibit its function.

    Once we have screen the whole database, we will take the best hits and test them for efficacy in a series of in vitro experiments. Hopefully we will find inhibitory compounds which can then serve as the basis for future drug development.

    Matt



  • 2014-03-27: Custom Android client

    Dears, we are playing with a customized skin of the BOINC client. It attaches to GPUGRID by default (but allows you to add other projects manually).

    Feel free to try the (unsigned) apk at www.gpugrid.net/download/apk/edu.berkeley.boinc.AndroidBOINCActivity.apk.

    Let us know.



  • 2014-03-26: WU: A2AR

    A big hi to all the users! I'm currently undergoing my master thesis in the lab and I'll very proud to participate in this fantastic community for the first time by sending some simulations to gpugrid.

    You will identify them with the ID A2AR, which stands for A2A adenosine receptor. It is a membrane protein from to a huge family called GPCRs that is key on neurodegenerative diseases such as Parkinson and therefore an important target of drug development. With these simulations we will try to prove the affinity of a couple of known ligands in silico.



  • 2014-03-24: WU: CMYB_equil

    Hello all,

    I have submitted some simulations of a small peptide to the short queue. This is a special type of simulation, and it is also the first time I am running them, so there may be errors with them. Please let us know what you see. There should be pass through quickly, however, so hopefully they don't cause too many problems.

    Nate



  • 2014-03-24: New CPU WUs - DUDHIVPR

    Hi All,

    I've just submitted our first large batch of work units for the CPU application, named "DUDHIVPR*". The purpose of these WUs is to test the correctness of operation of our application by attempting to reproduce published benchmark data.

    Matt



  • 2014-03-21: Thanks to Anonymous for donation

    Hi,
    we have received a high donation from a person who likes to remain anonymous.

    This message is just to thank this person. The money will contribute to pay a PhD student.

    In the current economic situation we need more donations. Anybody who would like to contribute please do so using the donate link above.

    GDF



  • 2014-03-19: acemdlong application 815 updated for Maxwell

    The cuda60 version of application version 815 is now present on acemdlong for those of you with the latest driver or a Maxwell card.

    Matt



  • 2014-03-10: New app on acemdbeta with Maxwell support

    There's a new application on acemdbeta, version 811 for CUDA 60 which supports the Geforce 750Ti. You'll receive this app if your driver version is 334.21 or greater.

    Please report problems here.

    Matt



  • 2014-03-05: Maxwell GTX750Ti

    Hi Guys,

    Just a line to say we've got our first GTX750Ti card up and running. The performance out-of-the-box matches a GTX480. We'll have a public app for GPUGRID just as soon as CUDA 6.0 is publicly released, which will probably happen at GTC at the end of the month.

    Matt



  • 2014-03-05: WU opi: Simulations on opiod receptors

    Hi,
    I have just submitted several hundred simulations on a collaboration study on opiod receptors. They are not much.

    Any problem use this thread.

    thanks,
    gdf



  • 2014-03-05: WU opi: Simulations on opioid receptors

    Hi,
    I have just submitted several hundred simulations on a collaboration study on opiod receptors. They are not much.

    Any problem use this thread.

    thanks,
    gdf



  • 2014-02-24: "Power To Give" - volunteer distributed computing for smartphones

    HTC have just announced "Power To Give", a new BOINC-based initiative for volunteer distributed computing on Android smartphones. HTC deserve to be commended for putting effort into helping the development of a polished BOINC client for Android.

    You can read all about it here: http://www.wired.co.uk/news/archive/2014-02/24/htc-power-to-give and see a video here https://www.youtube.com/watch?v=_0oJ39vs_Kk

    GPUGRID's very own Gianni De Fabritiis presented at the launch, happening as part of the Mobile World Congress in Barcelona. Video to follow soon, but you can read as-it-happened coverage here http://www.gizmodo.com.au/2014/02/htc-mobile-world-congress-press-conference-live-blog-follow-all-the-news-as-it-happens/

    We're very excited about this! Expect more news soon...

    Matt



  • 2014-02-20: Achievement: GPUGRID first project worldwide in boinc

    At least yesterday GPUGRID was the first project worldwide according to BOINCSTATS.

    Just a note to thank all the crunchers for contributing to our research.

    gdf



  • 2014-02-17: NTL workunits

    I have submitted a thousand simulations try to fold a small protein called ntl9.
    This is mostly a methodological work.

    thanks for crunching,
    gianni



  • 2014-02-17: WU: NTL

    I have submitted a thousand simulations try to fold a small protein called ntl9.
    This is mostly a methodological work.

    thanks for crunching,
    gianni



  • 2014-02-12: Uncovering the role of membrane lipids in modulating enzyme activity

    Hello everyone,

    At the end of last year, we updated the badge system to include several new publications we had just published. Today we want to highlight one of those pieces of work.

    Starting in Mid-2011 (an eternity ago), we began collaborating with a research group in Italy to better understand something strange they had been seeing in their experiments. Specifically, they were seeing that when they modified the composition of lipids in a cell membrane, the activity of an enzyme named FAAH increased. They came to us to try to better understand why that was happening. Through simulations performed here on GPUGRID we discovered that, contrary to expectations, the lipids modified the function of the enzyme by directly interacting with it and its endogenous ligand. It had been expected that structural changes in the membrane would be the culprit, but that was not the case. Additionally, we report the first unbiased binding of a lipid to a membrane protein. This is one of the first experiments of this kind ever performed, and was possible only because of the compute power we have here at GPUGRID. You can read more about it on the science page here, as well as check out the video of the binding event.

    Please note that (almost) all the papers we publish are available on our lab webpage. They can be found here. The versions of the documents there are the pre-print versions, basically meaning they are not formatted to look pretty. This is due to restrictions placed on us by the publishing companies. The text and figures are identical to those in the "pretty" version published in the journal, however. We are working on putting out copies of any papers missing from that page.

    Lastly, we remind you that GPUGRID accepts donations beyond compute time, and if you're interested you can see how to do so on our Donations page. Of course, the crunching time donated by all of you is greatly appreciated.

    Thanks and onward,
    The GPUGRID Team



  • 2014-02-07: First low parts Maxwell GPUs out 18th Feb

    GTX 750 and 750 TI will be out 18th Feb. These are based on the GM107 maxwell chip, so a small maxwell. Performance wise they should be around 40% the speed of a GTX780 but consume only 75W.

    More details here.
    http://en.wikipedia.org/wiki/GeForce_700_Series

    We are going to Nvidia in US in few weeks, let's see if can get one to test.

    gdf



  • 2014-01-23: acemdlong application 815 discussion

    I've promoted the version 815 application from acemdshort to acemdlong.

    Post problems here, please.

    MJH



  • 2014-01-21: Plenty of Workunits to crunch

    There are over 10,0000 workunits to crunch now at GPUGRID. Take your share.

    gdf



  • 2013-12-20: Off on Holydays

    Happy holidays everybody,
    we will be around but most of us are back for the new year.

    There should be enough workunits to crunch since then.

    gdf



  • 2013-11-21: New Badges for four new articles

    Hi everyone,

    As some of you may have already noticed, we have updated the badges to include four recent publications. In other words, many of you should have new colored water badges with rankings in your profiles.

    In the coming days/weeks we'll be updating the Science pages with details about the new publications, as well as posting here and on the Facebook page to give you all some background about the works.

    If you have not received any badges in this round, please note that many of the workunits for this round were performed 1-2 years ago (inlcuding my infamous NATHAN_FAAH workunits, started in September 2011!). These papers have been a long time coming, and we are very glad to finally have the results published. Do not worry if you were not included in this round, because we expect to have another update in the coming months. Lots of good results in the pipeline, we are just trying to get them published.

    Finally, just a reminder that GPUGRID accepts donations beyond compute time, and if you're interested you can see how to do so on our Donations page. Of course, the crunching time donated is greatly appreciated.

    And as always, thanks and onward.
    The GPUGRID Team



  • 2013-10-30: WU: NATHAN_benfix

    Hey guys,

    Minor group of workunits here on long queue. Just a small fix/check on some work we have sent for publication. You should barely notice them, and they should finish quickly.

    Regards,

    Nate



  • 2013-10-25: WU: RL1_run

    Hi all,

    Just sent a bunch of ~1600 WU to the short queue. It won't last very long, only one step.

    Thanks!!!
    Noelia



  • 2013-10-11: WU: FXArep

    Hi all,

    I have just sent a good bunch of WU (4000) to the long queue. Only two steps, 90000 credits each. With the analysis of this last batch, we will be able to finish a project on drug discovery for the thrombosis disease. Please let me know if you find any problem, although these simulations were already on the long queue some moths ago and should run fine.

    Noelia



  • 2013-10-08: Update to 331.40 to fix access violations on Windows

    If you have been unfortunate enough to have been afflicted by the problem of repeated crashing with 'access violation' errors, please upgrade the Nvidia driver to 331.40 to rejoin us in the happy land of mostly-crash-free crunching.

    MJH



  • 2013-10-08: Access Violation Problems / Switching between WUs

    For anyone getting the access violation problem, or very frequent switching between WU's, users of the forum have reported that the problem disappears with the new BETA v331.40 drivers.

    See discussions:
    http://www.gpugrid.net/forum_thread.php?id=3462&nowrap=true#33350
    http://www.gpugrid.net/forum_thread.php?id=3498&nowrap=true#33384



  • 2013-10-08: Access Violation Problems / Switching between WU's

    For anyone getting the access violation problem, or very frequent switching between WU's, users of the forum have reported that the problem disappears with the new BETA v331.40 drivers.

    See discussions:
    http://www.gpugrid.net/forum_thread.php?id=3462&nowrap=true#33350
    http://www.gpugrid.net/forum_thread.php?id=3498&nowrap=true#33384



  • 2013-10-07: New Linux driver version 319.60 for 780s

    If you are using Linux and have GTX780s, you should upgrade the driver to 319.60 to improve stability.

    MJH



  • 2013-09-03: WU: NOELIA_INS1P

    Hi all,

    New WUs in the long queue, big-box size, 120000 credits each. The batch has been previously tested and should not report any issues, but please comment any problems you might have.

    Noelia



  • 2013-09-02: Beta application

    The Beta application may be somewhat volatile for the next few days, as we try to understand and fix the remaining common failure modes. This will ultimately lead to a more stable production application, so please do continue to take WUs from there. Your help's appreciated.

    Thanks,

    Matt



  • 2013-09-02: acemdbeta application - discussion

    The Beta application may be somewhat volatile for the next few days, as we try to understand and fix the remaining common failure modes. This will ultimately lead to a more stable production application, so please do continue to take WUs from there. Your help's appreciated.

    Thanks,

    Matt



  • 2013-08-29: WU: NATHAN_KIDKIX...

    Hi all,

    Workunits with a similar name have been running for the past month or so on the long queue, but in keeping with our new policy I wanted to create a thread about them here. My original message in a previous thread was:

    With these workunits, I'll be looking at the folding of a small peptide using a special force field. The biophysics community uses different force fields to represent the motions of proteins and other molecules, and we are attempting to test a new one so we can check some previous work and feel comfortable in work we are planning to do.

    This work is a continuation of that, where we are now looking at the interaction of that peptide with another protein. The idea is to understand the interaction process, and later to see if the lessons we learn extend to other such interactions. There are MANY diseases in which these kinds interactions are important, from many cancers such as prostate cancer to neurological disorders like Parkinson's disease. They are fundamentally important to the function of cells. This is something I'll be looking at in the coming months.

    If there are any problems or you have further questions, post them here!

