Posts by Feet1st

21) Message boards : Rosetta@home Science : predicting protein shapes (Message 69692) Posted 22 Feb 2011 by Feet1st Post: Lots of interesting details about how protein design impacts disease. http://www.isgtw.org/feature/designing-better-drugs
22) Questions and Answers : Web site : Team name, HTML versions not working? (Message 69552) Posted 31 Jan 2011 by Feet1st Post: I'm having the same problem trying to use the same syntax on an existing team. I also tried " and %27 notation just to be sure.
23) Message boards : Number crunching : Project File Upload Handler Is Missing (Message 69275) Posted 13 Jan 2011 by Feet1st Post: Right, "pending" status and granting of credit are done by the validator and assimilator. It doesn't happen directly with your scheduler request. Under such recovery conditions, the assimilator is likely going to be noticably behind for 6-12 hours.
24) Message boards : Number crunching : Project File Upload Handler Is Missing (Message 69271) Posted 13 Jan 2011 by Feet1st Post: Hurray!! Servers all just came back online, my uploads finally went through, and scheduler request completed by sending me new work.
25) Message boards : Number crunching : Project File Upload Handler Is Missing (Message 69250) Posted 12 Jan 2011 by Feet1st Post: I actually keep some traces and finally sat down to check them out. Prior to the crash my uploads always went to SRV1 (probably varies depending upon your timezone), since that time I've got some on SRV5, some on SRV6. Sounds to me like they've added additional servers to help service all of the requests so the project could come back up to speed sooner. Perhaps that is why Ralph is still down. ...and I've still got a very old task trying to upload to SRV1 and it keeps failing with the upload handler missing error. Meanwhile, as others have reported, I've had newer tasks complete, upload and then removed from the list as normal. ...probably uploaded to one of the other servers. So this probably explains why some tasks are going through and others are not. Until the old servers digest all of those old tasks, they are probably thrashing terribly. I wouldn't go around changing any of the xml files of the tasks. It could work, but it could trash the tasks as well. And either way, it certainly isn't something to expect 50,000+ contributers to be doing manually.
26) Message boards : Number crunching : Hosted CPUs (Message 68934) Posted 29 Dec 2010 by Feet1st Post: Have you seen prgmr.com? I see nothing there indicating any definition of the amount of CPU time guarenteed nor expected. The SLA simply refers to up time. If I asked you to host a CPU for me, with internet connectivity, some disk space, etc. how much would you have to charge to break-even? Power, cooling, floorspace, routers, firewalls, software updates, insurance, internet bandwidth... The only way to offer something for less then the electricity costs of a single CPU is to provide less then a single CPU.
27) Message boards : Number crunching : Hosted CPUs (Message 68927) Posted 29 Dec 2010 by Feet1st Post: I've run Rosetta on Amazon Linux instances before. I've also studied many other hosting services and never found one that met the needs of Rosetta for anything near the $15/month figure you mentioned (except for a single CPU Amazon Spot priced instance when they go for around 2 cents an hour). They either don't allow you to install software on their server, they don't give you any significant CPU time, they cost more then Amazon full price, or all of the above. Amazon provides full SSH access to the instance. What I did was just wget the BOINC code and install and run it as per the Linux instructions from BOINC. But, and especially with the spot instances, you have to remember that your running image could be shut down at any time. I used EBS for BOINC's storage to partially prepare for that eventuality. I also configured BOINC preferences to immediately report completed results (but that's producing more hits to the project servers). So, you don't need to create an image at all, you can just use one of the existing AMIs, but when the instance is ended (i.e. someone out bids you for spot pricing) it is a manual process to get started again. The next step on what I've done is essentially to facilitate a farm of hosts and automate the steps. Create an image that boots itself by loading up a current (or stored) BOINC version, checks with some central host to see if any partially completed images are available, and then either picks up where another ended instance left off by attaching to the corresponding EBS (so long as the instance types are identical, BOINC will just think the machine was rebooted), or create a new one with files set up in a mannar to automatically connect to the project with your EMail address and password. There's some BOINC doc on doing that in the wiki at Berkeley.
