RNA World

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Gavin Shaw
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RNA World

Post by Gavin Shaw » Tue Jan 19, 2010 8:56 am

Anything related to RNA World

RNA World

Description:
RNA World (beta) is a distributed supercomputer that uses Internet-connected computers to advance RNA-related research. You can participate by downloading and running a free program on your computer.

RNA World (beta) is based at the Rechenkraft.net e.V. research facility located in Germany.

Team attach: Calm Chaos
RNA World - BoincStats
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Re: RNA World

Post by Gavin Shaw » Tue Jan 19, 2010 8:57 am

16 Jan 2010:

Last night our server was total overloaded. Also the disc is now nearly full. We need now to rent a much more power full server with much more disc space. For this we need donations or sponsors to help us with the costs. If some people, company or organisation wants to donate something or to be a sponsor, you are welcome. Just contact us. Only with a bigger server we can go public with the project.

18 Jan 2010:

The server is currently preparing another set of approx. 8500 work units. Following that I will add even more. Our change in HR settings seem to work just fine so we are getting closer and closer to finally going public. However, it seems that our server might be too weak for full operation since it is also hosting the Yoyo@home project. As a consequence, we will move RNA World to a different machine. ;-)
Michael.

RNA World is no available in the Boinc translation system (BTS). The project can now be translated to any language. Currently there are only 4 languages available. If you want to translate to an additional language, just give me a note and I add the template.
yoyo
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danielmid
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Re: RNA World

Post by danielmid » Tue Jan 19, 2010 7:31 pm

RNA is only accepting new accounts with an invite code for now.
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Re: RNA World

Post by Buga1 » Wed Jan 20, 2010 3:19 am

KM said something about them opening it up in a month or so. Haven't went and looked myself. At least at that part of it. I found it funny that the leading team in the project has almost if not a million credits, with lots of people on that team can join. Now it is a project that that team started, so I can understand a bit. But for it to already be added to stats sites, just seems odd.

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Re: RNA World

Post by danielmid » Wed Jan 20, 2010 7:41 am

What team is it?
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Re: RNA World

Post by Gavin Shaw » Wed Jan 20, 2010 8:33 am

The top team is Rechenkraft.net.
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Re: RNA World

Post by danielmid » Thu Jan 21, 2010 5:56 am

Yes, the site belongs to them lol
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Re: RNA World

Post by Gavin Shaw » Sun Jan 24, 2010 1:37 am

22 Jan 2010:

...again. ;-) There should be almost 9000 out by tonight. I have a set of additional work archives ready for delivery, but we always need to be a bit careful with the current server since it also hosts the Yoyo@home project and we have currently little space on that machine. So it is always possible that there is a lack in work supply. But that should be resolved as soon as we move to the new server. ;-)
Michael.
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Re: RNA World

Post by Gavin Shaw » Wed Jan 27, 2010 11:27 pm

26 Jan 2010:

Probably on Friday evening (UTC) we will start to setup the new server and move RNA World to it over the weekend. There will be probably some RNA World outages during weekend. To limit the risk of loosing credits and/or results, you should report your results before Friday evening. Thanks to all donations to make this possibe!
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Re: RNA World

Post by Gavin Shaw » Tue Feb 02, 2010 5:13 am

31 Jan 2010:

RNA World has successfully moved to a new server based on an Intel i7-920 Quad-Core machine with 12 GB of RAM and a dual 1.5 TB RAID system, as announced earlier. The server now also runs everything on a 64 bit basis, in contrast to the previous one where everything was 32 bit. As a consequence, a lot of stuff had to be de novo installed, recompiled and currently we run test work units to check for proper function of the system. If you receive an ERROR 403 please just clear your DNS cache (simply restart your machine) to solve this issue. Thanks to the many generous donations and Yoyos ambitious commitment we could put this significant project improvement quickly into practice. Please note that it might still be possible that we detect the one or the other issue.
Michael.
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Re: RNA World

Post by Gavin Shaw » Thu Feb 04, 2010 3:01 am

02 Feb 2010:

We are currently looking for a few people willing to help in our testing efforts who exclusively use Windows 2000 as operating system. Please contact us.
Michael.
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Re: RNA World