    Regards,
    Nate



  • 2013-08-29: Titan and GTX780 welcome

    Hi,
    with the new applications online for productions, we are happy to have Titans and GTX780 users on board.

    IMPORTANT. Just make sure to have the appropriate drivers for these two cards (or newer):
    http://www.nvidia.com/object/linux-display-amd64-325.15-driver.html
    http://bit.ly/13k1Ajc
    as these fix an important bug.

    gdf



  • 2013-08-28: WU: NOELIA_KLEBEs

    So far I've had
    one long wu error after 13s

    one short wu complete OK
    one long wu stall, ran for 2hr on a 660 but little progress, so got the bullet

    Be on your guard!



  • 2013-08-27: acemdlong application 8.14 - discussion

    We decided to go live with the new application on ACEMD-Long.

    It is version 8.00, and the server will automatically assign you a CUDA 4.2 or 5.5 version, depending on your driver version.

    Any problems on this thread, please.

    MJH



  • 2013-08-27: New acemdlong application

    We decided to go live with the new application on ACEMD-Long.

    It is version 8.00, and the server will automatically assign you a CUDA 4.2 or 5.5 version, depending on your driver version.

    Any problems on this thread, please.

    MJH



  • 2013-08-27: acemdlong application 8.03 - discussion

    We decided to go live with the new application on ACEMD-Long.

    It is version 8.00, and the server will automatically assign you a CUDA 4.2 or 5.5 version, depending on your driver version.

    Any problems on this thread, please.

    MJH



  • 2013-08-24: Project servers stopped.

    Problem with the database. Should be back online soon!

    MJH



  • 2013-08-24: Project servers up again

    Problem with the database. Should be back online soon!

    MJH



  • 2013-08-23: WU: SDOERR_VillinAdapt

    Despite its name, this protein is not villainous!
    Similar technique as with BenAdapt but now with a different protein system. Lets see how fast we can fold this protein :)
    I sent it to the long queue. Work units should take around 6.7 hours on a GTX 580

    If you want to bask at its folded beauty (which I would hope to achieve) take a look at this rendering (not by our group):



  • 2013-08-18: New acemdbeta application

    Dear all,

    I'm working on putting out updated Windows and Linux applications that will have full support for 780s and Titans. If you have one of these card types, please sub to "acemdbeta" and try some WUs. The beta app version is 7.02 for both architectures.

    Please post experiences here.

    MJH



  • 2013-08-18: New acemdshort application

    Dear all,

    I'm working on putting out updated Windows and Linux applications that will have full support for 780s and Titans. If you have one of these card types, please sub to "acemdbeta" and try some WUs. The beta app version is 7.02 for both architectures.

    Please post experiences here.

    MJH



  • 2013-08-18: acemdshort application 8.11 - discussion

    Dear all,

    I'm working on putting out updated Windows and Linux applications that will have full support for 780s and Titans. If you have one of these card types, please sub to "acemdbeta" and try some WUs. The beta app version is 7.02 for both architectures.

    Please post experiences here.

    MJH



  • 2013-08-18: acemdshort application 8.14 - discussion

    Dear all,

    I'm working on putting out updated Windows and Linux applications that will have full support for 780s and Titans. If you have one of these card types, please sub to "acemdbeta" and try some WUs. The beta app version is 7.02 for both architectures.

    Please post experiences here.

    MJH



  • 2013-08-14: WU: SDOERR_BenAdapt

    Hey all, I will be sending under this WU name some workunits to test a new method that we are developing. If everything goes well it will allow us to simulate more "intelligently" allowing us to see even slower biological events.
    Otherwise the system itself is of little interest as we have studied it before. These WU's are for testing the method as we know what to expect from this system. Therefore, the simulations will be very few and rare for the moment.

    It's a heads-up in case you are one of the lucky few to get one of these WU's, hehe.

    Edit: I forgot to mention, they should be relatively short for the long queue (estimated 3 hours on a 680)



  • 2013-08-14: IMPORTANT: Patched Nvidia drivers for Titans and GTX780

    If you have a titan or gtx780 please use these latest drivers from nvidia which fix an important bug.

    Titan/780 drivers:
    - Linux 325.15 http://bit.ly/13Qq4kf
    - Windows 326.41 http://bit.ly/13k1Ajc

    gdf



  • 2013-07-19: Update on titans and gtx780s

    Hi,
    so an update is due with titans and gtx780s.
    The current gpugrid application is not supporting it and we have not updated it for a reason.

    At the moment Titans and GTX780s do NOT work. After a short time the application crashes. Nvidia has now recognized the problem and it is working on a fix for Titans which should be out in a month or so. It could be a new driver or a bios update.

    For GTX780, the fix would be either together with the titan fix or it would not come for sometime or ever.

    Best for crunching at the moment are GTX770.

    gdf



  • 2013-05-28: New group member ... new simulations

    Hi guys,

    I recently disembarked at the multiscale lab attracted by the high-computing facilities you all provide! I am an experience researcher in the structural biology field.

    My first studies will be devoted to activate apoptotic proteins at atomic resolution, a family of proteins which control cell suicide and therefore are major players in cancer and neurodegenerative diseases.

    S.



  • 2013-05-22: New Nathan WUs on long

    Hey guys,

    I have put some new work on the long queue. These workunits are small and don't require any special algorithms, so should be no problems.

    With these workunits, I'll be looking at the folding of a small peptide using a special force field. The biophysics community uses different force fields to represent the motions of proteins and other molecules, and we are attempting to test a new one so we can check some previous work and feel comfortable in work we are planning to do.

    Happy crunching.

    Nate



  • 2013-05-20: New beta app for Titan owners

    Hi,

    If you have a Titan, please try out the new ACEMD beta application (You will need the option "run test jobs" selected too)

    Please report any problems here on this thread.

    MJH



  • 2013-05-16: Canceled SDOERR WU's

    I apologize for all whose WU's were cancelled today in the process of stopping the old ones and re-sending the new fixed ones.
    At the beginning I didn't realize the effect and extend of the cancellation (since it was not intended to work this way), but I see now that many hours of computation and credits were lost due to this.
    It seems to have been a bug in a script that had not been seen before until now, so we will refrain from using it until it has been fixed.
    I realize that the computation time is very important for everyone so we hope that such hiccups won't happen too often in the future.

    Many thanks for your patience and calculations!



  • 2013-05-15: Titan and GTX780 support

    We are probably merging the two updates at this point and update the applications to support titans and gtx780.

    It all depends how long it takes to get gtx780.

    gdf



  • 2013-05-14: Donating via Amazon

    Hey guys,

    We've added a new way for users to donate to GPUGRID. We've set ourselves up as an Amazon Associate, and if you click the link in our donations page before making a purchase with Amazon, we'll receive some small percentage of the value of your purchase. This way you can make a donation while going about your normal purchases.

    We are also considering updating the advertising banner(s) at the bottom of the page. We will likely keep it non-intrusive, non-annoying text, much as it is now. Certainly no flash animations.

    As always, Thanks!



  • 2013-05-13: New VIL workunits

    Hi,
    I have submitted some small workunits on folding. If they work fine, I will submit more, they are in the short queue.

    gdf



  • 2013-04-29: Deprecating Cuda3.1 application

    As everybody moved to the cuda4.2 applications already, we are going to deprecate the cuda3.1 short queue.


    gdf



  • 2013-03-07: Current Noelia WUs

    We have checked the error statistics and they are too high to be normal, so we are going to abort them.

    They work perfectly over here, so it's not clear what is the problem. We might need to run few in beta to try to understand it.

    gdf



  • 2013-03-04: GPUs supported by the "ACEMD Long" application

    Starting with this update to the ACEMD Long application, we are no longer supporting GPUs of compute capability 1.2 and lower. In practice this is everything below the spec of the GTX260 (8000-series, 9000-series, and low 2x0 and 3x0 cards).

    There are two reasons why we are doing this:

    1) It simplifies the application development because we have to support fewer hardware generations.
    2) We are able to improve the specification of the Long WUs to better reflect the majority of the GPUs crunching them.

    We are very grateful for everyone's contribution to GPUGRID, and I hope none of you with one of these older cards is upset by the exclusion. Work will still be available for you on the short queues.

    Thanks all,

    MJH



  • 2013-03-01: New project in long queue

    Hello all,

    After testing the new application, it is time to send a new project. I'm sending at the moment around 6000WUs to the long queue. Credits will be around 100000. Let me know if you have any issues, since is the first big thing we submit to the recently updated long queue and these WUs include new features.

    Noelia



  • 2013-02-27: long application updated to the latest version

    Among the advantages are reduced upload files.



  • 2013-02-27: Final beta unit test

    We have uploaded 100 workunits in the beta queue.

    Please report any anomalies.

    gdf



  • 2013-02-26: For photos and videos

    we will be posting photos and videos on the facebook page of gpugrid.

    If you want to be notified just follow us:
    http://www.facebook.com/gpugrid

    gdf



  • 2013-02-21: New WUs on Short 4.2 queue

    Hey guys,

    I have put about 1,000 new WUs on the Cuda 4.2 Short queue. In these simulations we're trying to get some information about the basic motions of proteins, and also study our force fields used to define their properties. The simulations are small and simple, so shouldn't suffer from CPU or memory issues. Happy crunching.

    Nate

    p.s. On the "Server status" page, the Cuda4.2 Short queue is actually the short queue on top. I will add some text indicating which is which.



  • 2013-02-13: New app is out for testing

    We have finished beta testing and we are now submitting workunits into a new queue for short runs.
    If all works, we are going to update also the long queue.

    Only cuda4.2 for the new app of course. Soon we will disable cuda3.1 as the application is way too old.

    gdf



  • 2013-02-07: ?eta and short queue jobs

    Hi guys!!

    I will be sending a good bunch of WUs to the short queue during the following days. Group names "RC1_run" and "RL1_run". A total of 13624 jobs will be submitted in total, once the first step -currently ongoing in the betaqueue- is finished for each of them. Around 1200 already submitted.

    Thanks a lot!!!!



  • 2013-02-04: Server restarted

    The server should be up and running again. Thanks for your patience!



  • 2013-02-04: Server problems

    We are having some problems with the server disks.
    The server may go down soon trying to recover from the problem.

    gdf



  • 2013-02-03: 1Pflops milestone

    GPUGRID has been constantly above the Petaflop in the past few days. Although just a symbolic number it feels good to reach such an impressive target for us.

    Every volunteer should feel proud too, because it's all thanks to you.

    gdf



  • 2013-01-22: Beta testing starting soon

    We will start some beta testing today or tomorrow with the new app for cuda4.2.
    If it works we plan to update acemdlong.

    gdf



  • 2013-01-09: New tasks in the Short queue - Method validation

    Hey guys,

    I've put some new tasks in the short queue. These simulations are validation for methods development work we did previously. As you know, part of what we do at GPUGRID is develop new methods for running and analyzing simulations. These types of simulations are important because they help us learn how to extract information from simulations that are relevant for all kinds of biological systems in the future. For an overview of methods we've previously developed, go to the Science>Methods page.

    Nate



  • 2013-01-02: No longer cuda3.1 apps in acemdlong queue.

    As announced we have deprecated the cuda3.1 application for the acemdlong queue.
    The acemd2 queue stays with both applications.

    From now on you should not be receiving acemdlong cuda3.1 apps.

    gdf



  • 2012-12-31: CUDA upgrade for long queue

    Starting in the next few days we will remove the cuda3.1 application from the long queue.
    If you want to crunch on acemdlong you need Nvidia latest drivers.