28) Message boards : Rosetta@home Science : Ribosome swivel accommodates proteins synthesis (Message 68758) Posted 6 Dec 2010 by Feet1st Post: Perhaps the investment is the supercomputers at Los Alamos are already showing results: http://www.hpcwire.com/offthewire/Scientists-Ratchet-Up-Understanding-of-Cellular-Protein-Factory-111146994.html
29) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (5) (Message 68700) Posted 24 Nov 2010 by Feet1st Post: Good to hear that Gates is still supporting key research. Could you talk a bit more about how the dormant HIV situation differs from say curing me of an H1N1 infection? I'm thinking in one case you are targetting surface proteins and in the other you have to get within the cell first, hence the importance of "delivery" of the endonuclease that is devised. Any updates on the carbon sequestration efforts? Or the biomass catalyst to break down cellulose into something that can be refined into fuel?
30) Message boards : Number crunching : Report long-running models here (Message 68631) Posted 15 Nov 2010 by Feet1st Post: Me too, AR3436A_blind_LESSPCSCST_BOINC_abrelax.default.v1_SAVE_ALL_OUT_22535_647_0 First model of this task has already taken nearly 12 hours of CPU and is still not complete. On step 177,000 with 24hr runtime preference.
31) Message boards : Rosetta@home Science : podcast about X-ray crystallography (Message 66788) Posted 6 Jul 2010 by Feet1st Post: Some interesting details about Xray crystallography and WCG here: http://www.isgtw.org/?pid=1002589
32) Message boards : Number crunching : Newbie Q&A, if you're new, have a view! (Message 65978) Posted 5 May 2010 by Feet1st Post: Rosetta's behavior should not be related to other applications running on the machine. Perhaps you don't really have enough memory to do everything you are asking it to do? The reason for less points sounds like the tasks were cut off early, and so they didn't get as many models completed. So, less credit, but less computing time used as well, due to the premature end. The current BOINC versions allow you to define that BOINC should stop running any time the machine's CPU % crosses above your configured threshold. The intent behind creating this new setting was, I believe, to help set things up so that BOINC would automatically stop when your machine gets busy with video or something and so reduce memory conflicts etc. with other applications.
33) Message boards : Number crunching : R@h crosses 10 BILLION total credits issued!!! (Message 65831) Posted 26 Apr 2010 by Feet1st Post: Congratulations to Rosetta@home on adding another digit to total credit! And for being a long-lived, successful illustration of how volunteer computing can be beneficial to everyone. Good luck with CASP!
34) Message boards : Rosetta@home Science : Possible cancer cure found in plant (Message 65301) Posted 12 Feb 2010 by Feet1st Post: I think the main way that DC helps advance medicine is that computer models can be used in many cases to predict toxicity, and therefore identify things that are NOT going to work much earlier in the process. This saves you from attempting clinical trials on ideas that will (at least according to the model) eventually fail to be safe. I know that sounds negative, but if you consider that you must try 1000 things to make a lightbulb (or a cure), and you can iterate through that list of things faster, then that is progress towards the final answer.
35) Message boards : Cafe Rosetta : BakerLab awarded 50 million supercomputing CPU hours in 2010 (Message 65144) Posted 29 Jan 2010 by Feet1st Post: See page 9: http://www.er.doe.gov/ascr/incite/2010INCITEFactSheets.pdf In spite of what I said this morning in my blog, I am glad to see a portion of this national resource going toward my personal preferred project. BTW, according to boincstats, there are 77,159 active hosts running on Rosetta as of today. If we assume these average just 8 hours of a single CPU to Rosetta per day, that is over 200 million CPU hours per year. Dwarfing the federal award. BakerLab has so many things going on. They run protein models for other research organizations for free under a program they call Robetta (note the "b" as in robot). I suspect the awarded CPU hours will be used to help process this work.
36) Message boards : Cafe Rosetta : a malaria story (Message 65001) Posted 16 Jan 2010 by Feet1st Post: More then one way to address malaria: Father/son team designs solar device with no batteries, that depends on a sweatband worn by the device user. Uniquely creative ideas come up on Innocentive
37) Message boards : Cafe Rosetta : Seti@home's Number 1 Cruncher Fired At Work... (Message 64398) Posted 7 Dec 2009 by Feet1st Post: I for one am hopeful that somehow the free publicity resulting from the dispute will actually benefit the BOINC community. I've started blogging about BOINC and distributed computing and current scientific challenges. Perhaps that is one way to help spread the positive word about BOINC. R@h and protein folding is my second blog topic. I think I misspoke in my headline when I said H1N1 is different in a few of it's proteins, I believe I should have said it is a bit of DNA that differs. Oh well, bloggers aren't perfect. I invite any input about future topics you'd like to see in my blog that you think will help interest the public, and the researchers in BOINC projects.