Post by Gavin Shaw » Fri Feb 05, 2010 3:00 am

04 Feb 2010:

After completion of the current work packet, we will have to do some in-depth data analysis. During that idle time, new work units will be prepared. It is possible that there will be no additional work available before next week.
Michael.
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Re: RNA World

Post by Gavin Shaw » Mon Feb 08, 2010 12:05 am

06 Feb 2010:

Although we are still in testing mode and currently have few if any work units since we have to perform thorough in-depth data analysis of our previous test runs, we have now transiently opened RNA World registration without further invitation code requirements. ;-)
Michael.
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Re: RNA World

Post by Gavin Shaw » Wed Feb 10, 2010 2:47 am

08 Feb 2010:

A warm welcome to the many newly registered participants. ;-) I will release a set of new work units today so that you guys get an idea about what computing for RNA World feels like. As always, we will be doing useful stuff, so these are no dummy WUs or so. ;-)
Michael.
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Re: RNA World

Post by Gavin Shaw » Wed Feb 10, 2010 2:47 am

09 Feb 2010:

I am preparing new work units since yesterday night and was actually baffled how fast the current projects were completed. That's plain excellent! By tomorrow at the latest we will have additional work. I will need to keep a better eye on the work queue but for that I need a more solid estimate of what you people can do with your machines. Thanks for your understanding.
Michael.
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Re: RNA World

Post by Gavin Shaw » Fri Feb 12, 2010 10:03 am

10 Feb 2010:

As announced, the server is currently getting fed with new work.
Michael.
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Re: RNA World

Post by Gavin Shaw » Sat Feb 13, 2010 8:06 am

12 Feb 2010:

The current set of work units have remarkably short run times, so our server is currently preparing WUs which are almost immediately getting downloaded and will be returned successfully within a few minutes - sometimes even just within a few seconds. So, the server intentionally gets some hard beating today. For us, this is important to check out the limits such that we can combine the work packet contents more effectively in the future, i.e. avoid releasing short WUs only, but sort of "sprinkle" them amongst larger ones.
There is more CMSEARCH work in the pipeline and some time during the weekend I intend to put a set of "heavy duty" CMCALIBRATE work units online. For reasons of internal result comparison, this time, they will be assigned exclusively to Linux-64 machines.
Michael.
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Re: RNA World

Post by Gavin Shaw » Sun Feb 14, 2010 12:47 pm

13 Feb 2010:

The new CMCALIBRATE (CMC) WUs for Linux x64 have been generated and uploaded to the server. Following their completion, a second set of CMC WUs will be released for Windows x64. Afterwards, results will be compared and then there should be no more WU shortage since on the basis of the CMC results we will most likely commence with CMSEARCH mass production.
In parallel to this weekends CMC WUs, additional CMSEARCH WUs will be fed into the system to ensure that those of you who do not run Linux x64 systems will have something to munch on.
For the CMC guys, please note as stated in the FAQ: You may experience huge hardware demands for some of these WUs with RAM requirements above 1.5 GB per WU and run times of maybe even a week. If you have a multicore machine, be aware that the RAM requirement in the worst case might have to be multiplied by your core number. Now you will understand, why we run CMC exclusively on x64 machines at present. Of course, I exaggerate a bit here, but it is better to be prepared than to experience unwelcomed surprises. I do not think that there is another DC project out there at present that beats us in what we have to demand from our participants. Consequently, your efforts are most welcome.
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Re: RNA World

Post by Gavin Shaw » Tue Feb 16, 2010 1:20 am

14 Feb 2010:

You probably have notice already that the server status page indicates some issues with the server. In fact, we are manually tweaking a bit with the database settings so that is why you see these messages. The DB is sort of slow and Yoyo tries to find out what is happening, so from time to time the machine has to be restarted to check effectiveness of some setting changes. Still, apart from some occasional work serving delays, all computations may continue and especially the CMC guys hopefully have enough to do with completion of what has been served so far. Please also note that there are additional CMS work packets in the server's processing queue. These will be fed into the system as soon as the DB issue is alleviated.
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Re: RNA World