    In a week or so, we wil also upgrade the applications to a newer version with mainly science related improvements, but also an output file of 1/3 of the current size.

    gdf



  • 2012-12-26: 20,000 wus in queue New Year experiment

    Hi,
    so we have queued around 20,000 new wu in these days. This is unusual for us.

    The WUs will last only two steps, so they should be all over by early January ready for analysis.
    They look a lot, but in fact each is a much shorter sequence of other WUs which last for even 100 steps and take months to complete.

    The idea is to have very many different runs which come back very quickly. Instead of taking months, we will take just weeks to do an experiment this way. Of course we need to see if the analysis says that it's ok.

    As we never run so many and so long each step, we had some problems in the process. Some of which were visible, like the upload size too large and some were not visible to you (e.g. storage on server).

    All this is also useful to learn and prepare the system to execute such large batches without problems.
    The new application in January will also help in this.

    thanks everybody and happy new year.

    gdf



  • 2012-12-19: New systems in Long queue

    Hi all!

    A good amount of new WUs will be around for the next weeks in the long queue. The systems are called hfXA_long and will provide around 90000 credits each.

    Thanks and Merry Christmas to all!!
    Noelia



  • 2012-12-04: New PNAS paper has been published using results from GPUGRID

    A great new paper entirely done on GPUGRID. Thanks guys.
    http://www.imim.es/news/view.php?ID=159

    Photos and comments on facebook:
    http://facebook.com/gpugrid

    gdf



  • 2012-11-21: 50 facebook 'likes' in one day

    After one day, we are on our way to the target of 100 followers.

    Thanks everybody. Please help us reach out new people so that gpugrid can grow.

    gpugrid team



  • 2012-11-20: New facebook page

    www.facebook.com/gpugrid

    Hi,
    in order to communicate better our results, videos and images, we have now open an official gpugrid page.

    This will help you to reach scientist and to discover what we do in an easier way.

    Like the page for updates.

    gdf



  • 2012-11-14: New WUs on long queue

    Hey all,

    I submitted last week some new work units to the long queue. It's an old system, but new kind of simulation. We're working with an experimental group to see if we can reproduce some interesting results they saw. If we're successful it could give us more ways to find out important information about proteins. Of course, the results could also be negative, which is why we must do the experiment.

    The work units seem to be running well right now. They seem to have a pretty low failure rate. Please let us know if there are any issues.

    Edit: They have the name similar to NATHAN_benHP, for those that are interested.

    Nathaniel



  • 2012-11-03: CUDA upgrade notice

    By beginning of next year, we would like to remove the cuda3.1 applications.
    These are still the old apps and don't have several of the new features available in the new app which we need to do the science.

    We will probably have a cuda4.2 app only, so within the next few months, drivers should be upgraded to at least this version. In our machines, the latest driver 304.51 works quite nicely under Linux, very robust.

    gdf



  • 2012-10-11: New systems in long queue

    Hi guys,

    Just sent a good amount of WUs to the long queue. Credits will vary from 60000 to 70000. Thank all for your time!

    Noelia



  • 2012-09-25: another sys on acemdlong

    Hi,

    I am submitting 500 WU on long queque of one of my last systems, that will be 57400 for each WU.


    :)

    Cheers,

    Paola



  • 2012-09-18: New WU on long queque

    Hi guys,

    I have submitted 500 WU of 69000 credits each.

    Thanks for your computing time,

    Paola



  • 2012-09-11: Server problem fixed

    The out of disk space error should be solved now.

    Sorry for the inconvenience.

    GDF



  • 2012-08-21: hsp90 with high ligands concentration

    Hi guys,

    I am trying to enhance the sampling in a difficult system....hoping to improve the sampling HSP-90 chaperon.
    I sent 500 WU on acemd long 76460 credits each

    Thanks for your computing time,

    Paola



  • 2012-08-20: Lots of WU in short queue!

    Hi guys,

    It just finished uploading 14000 WU (same systems where in the beta queue last week) to the short queue. There are two types of systems and will provide either 1400 or 9500 credits each. Last week I posted half of these systems where going to be sent in the long queue, but we have more appropriate systems for this queue ready to be sent there in the following days -so expect high activity of your cards this week in both queues!-
    These systems will allow to determine and ranking the best ligands within a large set of compounds for trypsin enzyme.

    Thank you for your time,
    Noelia.



  • 2012-08-10: New system: amidotransferase

    Hi guys,

    I am submitting 500 WU, 14400 credits each on acemd short. The group name is 1XFG_HGA.

    The system is an amidotransferase, that is involved in several biosynthetic reactions.

    Cheers,

    Paola



  • 2012-08-08: More acemdbeta

    Hey guys,

    Be expecting a good bunch of workunits in acemdbeta!! ( around 14000). As before, this is not that we want to test the system, this is already the real thing that can only run in the beta queue. The systems are short and will provide either 3000 or 450 credits.

    Thanks!
    Noelia



  • 2012-08-08: ENDOCHITINASE in complex with a purin derivative frag

    Hi guys,

    I am submitting 500 WU, 21800 credits each, on acemd short queque. The system is a chitinase in complex with a purin derivate. Chitinase hydrolyses chitin, an essential fungal cell wall component, playing a role in cell wall morphology, so inhibitors should have antifungal properties.


    Thanks for your computing time,

    Paola



  • 2012-08-08: ENDOCHITINASE in complex with a purin derivative frag

    Hi guys,

    I am submitting 500 WU, 21800 credits each, on acemd short queque. The system is a chitinase in complex with a purin derivate. Chitinase hydrolyses chitin, an essential fungal cell wall component, playing a role in cell wall morphology, so inhibitors should have antifungal properties.


    Thanks for your computing time,

    Paola



  • 2012-08-02: new system trypsin mutant L99A

    Hi guys,

    I am submitting 500 WU (17900 credits each). The protein is a trypsin mutant, to see if and how that mutation (Leucine 99 substituited by Alanine) affect the binding to benzamidine, following Ignasi's work :D

    Paola



  • 2012-07-30: EXOGLUCANASE I bounded to an amphipathic fragment

    Hi guys,

    I have submitted 500 WU with group name 1H46_RNP on acemd(short), 21600 credits each :)

    Cheers,

    Paola



  • 2012-07-24: New system in beta queue && long queue

    Hi guys!

    I've just sent 500 WU to acemdbeta with 5250 credits each for the first phase of the simulations. This equilibration step can only be done in the beta queue, so this is not a test, but already the real simulation.
    Once all this WU are finished I will be able to prolong all them in the long queue, giving a total batch of 3500 WU with around 50000 credits each, likely in the next two days.

    The new system have already been in gpugrid: it is the domain SH2 but focusing on the interaction with fragment(s) and not with polypeptides as before.

    I will keep you updated once I send the second part!


    thank you ;)
    Noelia



  • 2012-07-20: FInding the best receptors

    Hi all,

    I submitted this afternoon a set of new systems to acemdlong with credits ranging from 40000 to 70000. This will allow to check which are the best binding candidates in a family of receptors for a given drug, and ultimately, extend the method to other families.

    Thank you all for your computational time.
    And have a nice weekend!!!

    Noelia.



  • 2012-07-20: Finding the best receptors

    Hi all,

    I submitted this afternoon a set of new systems to acemdlong with credits ranging from 40000 to 70000. This will allow to check which are the best binding candidates in a family of receptors for a given drug, and ultimately, extend the method to other families.

    Thank you all for your computational time.
    And have a nice weekend!!!

    Noelia.



  • 2012-07-19: New systems in beta queue

    Hi all,

    I just sent 500 WU on acemd beta, half of them with 450 credits and the other half 3000, only for the equilibration step. So this is a perfect occasion to check how the beta queue works ;). Once this is finish I will sent the complete simulations. This will allow to compute the energy of binding for about one hundred of different ligands to trypsin, and if this works, we'll extend to more than one thousand!!

    Noelia.



  • 2012-07-13: new system THYMIDINE KINASE- HYDROXYPROPYLADENINE

    Hi guys,

    I am going to send a new system, a THYMIDINE KINASE in complex with an adenine analogue inhibitor
    500 WU on acemd short, 21700 credits each
    and if it works fine, I will send asap even the complex with the enantiomer :)


    cheers,

    Paola



  • 2012-07-10: Welcome to Noelia

    Hi,
    Noelia will start a PhD with us at gpugrid, so she will be sending you lots of work very soon.

    We will be uploading pictures and descriptions soon.


    gdf



  • 2012-07-06: New 40% faster applications are now fully deployed

    The new cuda4.2 applications are now fully in use for Kepler and Fermi.
    cuda3.1 applications will still be given out if you have an older driver.

    gdf



  • 2012-07-05: New system submitted beta-lactamase

    Hi dear volunteers,

    I submitted tonight 500 WU on acemd (short) 12500 credits each.
    The system is a beta-lactamase in complex with a negative charged fragment.

    cheers,

    Paola

    p.s. sorry for the delay of the post....I am on vacations, but still thinking about work :)



  • 2012-07-02: Farewell

    Dear crunchers,

    My time has come. Now that I got my PhD I must move on. I am leaving the lab and therefore GPUGRID.net as scientist although I'll be following it closely from wherever I am.

    It's been a pleasure to work with you all and I hope you still keep your volunteering spirit for the years to come. You're really the fuel of the scientific project behind.

    Thank you very much.

    All the best,
    Dr. Ignasi Buch



  • 2012-06-29: let's sample the binding site....

    Hi all,
    I am submitting 450 WUs on acemdlong, 53600 credits each.
    The group is ADAPT. I want to improve the sampling in the binding region.

    Thanks to all for your computing time,

    cheers,

    Paola



  • 2012-06-29: Ignasi's thesis defense TODAY- streamed online!

    Guys,

    I am told that in this address http://84.88.71.16:8080/auditori and using Windows Media Player, you can follow my thesis defense today scheduled at 15:00h Barcelona time (UTC+2). Double check your time difference, just in case...

    Sorry for the short notice,
    i



  • 2012-06-25: New CUDA4.2 applications are out for Kepler GPUs

    We have finally uploaded the new applications for Kepler supporting cuda4.2.

    You should be receiving them if you have a recent driver. The new applications are substantially faster.

    gdf



  • 2012-06-11: 3EKO_8LIG 3EKO with high ligand concentration

    Hi all,
    I am submitting 500 WUs on acemdlong, 53900 credits each.
    The group is 3EKO_8LIG. It is the same protein target of my previous runs, a molecular chaperon (HSP90) involved in many cellular functions. I put an high concentration of the small ligand in order to improve the sampling.

    Thanks to all for your computing time,

    cheers,

    Paola
    ~



  • 2012-05-30: Plenty of WUs in queue!

    Guys, there are some big nice simulations waiting for you to come crunch them!



  • 2012-05-28: New task on long queue from Nate, named RSP1120528

    Hey everyone,

    I have submitted some new tasks to the long queue. This is a new system that hasn't been run before on The Grid, but since I'm not doing anything new configuration wise, I don't expect any problems. These will be higher priority tasks than most, and if all goes well we hope to get some positive results quickly. I'll elaborate on the goal of these simulations later. They should run for about 7 hours on the fastest cards. I'll be keeping a close eye on them over the next few days, but please report any problems when you see them.

    Nate



  • 2012-05-25: Install new drivers for new application

    The new application will soon make it to production.
    You need to have the latest drivers to use it, because it is compiled with cuda4.2.

    Linux: 295.41 or greater
    Windows: 301.32 or greater



  • 2012-05-24: This is what *xTRYP* WUs were about

    Check this video out.

