Posts by Michela
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Message boards : Number crunching : low credit on some WUs ( Message 6386 )Posted 2224 days ago by 
Michela
Yes, 1hsg-1hvi complex was a tough one :-) The ligand did not wanted to dock in the protein at all. The good news is that the code is robust and does not crash but sends us back the information that the ligand is not fitting in the protein pocket. This is science :-) |
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Message boards : Docking@Home Science : Can you give us a science update? ( Message 6385 )Posted 2224 days ago by
Michela
Any news?? Yes, but it is not good news. Our most recent work with Docking@Home was reported in a paper we submitted to the Supercomputing conference. The paper got rejected because with too much science and not enough HPC. We really like the work we were able to do with your computing support and we do think it can be very useful for the community. Now we are reviewing the manuscript and plan to submit it to a conference that has a more computation biology scope. I really would love to share with you all the paper to start a discussion with you. Let us review the manuscript, submit it to the conference and as a technical report, then I can share it with you all. Thanks for your help! |
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Message boards : Number crunching : HELP - Consistant 0% Progress - Client Problem? ( Message 6363 )Posted 2250 days ago by
Michela
This is a report of the jobs associated with 1hvi1hpv. The testing process that is performed before to distribute a new complex to volunteers did not capture any major problem. There are 11,684 jobs with server state = over, 692 of them with outcome = client error. It is around 6% of them (including aborted and failing) and the failings come from the same hosts (around 30-40 of them). The job distributed but not returned are 17,958; the jobs generated but not distributed are 252; the job to be generated are 0 since we moved on to the next complex. Please abort jobs with 0% progress. Docking is not a deterministic simulation and some docking attempts can fail. Our testing can successfully capture most of the cases but not all. Thanks! MT |
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Message boards : Number crunching : Win7 64bit problem with Docking ( Message 6362 )Posted 2250 days ago by
Michela
This is a report of the jobs associated with 1hvi1hpv. The testing process that is performed before to distribute a new complex to volunteers did not capture any major problem. There are 11,684 jobs with server state = over, 692 of them with outcome = client error. It is around 6% of them (including aborted and failing) and the failings come from the same hosts (around 30-40 of them). The job distributed but not returned are 17,958; the jobs generated but not distributed are 252; the job to be generated are 0 since we moved on to the next complex. Please abort jobs with 0% progress. Docking is not a deterministic simulation and some docking attempts can fail. Our testing can successfully capture most of the cases but not all. Thanks! MT |
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Message boards : Number crunching : Win7 64bit problem with Docking ( Message 6361 )Posted 2250 days ago by
Michela
Same issue here.. My Win7 64bit docking WU's stay at zero and reset themselves to zero time elapsed every minute or so. We are looking at the issue. It was not present in the pre-testing phase of the complex on our testing machines. More very soon, Michela |
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Message boards : Number crunching : HELP - Consistant 0% Progress - Client Problem? ( Message 6360 )Posted 2250 days ago by
Michela
For some reason all my workunits on my new computer i7 2600k are stalling at 0.000% progress while those on my old computer Intel core duo are still running fine. Any idea on how to fix this? My new computer is burning through workunits on other projects, and I want them to do the same here. We are looking at this. Thanks for the note! Michela |
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Message boards : Docking@Home Science : ExSciTech?? ( Message 6357 )Posted 2253 days ago by
Michela
What about? Is a standalone app? And when will be released?? We are working on an extension of VMD (open-source package available at http://www.ks.uiuc.edu/Research/vmd/) independent from the BOINC client. We are working hard to get a alpha release for a small group of D@H testers for the end of the summer. I should have more news to share with you all for the end of June. Michela |
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Message boards : Number crunching : AC unit failed = server down ( Message 6353 )Posted 2263 days ago by
Michela
Tell you what: with all of these problems, I am going to suspend to project, no new tasks. you guys have RSS. When things are fixed, get a message up in RSS, and also tell everyone in the crunching topic. We fixed the issue a long time ago. Are you experiencing still problems? |
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Message boards : Docking@Home Science : Poem@home display Wu and use GPU ? like Folding@home ? ( Message 6347 )Posted 2274 days ago by
Michela
Docking@home display Wu and use GPU ? like Folding@home ? No, we are not distributing jobs on GPUs at this point. One of the reasons is that CHARMM does not run on GPUs. We look at GPUs with interest and have been working on a MD code for GPUs. One of the students in the group is testing a small framework with BOINC and our MD code for GPUs. This could become a very interesting follow-up for Docking@Home but we will need some time. |
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Message boards : Docking@Home Science : Poem@home display Wu and use GPU ? like Folding@home ? ( Message 6345 )Posted 2280 days ago by
Michela
Any news??? Not really. We should have a first prototype in a couple of weeks for a small, internal grid of machines. |
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