Post by Gavin Shaw » Tue Feb 16, 2010 1:21 am

15 Feb 2010:

Well, the current test sets of CMS work units are near completion and we will now have to wait until all CMC WUs are done as well before we can go for the real big hunt. Since currently only Linux x64 systems can be served, this might take a few days, so I would suggest that meanwhile you guys add another project to your BOINC manager if you have not done so already. It is of course possible (and even likely) that I will submit new sets of CMS WUs for other OS inbetween but first I need to take a deep look into all the nice things we have produced already.
Please stay tuned, you all have done an excellent job so far. ;-)
Michael.
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Re: RNA World

Post by Gavin Shaw » Fri Feb 19, 2010 10:47 am

19 Feb 2010:

Last night we have run a thorough HD hardware check over several hours to identify the reason for why our RAID system on the server occasionally slows down. However, the HD is error-free.
Anyway, new CMS work units for all operating systems will be released some time this weekend in addition to the remainder of the CMC work for Linux x64 machines. It would help us to speed up things (and generate even more CMS work) if the Linux x64 users could transiently disable the cmsearch application and focus on completion of the CMC packets.
Michael.
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Re: RNA World

Post by Gavin Shaw » Sun Feb 21, 2010 12:40 am

20 Feb 2010:

We are making good progress with the remaining CMC work units. The announced CMS WUs have already been prepared. It should be around 300,000 this time. Because the CMS WUs coming up will have significantly shorter deadlines than the remaining CMCs, I would like to once again ask Linux x64 users to make sure to disable the cmsearch application as long as their machines are still receiving CMCs. By doing so, you help to significantly speed-up the proejct as a whole and allow us to much earlier generate lots of new CMS work units for all machines. Thanks for your help!
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Re: RNA World

Post by Gavin Shaw » Mon Feb 22, 2010 11:31 pm

22 Feb 2010:

Due to the extremely short WU completion times we have transiently halted the transitioner and validator which both will be reactivated this evening. The WU generator continues to run.
Michael.
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Re: RNA World

Post by Gavin Shaw » Tue Feb 23, 2010 9:11 pm

23 Feb 2010:

I think we will need to design a filter on the server side that, based on the run time estimates, prevents such small WUs from being sent out to clients in the future. Although we have more than 200,000 WUs left, little is computed due to the extremely heavy MySQL load that is caused by the massive connections. So, another lesson learned, I would say. These small WUs in fact can easily run on some of the (mostly idle) server CPU cores and should also finish within a few days.
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Re: RNA World

Post by Gavin Shaw » Thu Mar 04, 2010 11:50 pm

04 Mar 2010:

The entire set of CMC work units for Linux x64 machines is almost complete now and so is the current CMS bundle. We have already prepared the first eukaryotic organisms which will cause significantly more traffic during download and correspondingly require more HD storage as well. As soon as the results have been assembled (a matter of just a few days), we will normalize the client server communication intervalls such that all the problems that occurred with the last CMS work units will not reappear. We will then release a set of CMC work units for Windows x64 only plus a first test set of the eukaryotic CMS WUs for all systems to check whether it runs smoothly. If that is the case, we will fill up the server with more work. Exact dates will be announced here.
Thank you all for your patience and help with the trouble shooting.
Michael.
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Re: RNA World

Post by Gavin Shaw » Thu Mar 04, 2010 11:50 pm

04 Mar 2010:

With the last 2 cmsearch runs we send and received round about 900.000 results and transfered 1 TByte of data.
yoyo
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Re: RNA World

Post by Gavin Shaw » Fri Mar 05, 2010 11:56 pm

05 Mar 2010:

I have good news for those of you whose machines failed on the CMC "monster WUs" delivered to Linux x64 systems. Tonight we most likely solved the problem which indeed has to do with memory allocation. A new parameter setting has been applied and these WUs are now out again in the wild for those who dare munching on them once again. Solving this problem was only possible with the valuable help of some of you who ran the diagnostics which we had posted to diverse forums. Thanks again for your help.
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Re: RNA World