    We are already working on the publication with the Dr. P. Carpentier the crystallographer from the ESRF Synchrotron in Grenoble (France) who's been able to crystalize some of the intermediate states of benzamidine binding that we see in our simulations.

    cheers,
    ignasi



  • 2012-05-16: 3EKObis another conformation

    Hi all, I am submitting 500 WUs on acemdlong, 56000 credits each. The group and name are 3EKObis...because I have already completed one, but we need more data and I hope that this new conformer should give better results.

    The system is a molecular chaperon involved in many cellular functions.

    Thanks to all for your computing time,

    cheers,

    Paola



  • 2012-05-09: Ignasi's PhD thesis

    Dear all,

    I finally have my thesis printed.
    I thank you all (once again) for your crucial contribution to it. And of course, Gianni, Toni, Kashif, Matt, Nate and Paola for many many reasons.



    The defense is programmed for the 29th of June and you are all invited if you can make it to Barcelona. Drop me a line if you really want to come. There shall be a party :)

    cheerios,
    i



  • 2012-04-22: Problems with fragxa4 and fragxa3 WUs

    We had to cancel these WUs on-the-fly. fragxa3 were 10 times longer by mistake and would not have finished in most computers.
    On Monday we will look into compensating who was affected by this.

    Sorry for the inconvenience.

    gdf



  • 2012-04-18: New *xTRYP* WUs

    We are submitting a new batch of WUs (~1000) of our beloved trypsin and benzamidine system for a beautiful experiment in collaboration with a crystallographer.

    It seems that these crystallographers and us may have got to similar conclusions on how trypsin and benzamidine like to interact. The nice thing is that we'd have got to the conclusions from VERY different approaches. They make crystals of trypsin/benzamidine and take pictures of their structures using a synchrotron and we make MD simulations of already solved structures and take many snapshots of what happened. And then we compare them.

    If experimentalists (protein crystallographers in this case) are able to reproduce what we obtained from computer simulations or viceversa, it would be a beautiful (and necessary) validation of our methods.

    Let's hope that all goes well.

    Cheers!



  • 2012-04-02: New WUs of TRYP (*adTRYP*)

    We have submitted a new batch of TRYP (*adTRYP*), significantly longer than the latest TRYP (met*, eth*, pro*,...).

    The latest TRYP were a real production attempt to straighforwardly obtain binding for small inhibitor molecules. It finally proved harder than first expected, therefore we are improving the underlying analysis method as well as implementing a cleverer scheme to obtain the data. That is what *adTRYP* are for, to prepare a systematic methodological study on how to produce efficiently many events of binding for small protein inhibitors. See experiments section for more info.

    Cheers



  • 2012-03-23: Tests on GTX680 will start early next week [testing has started]

    We are looking forward to testing the new nvidia architecture. We will report the performance soon and really thank one anonymous cruncher for the donation.

    gdf



  • 2012-03-23: Tests on GTX680 will start early next week

    We are looking forward to testing the new nvidia architecture. We will report the performance soon and really thank one anonymous cruncher for the donation.

    gdf



  • 2012-03-21: New GPUGRID team member

    It is a pleasure for us to introduce you Paola Bisignano, PhD student at IIT (Italy) that is visiting us for 9 months. She has already started to send WUs to the queue, so soon you will be getting them.

    Her work is similar to ours (i.e. *TRYP*) where we try to predict small molecule binding affinities and kinetics to protein targets of biomedical interest.



  • 2012-03-19: New publication, new badges!

    Dears!

    We have recently published a new paper on the Journal of Chemical Theory and Computation: "Visualizing the Induced Binding of SH2-Phosphopeptide", authored by me, ignasi (shared co-authors) and GDF. In the paper we have made (hopefully :) good use of your donated GPU time to find out in detail what happens when a kind of signal is transmitted between proteins in a cell. The signal is the recognition of a short peptide (pYEEI for friends) by a partner "plug", called the SH2 domain. This kind of signaling is in fact very common in cells for responding to all varieties of messages (for example in receptor kinases).

    We updated the badges accordingly - and this time we also briefly go down the hall of fame. Of the 3113 contributors, these are the 10 users who contributed the most computation (rank, name, millions of credits):

    1 Retvari Zoltan 70.1
    2 Venec 66.8
    3 davidYuen 49.0
    4 WirelessDude 46.8
    5 Stoneageman 46.3
    6 CTAPbIi 26.0
    7 Helmholdt 24.8
    8 Nikke 24.3
    9 CNT - IQE 24.0
    10 Ketzer7 24.0



  • 2012-03-13: Update to FAX3 tasks on long queue

    see details here: http://www.gpugrid.net/forum_thread.php?id=2903&nowrap=true#23933



  • 2012-03-10: New task on long queue, significantly longer than traditional tasks

    Hi all,

    I have submitted some new work units that will replace some I submitted earlier in the week. The names will be "NATHAN_FAX3". These tasks are in the true spirit of the long queue, and will take about 12+ hours on the fastest cards. Some have already been returned and indeed have been around 13 hours. This is markedly longer than what you have expected traditionally, but we really want the long queue to be for critical tasks, computationally intensive tasks, and the like. I suggest you all take note of how these tasks run on your computers and be mindful of temps and errors as you start to receive them.

    I have noticed some crunchers expressing concern/dismay that perhaps they will not be able to get the 24h bonus with such long tasks. We are mindful of that concern, and will keep an eye on this group as an experiment. If we think it is too unfair to people with fast but not the fastest cards, we'll be sure to correct that in future groups. But the less send/recieve we have to do, the better. We are also mindful of the fact that longer tasks might be more susceptible to errors/crashes, and we want to see how this goes. I'll be looking out for the severe error percentage over the next few days for any problems.

    Also, a note about tasks beginning with NATHAN_FA... These tasks are unique in that they are quite large simulations, compared to many others we have done in the past which are smaller (bigger biomolecules mean bigger simulations). They not only take longer per step, but require more memory. Cards with lower memory (below 1GB) may suffer additional performance loss. There is nothing we can do about this, unfortunately.

    Happy crunching.

    Nate



  • 2012-03-06: Server back online after power cut

    We are attached to a temporary powerline, so we need to restart sooner or later to attach it to the proper one.

    gdf



  • 2012-03-05: Do not use 295.x driver on windows

    The driver causes CUDA WUs to fail - here and on other projects. Please don't use it until NVIDIA fixes the bug.



  • 2012-03-05: New wus on long, old project that needs validation.

    Hey crunchers, I have put a batch of work units in the long queue that should make up for the drought. The work units themselves are not from a new system, but rather are an important validation of work I have already been doing. These work units require the long queue, and will likely take 12 hours on the fastest cards. Let us know if you have any problems or concerns and we'll do what we can to address them.



  • 2012-03-04: acemdlong also updated now

    The update process is finished also for acemdlong.

    gdf



  • 2012-03-04: New application acemd2 6.16 (WIN/LINUX)

    We have upgraded the acemd2 application to get some features which we need in order to execute new WUs.

    Soon, we will upgrade also acemdlong.

    All the rest in the application stays the same and you should not notice any change.

    gdf



  • 2012-02-24: monitor suspend/resume bug in 295/296 drivers

    There are some reports of bugs concerning the latest NVIDIA drivers (failures when monitor goes to sleep). GPUGRID may not be immune to the bug. If it occurs to you, either

    * rollback to previous drivers
    * or configure the monitor so that it does not turn off



  • 2012-02-24: Possible monitor suspend/resume bug in latest drivers

    There are some reports of bugs concerning the latest NVIDIA drivers (failures when monitor goes to sleep). GPUGRID may not be immune to the bug. If it occurs to you, either

    * rollback to previous drivers
    * or configure the monitor so that it does not turn off



  • 2012-02-16: New TRYP WUs

    I am submitting 700 WUs in the long queue as part of a new experiment.
    You'll note that they have the TRYP tag that was used for our publication in PNAS 2011:
    metTRYP
    ethTRYP
    proTRYP
    isoTRYP
    butTRYP
    penTRYP
    hexTRYP

    We are now extending the study to 7 different ligands to see if we can reconstruct their bindings too.

    cheers,
    i



  • 2012-02-09: AMD GPUs now available

    For running AMD gpus please check this thread:
    http://www.gpugrid.org/forum_thread.php?id=2839



  • 2012-02-09: AMD GPUs now available at different project

    For running AMD gpus please check this thread:
    http://www.gpugrid.org/forum_thread.php?id=2839



  • 2012-02-09: AMD GPUs are now usable at Donate@Home, a different project from GPUGrid.

    For running AMD gpus please check this thread:
    http://www.gpugrid.org/forum_thread.php?id=2839



  • 2012-02-07: New WUs: GIANNI_FR1

    This is a set of 600 WU in the acemdlong queue related to method development.

    gdf



  • 2012-02-07: New wus on the long queue

    We have put some not-so-long WUs in the (currently empty) long queue. They give normal credit (possibly with bonuses). This is part of an experiment to verify whether we can get low-latency results.

    They are named "TAKExx".



  • 2012-02-06: New batch of WUs: KKAL4

    I've created around 1000 new WUs on the "normal" queue. They give 9100 base credits each. The type of WU uses a standard setup and we already had them around in the past.



  • 2012-01-27: New windows beta application is out

    Same as Linux which was fine. If it works we will update the production apps.
    Again only minor changes.

    gdf



  • 2012-01-25: New acemd linux beta test app

    A new app is up for test.
    Only minor revisions.

    gdf



  • 2012-01-23: Badge system up and running!

    You are seeing it :). Check your Account page too.



  • 2012-01-20: Ladies and gentlemen, the GPUGRID Badges!

    The Amino acids, components of proteins, the main characters in GPUGRID simulations. Given per total number of credits and milestones in 20 levels, the number of amino acids encoded by the universal genetic code (ordered by molar mass ~weight). Amino acid/credits equivalences below.



    The Waters, basic component of life and a distinctive trait of our long and accurate simulations. 7 levels (Plastic, Bronze, Silver, Gold, Ruby, Emerald, Sapphire) to represent relative contribution to our scientific publications. Each water badge will be linked to the corresponding publication and Science topic. Water/percentage equivalences below.



    The donor badge is changed to the crown

    The complete information is available in the Volunteers page. We will update the server at the start of next week!



  • 2012-01-16: More workunits in the long queue

    Dears, we're sending 1000 more WUs related to the modeling of neural system.

    These are named TONI_FAAEAC1 and TONI_FAAEAN1. They should give out 47700.9 and 36228.6 credits respectively.

    As always, make sure you disable the "acemdlong" app in your GPUGRID preferences if you don't have one of the latest cards.

    Toni



  • 2012-01-13: GPUGRID's new Badge System coming soon

    This is the first formal announcement for the new Badge System. Next week, we will unveil the badge images, although the final implementation may still take two or three more weeks. We can already tell you that there will be two types of badges: one for the total number of credits (one badge per user) and one to acknowledge the relative contributions on our publications (one publication, one badge). More soon!



  • 2012-01-09: Web shortcuts in the Boinc client

    We have added BOINC-client shortcuts to commonly-accessed GPUGRID web pages. (Known as Client Web Links or GUI Urls in BOINC lingo.)

    You should soon see the following buttons appear in the Projects/GPUGRID tab: Your account; Your team (if any); Server state; Donations; Science; Forums.

    Best wishes for a great year 2012!



  • 2011-12-23: Happy Holidays!

    GPUGRID wishes you Merry Christmas and a Happy New Year 2012. We hope the world doesn't end in 2012 as we've got lots of work to do!