38) Message boards : Cafe Rosetta : What to get for holiday gift? (Message 64373) Posted 4 Dec 2009 by Feet1st Post: My Mother has simplified her holiday shopping. She askes everyone on her gift list what charity they would like to donate to. So, now that Rosetta@home accepts direct donations, the choice was obvious. I was wondering how much has been raised and if the money is earmarked for any specific endeavors within BakerLab?
39) Message boards : Rosetta@home Science : new supercomputer (Message 64261) Posted 28 Nov 2009 by Feet1st Post: http://www.popsci.com/technology/article/2009-11/digital-cat-brain-runs-blue-gene-supercomputer Interesting... I wonder how they prove to themselves that they are accurately modelling a cat's brain?? I guess you simulate inputs for someone wanting to play with the cat. Simulate them dangling a string, and if the model shows the cat deciding instead to lay in the sun and stretch, or jump into the lap of another person and lay on the newspaper they are trying to read, then that would prove it's working! ;)
40) Message boards : Cafe Rosetta : Distributed Thinking (Message 64131) Posted 22 Nov 2009 by Feet1st Post: In the Innocentive link I provided in the OP, they talk about how much of the oil from the Exxon spill in Alaska solidified in the extreme cold, and sank to the bottom and remains there more then 10 years later because we have no way to clean it up. The experts were unable to find a way to do it. But Innocentive tossed the idea out to a diverse group of people and was willing to consider all comers. A guy from the construction industry came up with a solution that is being used right now to recover the sludge and clean the environment. Did he make millions of dollars on licenses for a new patent?? No. He made $20,000, much of which he used to visit the site where they are actually implementing his idea. He wanted to see it in action. So, not only was a solution found to a problem that was believed unsolvable, but the price of $20,000 was nothing compared to the costs of all of the experts that had failed prior to that. There simply is no way to achieve innovation in a computer program. By definition, it only does what it was programmed to do. The point is there are specific tasks that benefit from more then one person participating. Indeed, BOINC has enabled BOSSA for just such projects. One distributed think project was run by NASA. They have telescope images which detail millions of galaxies and they wanted to build a database of which ones are spiral galaxies and which are ellipical. So they put together some material to teach folks how to distinguish the difference and then presented them with images and they selected the classification they deemed appropriate. The selections of several users were combined and if everyone had the same perspective, the selection was accepted. If not, it was deferred to an expert for review. The scientists may have viewed this as sort of a fool's arrand, because what difference does it really make if we classify them incorrectly? But the volunteers took it very seriously and didn't want to mess up the science by giving an incorrect answer. The volunteers helped the scientists realize there are actually three types of galaxies. Spiral, elliptical, and "irregular". This never could have happened with a computer program. Indeed, if human experts were tasked with it, they would have maintained the opinion that what they were taught in school is true, there are only two galaxy types. And in the 5 seconds they would have spent on each of the millions they have to do, they would have picked one of the two possible choices. Why do they need us? "The simple answer is that the human brain is much better at recognising patterns than a computer can ever be. Any computer program we write to sort our galaxies into categories would do a reasonable job, but it would also inevitably throw out the unusual, the weird and the wonderful. To rescue these interesting systems which have a story to tell, we need you." http://technocrat.net/d/2007/7/11/23050/ So, in addition to taking more then 5 seconds, using a computer program would have limited the potential for discovery. I've been reading a rather slow book, but it has some real points of insight. It is called "The Wisdom of Crowds" by James Surowiecki. He outlines specific conditions where a crowd of amateurs can work together to produce a better result then a group of experts. But they really have no way to study innovation in a mannar that is scientifically significant, so you have to sort of make the leap to that on your own. I mean you only innovate something the first time, so by definition, any experiment would not be reproducable.

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