Post by Gavin Shaw » Sat Mar 06, 2010 11:27 pm

06 Mar 2010:

This weekend we will release new work. As announced earlier, first we will send out two sets of CMC WUs exclusively for Windows x64 machines. These will be submitted this evening. In parallel to that we will upload our first CMS test set of WUs to analyze eukaryotic organisms including the human genome to all systems. Please note that these WUs will require a broadband internet connection since the sizes of the genomes of these organisms are one to two orders of magnitude larger than all what we have analyzed so far. Importanly, run times can be significantly longer as well with up to 100 hrs for a single WU.
Michael.
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Re: RNA World

Post by Gavin Shaw » Fri Mar 19, 2010 4:03 am

18 Feb 2010:

With cmcalibrate 0.22 for win32/64 and cmsearch 0.11 for win32/64 the screensaver shouldn't start multiple times anymore.
yoyo
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Re: RNA World

Post by Gavin Shaw » Wed Apr 28, 2010 4:09 am

26 Apr 2010:

As you may have seen, in parallel to the tuberculosis project, we have also initiated the systematic genome annotation analyses (GA projects) in order to globally map the presence of non-coding RNAs.
Michael.
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Re: RNA World

Post by Gavin Shaw » Thu Apr 29, 2010 12:38 am

28 Apr 2010:

...due to improvements we are currently working on to process the tiny WUs on the server in the future. The background is that batches of very short WUs cause severe server stress regarding the number of connections and MySQL requests despite our good server hardware specifications. Since these small WUs will re-occurr in future projects as well, we need to do something about this. At present, we have implemented a server response delay which is causing many machines to sit idle exclusively once these small WU batches enter the system - a situation which clearly is unacceptable. These WUs are usually consisting of plasmids or phages with very short DNA sequences and are consequently processed within just a few minutes - sometimes even shorter depending on your hardware - and therefore the server contact frequencies are massively increased. We could solve the issue by just adding a couple of servers as put into practice by some of the bigger DC projects. Unfortunately, our current project budget does not allow for such a solution, so we decided to process these small WUs on one or two of the server cores in the future.
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Re: RNA World

Post by Gavin Shaw » Sat May 01, 2010 2:11 am

30 Apr 2010:

The WU generator is working again, the small WUs will now be processed on the server, except for very, very few which we will deliver to some remote machines. Please also note that the server response delay has been drastically reduced such that connection issues should be resolved by now as well.
We have plenty of WUs, will not run out of work and hope for your further support which is very much appreciated. ;-)
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Re: RNA World

Post by Gavin Shaw » Fri Jun 18, 2010 8:25 am

17 Jun 2010:

Today I would like to inform you that we will present the RNA World distributed computing project at the RNA 2010 conference of the RNA Society held next week in Seattle/USA. Thanks a lot for your valuable contributions which ultimately made this presentation possible and hopefully will allow us to make new contacts to many RNA researchers in order to establish additional cooperation projects.
Please also note that this will be the second official presentation of the RNA World project within eight months, so we are quite happy about that and will now prepare to publish our first scientific results in a peer-reviewed journal.
Michael.
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Re: RNA World

Post by Gavin Shaw » Sat Jun 26, 2010 3:06 am

25 Jun 2010:

The RNA World project description is currently only available in English and German. We are searching for help to translate the project description into as much languages as possible. Please contact us if you want to help.
yoyo

Just a short note on the latest developments: I am currently experiencing remarkable interest in our project at the RNA conference in Seattle. It seems that quite a number of people is interested in cooperating with us in the future. Some of these people do have full trancriptome sequences available that would help us to validate our computational results on a lab experimental basis. So, I think these are really exciting news.
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Re: RNA World

Post by Gavin Shaw » Mon Jul 12, 2010 12:02 am

11 Jun 2010:

From now on we will post all NEWS messages in two languages: English and German.
Ab heute werden wir sämtliche NEWS-Meldungen zweisprachig herausgeben: Auf Englisch und Deutsch.
Michael.
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