  • 2011-12-20: HIV research update

    There has been further project development in the HIV research line which you may find on the Science page of the website.

    I would also like to personally thank all volunteers for their continued support of this research. Thanks to your crunching we have been able to uncover one of the fundamental processes in the maturation of HIV. Some further computing is required to complete the work (Tag: HIVPR) and we look forward to your continued support in the future.



  • 2011-12-20: GPUGRID has a new website!

    Guys, you are seeing it.

    Thanks to the awesome work done by Ignasi, GPUGRID.net has a new, stylish, (even steelish :-) appearance. The redesign affected essentially all the areas of the website.

    We (well, Ignasi) has paid especially close attention to the "Science" section - it's completely redesigned, and includes visual cues of the each major area we are doing research in. We hope you will enjoy it!

    Needless to say, the forums and user/task/WU/server status pages are also updated and in sync with the new style, but they maintain all the old functionality. The BBCode thing is now functional. For more details, comments, etc., please refer to the "server and website" forum.

    A whole-hearted thank you to Ignasi for this Christmas present to the group.

    Toni



  • 2011-12-17: New work units on long queue

    Hi all, I have submitted 1000 new workunits to the long queue. The simulations focus on the receptor CB1, and with them we hope to gain some insights that will have important implications for a wide range of diseases, including several neurological disorders, gastrointestinal disorders, pain, and cancer.



  • 2011-12-15: Workunit distribution normal

    WU and credit distribution should be normal now. Thanks for the patience. Feel free to report irregularities and concerns in the "Server and website" forum.



  • 2011-12-14: First part of server upgrade complete

    We upgraded the server software - if WU distribution, reporting, etc. is confirmed to work correctly, on Monday we will update the web pages.

    As a first consequence of the upgrade, you should be receiving "notifications" in your BOINC clients.



  • 2011-12-14: Server upgrade started

    GPUGRID.net will be down for several hours. Follow us on http://twitter.com/gpugrid!



  • 2011-12-12: Server upgrade imminent

    Dears, just another reminder that we'll soon be upgrading the server software. There will be some down-time.

    Even though we planned the transition carefully, we can't anticipate exactly how long will it last (hopefully in the order of hours). Feel free to increase the work cache.

    T



  • 2011-12-02: Winter is coming

    A totally renewed version of the GPUGRID website will be soon released together with a server update. More news to come.



  • 2011-11-03: Possible network shutdown on saturday 5 nov

    On Saturday November the 5th the IT department is going to replace some network equipment in the servers room. The GPUGRID server may be affected.



  • 2011-10-18: @gpugrid Twitter account

    GPUGRID finally goes social. We will be posting the News and other stuff through our Twitter account. We encourage you to follow us. Should be specially useful to communicate with you if the site is ever down.



  • 2011-10-17: New workunits AGGMI1 on protein aggregation

    I'm sending a number of these to further a study (almost complete) on the formation of pathological protein aggregates. I placed the WUs into the "short" queue - a GTX 275 (on Linux) should take around 8.5 hours for one.



  • 2011-10-06: Steve Jobs' 2005 Stanford Commencement Address

    A nice talk from Jobs in youtube. If you have not seen it yet, give it a try.



  • 2011-10-06: Steve Jobs' 2005 Stanford Commencement Address

    A nice talk from Jobs in youtube. If you have not seen it yet, give it a try.



  • 2011-09-30: Do not use BOINC 6.13.3 - 6.13.4 - 6.13.6

    These (unstable and withdrawn) version are silently causing WU corruption on upload and make other WUs fail.

    We encourage you to use the stable versions of BOINC clients.

    Thanks



  • 2011-09-16: 450 WUs more to fight cancer

    More WUs and counting for the Cancer-related project we are running. They come with the tag *EGFR* and are submitted to acemdlong only. Expect some 500 more in the next two weeks. Have a nice weekend.



  • 2011-09-10: Simpler deadline

    Since a few days, the deadline for the results is fixed at 5 days.There is not anymore any special mechanism for replication of results as before.
    This change should help people with slow cards to complete workunits.

    Make sure you select the right application (short 3h or long 12h) for your card.

    gdf



  • 2011-08-31: Welcome to Nathaniel

    Nate joined our group few months ago for a phd and he has just started to submit jobs in gpugrid for all of you.

    GDF



  • 2011-08-21: Gpugrid in the 6th Virtual Physiological Human newsletter

    The 6th public newsletter of the Virtual Physiological Human Network of Excellence includes an article about the recent scientific results obtained thanks to GPUGRID's volunteers. The article is on page 12; it features a couple of (very illustrative, in my opinion) figures which visualize the recent "TRYP" experiments.



  • 2011-08-19: Updated project icon

    It's just a small change (namely, 1600 pixels small) - we updated the project icon and got rid of the obsolete reference to PS3s. This is important for newer BOINC clients, whose simplified view only lists projects by icon.



  • 2011-08-09: Possible network outage on 10th August

    There could be a possible network outage tomorrow for network maintenance. It might affect also the new gpugrid server.

    gdf



  • 2011-07-28: 550 "WU shots" for the Summer

    Dear all,
    A batch of 550 very short WUs -WU shots- (compared to GPUGRID standard) has been sent for acemd2. Tagname is *PYRT* and expected computing time is 2-3h for a GTX275. Let's see how we (you and us) like it. Happy holidays & salut!



  • 2011-07-27: Crunch to fight cancer

    Dear users, we are submitting several WUs (*EGF*) directly related with colorectal cancer research. We are collaborating with MDs & researchers at the Hospital del Mar here in Barcelona to characterize some previously unreported effects of a well-known drug for cancer. Thanks for your precious contribution.



  • 2011-07-19: New server hardware fully funcional

    We have completed the port of the server on the new hardware.

    gdf, ignasi, toni



  • 2011-07-19: Server up again

    Please report any compute problem here.
    We are still fixing some parts of the web appearance.

    gdf



  • 2011-07-19: Server downtime

    We have a planned downtime today for a couple of hours maximum during the day.

    gdf



  • 2011-07-18: Server hardware update

    We are checking internally the new server. Hopefully there should be a transition to the new hardware soon.

    Nothing is needed on your side, but it is possible that the server can appear to be down for a couple of hours.
    gdf



  • 2011-07-06: New applications 6.15 are out with much improved efficiency and less impact on the system

    The new applications should be both more efficient than 6.14 and eliminate any lag in the user interface in Windows.
    gdf



  • 2011-06-15: New batch of work KKFREE4

    KKFREE4 should be fixing the problem of low credit of KKFREE3.

    gdf



  • 2011-06-12: New application acemdlong 6.14 is out

    This new application mainly present changes in terms of the science.

    gdf



  • 2011-06-07: New publication in PNAS!

    Dear users, we are grateful to announce a new publication from GPUGRID. This time at the prestigious journal Proceedings of the National Academy of Sciences of the USA (PNAS): http://dx.doi.org/10.1073/pnas.1103547108
    The work published is related to WUs tagged as *TRYP*. Thank you very much to all contributors!



  • 2011-05-28: CUDA2.2 application will be deprecated by June 3 - Update Nvidia drivers

    Please update Nvidia drivers to - at least -
    257.21 for Windows
    256.40 for Linux
    If you have a newer driver already, there is nothing to do.

    gdf



  • 2011-05-23: CUDA2.2 application will be deprecated soon - Update drivers!

    Please upgrade your driver to the latest available driver. If you don't upgrade the server will not be able to send you workunits anymore as old driver are not compatible with the cuda3.1 application.

    gdf



  • 2011-05-13: (Another) New publication: optimized methods to compute binding free energies

    May the party continue with our second publication from GPUGRID computations! The work, also to be published at the Journal of Chemical Theory and Computation, presents the optimization of a previously developed protocol to accurately compute binding affinities between proteins and small peptides. Such methods may be employed in the future for drug design studies. WUs related to this publication are all the *pYEEI*. Congratulations to you all!
    I. Buch, S. K. Sadiq and G. De Fabritiis, Optimized potential of mean force calculations of standard binding free energy, in press J. Chem. Theory Comput. (2011)



  • 2011-05-10: New publication: free energy of ion permeation through gramicidin A

    Dears, we are happy to announce that the results of various GPUGRID-enabled studies were recently published in high-impact journals.

    The first one I'd like to mention is "A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A". The paper is a numerical investigation on the convergence of a molecular dynamics (MD) technique called "steered MD" (SMD), which is used to obtain free energy profiles (i.e. probabilities of occurrence of certain biological events). The SMD technique is essentially based on statistics: one has to repeat the same experiment (computational or otherwise) over and over, many times, until a reliable result is obtained. How many times, and how reliable? Up to now, studies performed SMD on biologically-realistic systems were limited to just a few (~10) trajectories, and the corresponding error was therefore hard to assess. We used GPUGRID to perform increasing number of pulls, up to two thousands, to verify how much the precision of a free energy profile was gradually improved as a consequence. (The answer, if you were wondering, is that one needs quite a lot of simulations).

    T. Giorgino and G. De Fabritiis, A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A, in press J. Chem. Theory Comput. (2011).

    Thanks to all of the crunchers of the GA* series of workunits!



  • 2011-05-03: Social buttons and microdonations

    We have added buttons for Twitter, Facebook and Flattr (social micropayments) in our website. Help us spread the project! Thanks in advance.



  • 2011-04-25: Resuming long WU supply: ABxx

    I am also resuming the supply on the long queue. They are related to amyloid proteins, involved in diseases including Alzheimer's. The new tasks took 11h on a test GTX 275.

    Make sure you disable the "acemdlong" application from you GPUGRID preferences if you have an older card.

    Happy Easter!



  • 2011-04-22: Resuming WU supply: KKAL5

    After hopefully settling the scheduler issue, I'm gradually reopening the WU faucets. I'll be sending KKAL5/6/... workunits in the standard queue, which take ~6h on a GTX275. In addition to belonging to a protein of great interest , they are also part of a new approach which hopefully makes the best use of the simulated time, re-evaluating each day (or so) the simulation threads that are more promising. (And no changes is required on your side.)

    If you are not getting WUs, please post in the "server and website" forum.



  • 2011-04-15: Too many workunits: Please cancel them so that other can get them

    We have probably fixed the scheduler now, as there is no work, please cancel the workunits downloaded in excess so that everybody else without work can finally get them.

    Many thanks,
    gdf



  • 2011-04-15: Problem with scheduler

    In order to fix the problem that the scheduler was not releasing wus, we have switched two days ago to the matchmaker policy for the scheduler which is less strict. Well, it seems that it simply ignores all the rules, so we have now reverted to the old scheduling mechanism and will try some new fix.

    gdf



  • 2011-04-13: New science: AGG workunits

    For some days I will be running 600 workunit chains named "AGG" in the "acemdlong" queue. They belong to an investigation on aggregation processes, e.g. those that lead to Alzheimer's disease.



  • 2011-04-13: "No new work" problems SOLVED

    We have found what prevented most of users to receive work despite having WUs in queue. Everybody should be receiving work now. There's plenty of WUS to crunch!



  • 2011-04-13: "No new work/too much work" problems

    We have found what prevented most of users to receive work despite having WUs in queue. Everybody should be receiving work now. There's plenty of WUS to crunch!



  • 2011-02-23: Server poweroff: Feb 24th between 7-10am (UTC +1)

    Due to maintenance operations in the power system of the building, the server will be down between 7 and 10am (UTC +1) tomorrow Feb 24th. We appologise for the inconveniences.



  • 2011-01-31: New task selection option

    We are introducing the possibility for users to select between shorter (acemd2, approx 4 hours on GTX275 cards) and longer (acemdlong, 8 to 12 hours on GTX480) tasks. Simply go to your account preference to select which applications you want to crunch for. Long task are of course credited higher, but GPUs with less cores cannot simply compute them in time.



  • 2011-01-27: Server up again

    The server is up again and all should get back to normal very quickly.

    gdf



  • 2011-01-21: Power down scheduled: Thu, Jan 27th 10am UTC+1

    The server will be down for some minutes due to power maintenace operations in the building, next Thursday January 27th at 10am (UTC+1).



  • 2011-01-11: New Year, New WUs/experiment!

    Happy New Year,

    In this binary day 110111, I am sending some (150) new WUs tagged as *EGFR* for you to crunch. It is a brand new project that we are starting. Its goal is to find the (molecular) cause for the resistance to some anticancer drug -which is quite exciting!

    More to come,
    ignasi



  • 2010-12-27: Happy holidays!

    GPUGRID wishes you the best for the New Year.



  • 2010-12-14: Long WUs are out - 50% bonus

    Double sized WUs are out: *variant*_long* and include a bonus of the 50% on the credits.



  • 2010-12-14: Award for conference presentation

    We are glad to tell you that we received an award for best oral communication at the Young Modellers' Forum in London held the past 10th of December. The work presented was entirely based on the *IBUCH_TRYP* WUs for which the paper is in writting process. This is also your prize. Thanks for the hard work.

    ignasi



  • 2010-11-26: Proteins are complex molecules essential to life

    Check out our University's institutional video on our research group. http://www.youtube.com/watch?v=p1TeJ61FfpI
    We hope you like it.



  • 2010-11-10: Network unavailable from 00:00 to 02:00 CET

    There will be a planned network cut tonight from midnight to 2AM central European time zone.
    There is nothing special that you need to do.



  • 2010-11-04: For Fermi-CUDA3.0 users.

    If you have a GTX400 series card and are using our cuda30 application, please not that we have now deprecated it and only cuda31 applications will be distributed.

    To keep receiving workunits you need to update to CUDA3.1 drivers (256. or newer).

    thanks,
    gdf



  • 2010-10-20: 2,000 WUs on queue!

    We are back from our WU shortage we had to impose after storage problems. Still haven't recovered from them but new light-weight WUs are out already. Come and get them!



  • 2010-10-17: Storage server problem

    Our 32TB storage server is offline. The sysadmins are trying to rebuild it but until then we have access to only the smaller storage. Some workunits cannot be sent.

    gdf



  • 2010-09-03: Server up again

    We had several power cuts. The server now seems to work fine.

    gdf



  • 2010-09-03: Power down

    Tonight we had a power down of the servers. We are still recovering from it as one disk seems to be not functional.

    gdf



  • 2010-08-27: On new fatty WUs

    A batch of 500 WUs *_TRYP_* have been sent and will take TWICE as much to compute than normal.We are talking of 10 nanoseconds of simulation per WU! (for what most people still use big fat supercomputers). We need them for a very interesting publication we are preparing related to this experiment. Many thanks for the effort!



  • 2010-08-23: Welcome back from holidays with a new publication from GPUGRID

    Thanks to all volunteers for their contribution in the run of all *JAN* tasks which finally lead to this scientific publication:
    J. Selent, F. Sanz, M. Pastor and G. De Fabritiis, Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors, PLOS computational biology, 6, e1000884 (2010).

    Download it here: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000884

    In this work we show how sodium ion can modulate the activity of an important protein receptor (dopamine D2 GPCR) a drug target for the treatment of diverse central nervous system disorders (e.g. schizophrenia, Parkinson's disease).



  • 2010-07-06: PhD position available to work with GPUGRID

    A PhD position is available to work on
    "Molecular modelling of receptor dimerisation - a physical phenomenon with high relevance for schizophrenia" at GPUGRID.
    More information available at: http://multiscalelab.org/Jobs?action=AttachFile&do=view&target=PhD_position.pdf

    Please distribute the PDF of the position to reach maximum audience.

    gdf



  • 2010-07-02: New application for CUDA3.1 is now out

    A part for being faster for some workunits, it also solves the long standing bug of some older GTX260 cards.
    You need a CUDA3.1 driver to download the cuda31 application.
    (Windows only)
    gdf



  • 2010-06-30: New CUDA3.1 application for Windows now out for beta work

    We have uploaded the new CUDA3.1 application for Windows. It is given only to users who accept beta work. It will be released officially in the next few days for everybody.
    The CUDA3.0 application is still active for now.

    gdf



  • 2010-06-30: For Nvidia Fermi users - second reminder

    In the next few days, we will replace the cuda3 application with a cuda3.1 application. This might not work on older drivers, so please update to the latest Nvidia drivers.

    The CUDA3.0 application will be simply removed as there are many problems in the CUDA3.0 release that have been solved in CUDA3.1.

    gdf



  • 2010-06-29: For Nvidia Fermi users

    In the next few days we will update the Fermi applications to CUDA3.1. If you have a Fermi card, please update your drivers to at least 257.21 for Windows and 256.35 for Linux. No action is required from users with other cards.

    GDF



  • 2010-06-14: New publication from GPUGRID

    The article K. Sadiq and G. De Fabritiis,Explicit solvent dynamics and energetics of HIV-1 protease flap-opening and closing, is now in press in the journal Proteins.

    The work shows by means of MD simulations running on GPUGRID, several possible conformations of the HIV protease, a common target of anti-HIV drugs. In particular it was possible to release a new wide-open conformation which could present a possible useful target for new drugs.

    Thanks everybody for donating their GPU computer time. The work units were called *HIV*.

    A movie is also available at: Movie

    A copy of the paper is available at: Paper



  • 2010-06-08: Short movie for the outreach of molecular dynamics

    In an effort to give the "Ultimate Explanation" of what is MD to the non-initiated, a couple of scientists (50% belonging to the GPUGRID team) made a short movie in the context of a visual storytelling course at the science park we work in. We hope you enjoy it: http://vimeo.com/12055025



  • 2010-05-21: New 30% faster applications are now used for all runs

    The new even faster applications are now used for all the production runs. Fermi cards are also supported for Linux and Windows by the CUDA3.0 versions.

    GDF



  • 2010-05-14: New HIV-1 protease simulations

    Following recent discovery of the wide-open conformation of HIV-1 protease ( which can be found here: http://tinyurl.com/wohiv), we have sent some WUs to further investigate conformations of this enzyme. After initial testing we anticipate a large increase in the number of these WUs.



  • 2010-05-06: Fermi application 6.73 is not out

    After some beta testing the application is now available.



  • 2010-05-06: Fermi application 6.73 is now out

    After some beta testing the application is now available.



  • 2010-04-23: After months of waiting, Fermi arrives at GPUGRID!

    We have just received the first two Fermi card (GTX480 and GTX470). We are now installing it, stay tuned for a performance update.

    gdf



  • 2010-04-22: New publication - RBoinc: scientists interface to DC

    A new publication with the title "Distributed computing as a virtual supercomputer: tools to run and manage large-scale BOINC simulations" by GPUGRID scientists and developers Toni Giorgino, Matt Harvey and Gianni De Fabritiis, has been accepted for publication in the journal of Computer Physics Communications (DOI: 10.1016/j.cpc.2010.04.007) pdf. Scientists at GPUGRID have been using RBoinc already for a year and has proved to be a very safe and useful tool to manage work-flows in high-throughput experiments. RBoinc is already in the official BOINC source repository.



  • 2010-03-30: ACEMD beta for Fermi

    We have uploaded the beta application acemdbeta_*_cuda30 (for Fermi) compiled with CUDA3.0. You have to select to accept beta work in the preferences. Please help us to test it out.

    gdf



  • 2010-03-30: Server update

    We have upgraded the server software to support Fermi cards.

    GDF



  • 2010-03-19: Lecture on GPUGRID results, awarded

    We are proud to announce that a GPUGRID scientist was awarded the 1st Prize for oral communications after a lecture given at the 24th Molecular Modeling Workshop that took place in Erlangen (Germany) the 15-16th of March.
    This tells us that science done at GPUGRID is becoming more and more relevant to the Molecular Modeling community. Congratulations to you all! http://tinyurl.com/MMWslides



  • 2010-03-14: GPUGRID paper published!

    We are happy to announce that the Journal of Chemical Information and Modeling has published the paper about GPUGRID. In this publication we formally introduce GPUGRID to the scientific community (technically and in terms of applications) and we show some results of the *IBUCH*pYEEI* workunits. You can read the abstract here http://tinyurl.com/gpugridpaper
    Thank you very much. GPUGRID team



  • 2010-03-11: More workunits available, 3,352 workunits are in the queue now

    We have a backlog of 3352 workunits to be grabbed, help needed to complete them.

    GPUGRID team



  • 2010-03-05: GPUGRID wins a project to advance the understanding and cure of Schizophrenia

    GPUGRID will be the essential computational tool in a national publicly funded project (TV3-Marato) on Schizophrenia. The aims of the project is to perform in-silico modelling of antipsychotic drug actions. One of the previous task group called *JAN* were already starting to study this problem. Thanks in advance to all volunteers and stay tuned for updates.

    GDF



  • 2010-02-25: Small challenge

    We are doing a test of high-throughput production for a very small batch of WUs (29) named *challenge*.
    If you are lucky to get one, please prioritize them over the next 24h only.

    Many thanks.



  • 2010-02-19: Optimizing protocols

    We are already working on an optimized version of the protocol that will appear in the Journal of Chemical Information and Modelling as announced some days ago.
    So far, they look very promising.

    More WUs for the new application are already out!



  • 2010-02-16: Science update. New journal article.

    We are happy to announce that another set of scientific results was accepted today for publication. This is related to the jobs you have been running for months called *SH2*. Congratulations and thanks to everyone:

    I. Buch, M. J. Harvey, T. Giorgino, D. P. Anderson and G. De Fabritiis, High-throughput all-atom molecular dynamics simulations using distributed computing, in press J. Chem. Inf. and Mod. (2010).

    PDF

    gdf



  • 2010-02-11: New Nvidia application 60% faster is now out

    Along side the old application, we have uploaded the new faster application for Windows (6.01) and Linux (6.02). GDF.



  • 2010-02-09: Donations are back

    The donations system is up and running again.



  • 2010-02-04: Donations shut down temporarily

    Due to a spam attack, we have shut down temporarily the donations to GPUGRID.
    We will inform you when they are open again.



  • 2010-02-03: Production work for beta app submitted

    We have sent 1000 WUs for the new beta application.
    Please note that they are actually production WUs already.



  • 2010-02-03: New beta Nvidia application 60% faster.

    We submitted 1000 production WUs to the beta application.



  • 2010-02-03: New beta Nvidia application 60% faster.

    Really good news !



  • 2010-02-03: New beta Nvidia application 60% faster.

    The new Nvidia application is now out in beta. It is available by accepting beta work from GPUGRID.



  • 2010-01-31: Account creation active again

    Account creation active again as usual.



  • 2010-01-29: Akismet anti-spam system under test

    Let us know if you encounter problems.

    This was motivated by the latest "attack" and the precious time taken for fixing these annoyances.



  • 2010-01-27: Account creation temporarily disabled

    We have disable account creation temporarily. GDF



  • 2009-12-17: GPUGRID wishes you a Merry Christmas

    We also would like to introduce you the Xmas Donation Campaign to try to raise some funds for the project during these holidays. We are going to keep an eye over GPUGRID to make sure we don't go offline during the following days. Merry Christmas to you all and thank you very much for your support.



  • 2009-11-30: MD conference impressions and GPUGRID poster for download!

    As announced, GPUGRID was in the conference on MD here in Barcelona last week. We presented a poster, available for download here (Resources section), and a talk by Gianni. Both raised a lot of interest in terms of computational power available through ditributed computing and potential scientific impact of the experiments run. Best regards!



  • 2009-11-19: Conference "Expanding the frontiers of molecular dynamics simulations in biology" in Barcelona next week

    GPUGRID is participating to a conference concentrating the main talents in molecular dynamics in the world today. Gianni De Fabritiis will be giving a talk presenting the work on the Dopamine receptor, and Ignasi Buch will be presenting a poster (soon available in the web) on GPUGRID and the application Calculations of binding free energies (we have been recently busy with the paper! News soon). Remember to check out our gallery for pictures of the events.



  • 2009-10-21: 5th Pan-Galactic BOINC Workshop in Barcelona

    The 5th Pan-Galactic BOINC Workshop will take place tomorrow and on Friday here in Barcelona and GPUGRID will be there. We will also be presenting a remote submission system that we use in the lab to safely interact with the server, to send/retrieve WUs from it. For more information check the wiki site http://boinc.berkeley.edu/trac/wiki/WorkShop09



  • 2009-10-06: New top volunteers

    Congratulation to our top volunteers. JackofAll managed to become top host, while XtremeSystems and Stoneageman keep their top volunteers and top teams position.



  • 2009-09-30: Donor: Have your say, propose a research topic

    GPUGRID offers the opportunity to its highest donor, once reached the target, to choose a research topic (Cancer, Alzheimer, etc.). Would you like to have your say but can't afford a high enough donation? No problem! Donations made as part of 'an interest group' (Team,...) will be considered as a unit. To donate, click here. Many thanks.



  • 2009-09-28: New large batch of workunits ready to download

    We have just uploaded over 4,000 new workunits. Good crunching.



  • 2009-09-25: Another scientific publication on GPUGRID application ACEMD

    A new publication on the ACEMD application run by GPUGRID has appeared on the Journal of Chemical Theory and Computation. M. J. Harvey and G. De Fabritiis, An implementation of the smooth particle-mesh Ewald (PME) method on GPU hardware, J. Chem. Theory Comput., 5, 2371–2377 (2009). PDF available also at the project website.



  • 2009-09-22: Windows application version updated

    The Windows application has been updated. Please check your host. Driver version 185 or higher and BOINC 6.10.3 recommended.



  • 2009-09-21: Linux version updated

    The new Linux application is now based on CUDA2.2 and requires drivers 185.xx.



  • 2009-09-20: Suggested client is now 6.10.3

    If you are using Linux please update to BOINC 6.10.3. The previous suggested version 6.6.36 was not working properly on multiple GPUs.



  • 2009-09-16: PayPal donations supported

    We now support PayPal donations! Please follow the instructions from the donations website. Many thanks.



  • 2009-09-14: Linux users: driver update

    The Linux application will be updated tomorrow to CUDA2.2. Please, update to driver version 185.xx at least.



  • 2009-09-08: Reminder to Linux users

    Please remember to update to driver version 185.xx at least. The Linux application will be soon updated to CUDA2.2



  • 2009-09-07: Top Contributors

    With the aim to increase visibility of our TOP contributors, we now display permanently on our Homepage, the TOP 3 contributors by User, Host and Team. Congrats to the current ones!



  • 2009-09-03: Request for donations. Get your research project, propose a target disease.

    We would like to ask your help to support us with donations. In this letter we explain why and how you can participate to the biomedical research we will be able to do.



  • 2009-09-02: Server disk changed

    We are now back online. The server will suffer a bit of traffic for the first few hours due to all the data being transferred.



  • 2009-09-02: Problems with a server disk

    We are experiencing some problems with one of the server disk. We might shut down the server for small periods of time to fix the problems.



  • 2009-08-27: GPUGRID distributes CUDA2.2 and CUDA2.3 applications

    Since last week we are now distributing the most appropriate application version to your hardware. This will allow you to use the driver that you prefer, the most recent or an older one.



  • 2009-08-25: GPUGRID gets first rank in the class

    With the title 'A distributed computing system for high-throughput molecular dynamics simulations', Ignasi's masters thesis got the highest mark of the course: 9.6/10. Thank you all and let's keep on working!



  • 2009-08-20: Suggested client version

    The suggested BOINC client version is now 6.6.36.



  • 2009-07-31: Windows application updated to CUDA2.2

    We have updated the Windows application (version 6.67) to cuda2.2



  • 2009-07-28: Server software updated

    We have updated to the latest server software.



  • 2009-07-27: Updating driver for LINUX users

    Linux users can now update to the latest version of Nvidia drivers. We have hacked the BOINC-driver bug. Version 185.xx will be required in the future to be compatible with CUDA2.2.



  • 2009-07-25: Updating driver for Windows users

    All Windows users should update their Nvidia driver to version 190.xx. This driver allows computation also in SLI mode. From next week, we will update the application to CUDA2.2 which requires the new driver. The current application for Windows will still work under the new driver in the meanwhile.



  • 2009-07-20: Computing preferences updated

    We have updated the 'computing preferences' page available under your user account in the website. Please, make sure they match your favourite computing setup.



  • 2009-07-15: GPUGRID fatured in the latest VPH project newsletter

    A 'technical report' on GPUGRID project is featured in the latest newsletter of the Virtual Physiological Human Network of Excellence (VPH NoE). The VPH is a large collaborative project that coordinates the efforts of the best European research institutes which work on the simulation of various aspects of the human body. See http://tinyurl.com/vph-newsletter-pdf (we are on pages 13 and 20)



  • 2009-07-09: Thousands of WUs

    It seems that we had some transitory issues with the scheduler, and no WUs were sent. Right now it is working fine. There are thousands of WUs waiting for you, come and get yours!



  • 2009-07-08: Freed server disk space

    Tonight (Mediterranean time) we ran out of disk space in the server, so most of you couldn't upload any WU. We optimized (once again) the disk space and are back normality now. Sorry for the inconveniences.



  • 2009-06-23: 2 billion credits reached!

    The GPUGRID.net project just awarded its 2 billionth credit! This means that in totat you donated around a sextillion (10^21) floating point operations, which we used to compute approximately 1 millisecond of simulated trajectories in total. Congratulations to all volunteers!



  • 2009-06-19: Server update

    We have updated to the latest server software. Also now the minimum required driver version is enforced to be at least 180.



  • 2009-06-15: Big queue of fresh WU!

    We have +2,000 WU in queue to be crunched waiting for you guys! Actually, and that's for real, the publication on the SH2 system may be able to drop off finally after these results. Not only these, but Ignasi is defending his Masters thesis this Friday and would be delighted to show these results (properly credited of course). Many thanks in advance!



  • 2009-06-05: The VPH project featured in 'The Times'

    The VPH project, in which GPUGRID participates, has been in the news. 'The Times' reported today that the use of animal experiments could be replaced by research on "virtual human beings" and tests on banks of living cells within a generation, following a series of talks given at the Cheltenham Science Festival on June 4th 2009. More information here.



  • 2009-05-28: New scientific paper on ACEMD, the MD compute engine of GPUGRID.net

    We are glad to announce the publication of our application, ACEMD, in the Journal of Chemical Theory and Computation. For more information: Journal link and pdf.



  • 2009-05-26: GPUGRID in the Virtual Physiological Human project

    GPUGRID participates to the VPH-NoE (www.vph-noe.eu), the EU-supported Network of Excellence for the Virtual Physiological Human. The VPH NoE initiative supports European research in biomedical modelling and simulation of the human body. It will improve our ability to predict, diagnose and treat disease, and have a dramatic impact on the future of healthcare. For more information check the VPH official site



  • 2009-05-22: WUs, WUs and more WUs

    We've recently sent hundreds of new batches of workunits. There's a long queue of them waiting to be downloaded. Come and get yours!



  • 2009-05-13: GPUGRID featured in latest EMBO Report

    The GPUGRID project is featured in "Science wikinomics", a paper in the latest EMBO (European Molecular Biology Organization) Reports, which discusses the philosophy of distributed scientific computing in the "wiki" scientific workplace. Article link



  • 2009-05-07: Donate to GPUGRID

    GPUGRID is now accepting donations from users who want to contribute further. We do accept either hardware or monetary donations. Monetary donations have a minimum of 1 Euro and can be done using a Credit/Debit card or via Bank Transfer. Many thanks to all of you considering a donation.



  • 2009-04-28: On recent WU cancellations and redundancies

    Yesterday we had to cancel several WU due to an emergency related to inherited problems from Easter's blackout and our efforts to improve our in-house developed submission system. In addition, the fact that the output of such cancellations wasthe same to that the 'redundant results' lead to some confusion between these two states. The GPUGRID team appologizes for any credit lost in the case of the emergency cancellations but reminds again its users that NO CREDIT NEITHER COMPUTING TIME is lost in the case of common redundancy in results. We refer to this post and [url=http://www.gpugrid.net/forum_thread.php?id=868&nowr ap=true#7762]this one[/url] for information information. Thank you very much for your patience.



  • 2009-04-24: New WUs are out - An HIV virus (AIDS) protein

    So we are submitting new WUs corresponding to a brand new experiment. We are starting to investigate the structural and dynamical properties of HIV viral proteins in order to help understand how at a molecular level, the virus becomes infectious. We will soon update the science section for it.



  • 2009-04-14: GPUGRID server is up and running again

    We suffered a network failure during these Easter holidays that couldn't be fixed until today. We are getting back to normality now. Thanks for your patience.



  • 2009-04-10: Heartquake in Abruzzo

    Da GPUGRID vogliamo esprimere la nostra piu' sincera partecipazione a questo triste giorno di lutto nazionale in Italia per le vittime del terremoto. GDF. (http://www.repubblica.it)



  • 2009-04-03: A new batch of workunits out

    We have just submitted a new batch of workunits which improve further the accuracy of the free energy calculations.



  • 2009-03-27: We are billionaires

    We just reached a 1 billion (1,000,000,000) total credits! Many thanks to all volunteers.



  • 2009-03-20: Spring upload

    More New WUs are out! We didn't want you to start spring with no new stuff to crunch. Have a nice weekend!



  • 2009-03-18: New workunits are out

    We are giving away new workunits for the SH2 system (see Science page for more info). These are similar simulations but with different ligands as the computing protocol we've been applying for the last months seems to do pretty well. We are very excited about it. Thanks to all who make it possible!



  • 2009-03-12: Server update and HTTP error fixes

    We have updated the server software. The problems of HTTP errors have been solved as well.



  • 2009-01-30: New GPU applications

    New applications for Windows and Linux released. CPU usage is now close to zero, so that you can keep crunching other CPU projects as before while also using the GPUs in your machine.



  • 2009-01-28: Account creation temporarily disabled

    We have disable account creation temporarily. GDF



  • 2008-12-17: NVIDIA Press Release

    GPU computing finally takes off in BOINC with GPUGRID, SETI@Home and Einstein@Home. Read today's NVIDIA press release 'NVIDIA CUDA Technology Dramatically Advances The Pace Of Scientific Research'.



  • 2008-12-11: Suggested BOINC version is now 6.4.5

    Please upgrade to version 6.4.5 to have a correct estimation of elapsed time.



  • 2008-11-27: GPUGRID t-shirt graphics and brochures available from website.

    We have created a new resource section which contains project brochures and t-shirt graphics and divulgation material.



  • 2008-11-12: PS3GRID and GPUGRID new website in two styles selectable by users.

    We have uploaded the new website with improved design and usability. Users can also choose between black (geek) and white (zen) styles. Try it out.



  • 2008-10-29: GPUGRID - BOINC version 6.3.19

    BOINC release 6.3.19 is now the suggested version for GPU users. Please update following the link from www.gpugrid.net.



  • 2008-10-24: GPUGRID video and photo channels

    The multiscalelab is pleased to announce its new video channel on vimeo: http://www.vimeo.com/user862246. We have uploaded a sample video of a simulation (more news soon) and a screencast on how to connect a GPU to the project using Vista. We want to remind as well, that we are already present on flickr: http://www.flickr.com/photos/multiscalelab



  • 2008-10-20: GPUGRID new applications

    The new application for Linux and Windows are now 25% faster on GTX200 Nvidia cards. We are now officially supporting Windows 32 and 64, XP and Vista.



  • 2008-09-29: Play Me a Molecule, PS3GRID/GPUGRID note on Science magazine

    A note featuring PS3GRID/GPUGRID has appeared on the September 12 issue of Science. Thanks to all volunteers for their contribution to the continuos growth of this project. Full text is at http://www.sciencemag.org/cgi/content/long/321/5895/1425b



  • 2008-09-12: GPUGRID new application

    We have uploaded a new GPU application version for Linux with practically zero CPU usage.



  • 2008-09-06: PS3GRID-GPUGRID milestone 1,000,000 RAC per day

    In the past few days PS3GRID-GPUGRID project reached and passed the 1,000,000 RAC per day. A computational milestone for the project ever reached before.



  • 2008-08-26: Server are up and running

    We had a network outage during Sunday due to electrical works. All normal now.



  • 2008-08-26: GPU new applications

    We have uploaded new applications compatible with CUDA 2.0 and latest Nvidia drivers (177.xx). Please reset project in order to get the right latest files.



  • 2008-08-20: GPU BOINC update

    ALL LINUX users of the GPU application should update to boinc version 6.3.8. Link available from www.gpugrid.net.



  • 2008-08-05: New article in press

    The impact of accelerator processors for high-throughput molecular modeling and simulation, in press Drug Discovery Today (2008).



  • 2008-07-17: Launch of GPUGRID.net, BOINC on GPUs

    Finally GPU computing on BOINC! After delivering BOINC on Playstation last year, we are happy to announce that from today we are are able to distribute workunits on Nvidia GPUs. PS3grid.net and the new website GPUGRID.net go along to create a large infrastructure for biomolecular simulations. To run GPU workunits simply follow the instructions on the website. Apart from us, this was made possible by a strong collaboration with BOINC developers and in particular David Anderson at Berkeley and Stefan and Keith from the BOINC community, already moderators at ps3grid. We also want to thank Nvidia for their important support.



  • 2008-07-17: PS3GRID at the European Science Open Forum

    Come and visit us at our booth at the ESOF08 event taking place in Barcelona this Friday. http://www.esof2008.org.



  • 2008-07-09: Sony Computer Entertainment Spain collaborates with PS3GRID

    PS3GRID announces a collaboration with Sony Computer Entertainment Spain which donated to the project 20 Playstation3 to build a PS3 cluster and funds to support a Master student project. The PS3 cluster will be presented at the European Science Open Forum, 18 July 2008 in Barcelona, http://www.esof2008.org. Photos of the cluster and the PS3GRID showcase will be made available after the event.



  • 2008-05-21: Server update.

    PS3GRID updated to the lastest server release.



  • 2008-05-09: Detail of the first numerical experiment.

    The first set of numerical experiments run on ps3grid.net produced 5,000 trajectories, 4 microseconds of simulated time, over 200 years of CPU time with a daily output of 100 ns and few GBytes, two orders of magnitude closer to single-molecule pulling experiments. Thanks to all volunteers for this effort.



  • 2008-04-10: Forums update.

    PS3GRID forums have been slightly reorganized to improve the usability.



  • 2008-03-31: Server is up.

    Server is up again after PRBB server room maintainance.



  • 2008-03-28: Master URL change for www.ps3grid.net.

    The master url of the project has changed to the simpler http://www.ps3grid.net. Previous master url will still work, although the boinc client will notify that you should use the new one.



  • 2008-03-27: Server downtime tomorrow March 28.

    Tomorrow Friday, there will be a general shutdown in the PRBB server room which will affect ps3grid.net. The server will remain down for approximatevely 4 hours. Everything should get back to normal after the server is booted again.



  • 2008-03-03: Boinc.cat and ps3grid.net on the press.

    An article featuring boinc.cat and ps3grid has just appeared in a Spanish newspaper.



  • 2008-02-26: New numerical experiment on TPI.

    We have released a new batch of workunits for a second set of molecular experiments.



  • 2008-02-11: New PS3GRID live pen drive released.

    We have released an updated version of the ps3grid live pendrive compatible with firmware version 2.10.



  • 2008-02-07: PS3GRID server storage upgrade.

    We are upgrading the disk space on the ps3grid server. It might be down for short periods today.



  • 2008-02-01: PS3GRID user photo.

    We are looking for photos of PS3GRID users with their PS3(s) for a Spanish national magazine. If you wish to appear follow this thread in the forum .



  • 2008-01-22: PS3GRID server update.

    PS3GRID may be down at times today for a server update.



  • 2007-12-14: PS3GRID new server.

    PS3GRID new server is now in place. Everything seemed to have worked smoothly.



  • 2007-12-13: PS3GRID new server.

    PS3GRID will move to a new server. The move will take place between today and tomorrow. During the DNS propagation the server may appear unreachable from your location.



  • 2007-12-03: PS3GRID Live on LaVanguardia.

    PS3GRID Live usb reported in the Catalan newspaper LaVanguardia.



  • 2007-11-19: PS3GRID Live download stats.

    PS3GRID Live usb has been downloaded 115 times in just 5 days.



  • 2007-11-14: PS3GRID Live Linux pen drive simplifies volunteer computing on the Playstation 3.

    PS3GRID has just relased a new usb pen drive image called PS3GRID live to start BOINC/Linux within minutes on a PlayStation 3.



  • 2007-11-10: PS3GRID project update.

    PS3GRID project has been updated to the latest BOINC version.



  • 2007-11-10: Network problems.

    University network returned to normal acitivity.



  • 2007-11-04: PS3GRID project is up.

    PS3GRID project is up.



  • 2007-10-30: New client for IBM CELL blades at PS3GRID.NET

    A new version of the PS3GRID BOINC client is available for download. This version has better support for IBM CELL blades. Playstation 3 users do not need to upgrade.



  • 2007-10-22: Research jobs at PS3GRID.NET

    PhD studentiship at PS3GRID.NET: Medium-throughput Modelling of Protein-Ligand Interactions Using Distributed Computing



  • 2007-10-20: Read about PS3GRID.NET

    Read about PS3GRID.NET in this new document uploaded on PS3GRID.NET.



  • 2007-10-08: PS3 price cut in Europe from 10th Oct

    A 40Gb PS3 version will be available from next month in Europe and elsewhere (not north America) at a discounted price. Read more



  • 2007-09-03: D. Anderson gives a seminar at the PRBB.

    Next Monday September 10 at 12:00 seminar Volunteer Computing in Biomedicine by D. Anderson, at the Barcelona Biomedical Research Park. All welcome.



  • 2007-08-28: PS3GRID on SuperQuark.

    The Barcelona Biomedical Research Park and PS3GRID featured on the national Italian television. Click here to watch (in Italian).



  • 2007-08-22: PS3GRID publication.

    A chapter on PS3GRID will appear in the book 'Distributed & Grid Computing - Science Made Transparent for Everyone. Principles, Applications and Supporting Communities'.



  • 2007-08-13: PS3GRID web site translations.

    Many thanks to toma01 for the Japanese translation and to Miquel P. for the Catalan and Spanish ones.



  • 2007-08-01: Work available.

    A new large batch of workunits is available. The first set of new work is already out.



  • 2007-07-23: Translation.

    PS3GRID website is now also available in Spanish and Japanese. Other translations to follow.



  • 2007-07-18: D. Anderson gives a seminar at the PRBB.

    Seminar title Volunteer Computing in Biomedicine by D. Anderson, September 10 at 12:00 at the Barcelona Biomedical Research Park. All welcome.



  • 2007-07-16: Website and server running.

    We are online now. The problem occurred is fixed and will be solved completely in the next days.



  • 2007-07-14: Database problems.

    We are experiencing problems with the database due to an other webserver hosted on the server. Unlikely that we can fix it before Monday.



  • 2007-07-12: PS3GRID Boinc Client.

    A new release of the PlayStation 3 BOINC client with an easier installation and execution script is now downloadable from PS3GRID.



  • 2007-07-09: Price cut for PS3.

    In USA Sony cuts PlayStation3 price by 100 dollars. Hopefully the same will happen in Europe.



  • 2007-07-06: New website.

    PS3GRID has a new website professionally designed by mantis.cat. Many thanks to them and Dani.



  • 2007-06-24: Public presentation.

    The first results computed for the PS3GRID project will be presented at the international symposium of biomedical informatics, 26-27 June Barcelona.



  • 2007-06-19: Server upgrade.

    Today server will be down at times for software upgrade.



  • 2007-06-16: Translation update.

    PS3GRID volunteers are translating the website in French, German, Italian, Spanish, Catalan, Portuguese and Japanese.



  • 2007-06-13: Favicon.

    Thanks to Krunchin-Keith for the new PS3GRID favicon and congratulations for the top user ranking.



  • 2007-06-13: Workunits.

    New work is now available.



  • 2007-06-11: Congratulations.

    Beta Users have successfully created over 50 molecular trajectories for something equivalent to over 632 days (1.7 years) of CPU-time on a PC.



  • 2007-06-08: Translations.

    We are looking for translators in French, German, Italian, Japanese and other major languages. Please contact ps3grid@gmail.com if you wish to help.



  • 2007-06-05: Project skin.

    Project skin images are now showing in the client. Thanks to Dani at boinc.cat.



  • 2007-05-29: Beta testing.

    Further workunits are available.



  • 2007-05-26: Beta testing.

    First workunits for 1875 credits are being distributed.



  • 2007-05-12: Beta testing.

    PS3GRID enters BETA testing phase. If you own a PlayStation3 and wish to participate, please write to ps3grid@gmail.com



  • 2007-05-09: AVUI (Catalan)

    An article on the journal Avui on BOINC and ps3grid



  • 2007-05-04: Innovation (French)

    Article on the journal Innovation on ps3grid



  • 2007-05-03: Tv3 News (by Dani) (Catalan/Spanish)

    Watch the news program on the ps3grid project on TV3



  • 2007-04-25: Radio interview at comradio (by Dani) (Spanish, 12min, 6Mb)

    Listen to the interview of G. De Fabritiis on the use of the Cell processor for scientific computing.



  • 2007-04-23: Beta testing

    Beta testing on PS3GRID will be starting in a couple of weeks



  • 2007-03-02: G. De Fabritiis

    Performance of the Cell processor for biomolecular simulations



  • 2007-02-13: Vilaweb

    PlayStation3 serving scientists -Catalan press-



  • 2007-02-10: El Mundo

    Potential of the PlayStation 3 for scientist projects development -Spanish press-



  • 2007-02-10: El Mundo Salud

    Potential of the PlayStation 3 for scientist projects development (on-line version) -Spanish press-



  • 2007-02-01: Hello World

    PS3GRID.NET started its website