RNA World (beta)
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RNA World (beta)
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Release of CMCALIBRATE mini WUs
I just uploaded a first mini set of the new CMCALIBRATE WUs for Linux-x64 that are based on Rfam-10.0.
Ein erster Satz CMCALIBRATE Mini-WUs für Linux-x64 Maschinen wurde gerade zur Abarbeitung bereit gestellt. Diese WUs basieren auf der neusten Rfam-10.0 Datenbankversion.
Michael.
26 Jul 2010 23:41:44 UTC
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Delay of CMCALIBRATE WU delivery
The announced CMCALIBRATE WUs have already been prepared. It seems, however, that there might be a minor inconsistency in the current Rfam 10.0 database data set which we would like to have clarified before we release the new work.
Obwohl angekündigten CMCALIBRATE WUs bereits zur Ausgabe vorbereitet sind, können wir sie erst ausgeben, sobald wir eine kleinere Datensatzinkonsistenz in der neusten Rfam 10.0 Version geklärt haben.
Michael.
25 Jul 2010 11:52:38 UTC
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New set of CMCALIBRATE WUs
Probably on the weekend we will release new CMCALIBRATE WUs for 64 bit-based Linux systems. These WUs will naturally be a bit more demanding than the CMSEARCH stuff we are mainly running at present, so make sure you adjust your project setting accoringly to receive only those WUs which your machines can handle - although the new WUs should not be much more demanding than what we had before with CMCALIBRATE (maybe with a few exceptions, however).
Wahrschenlich schon am Wochenende werden wir einen neuen Satz CMCALIBRATE WUs für 64-Bit basierte Linux Systeme in die freie Wildbahn entlassen. Diese WUs werden erwartungsgemäß etwas anspruchsvoller sein, als was wir aktuell mit CMSEARCH berechnen. Schaut also bitte, dass ihr eure Projekteinstellungen entsprechend anpasst, damit ihr wirklich nur diejenigen WUs bekommt, die eure Maschinen auch bewältigen können. Die neuen CMCALIBRATE WUs sollten allerdings nur unwesentlich anspruchsvoller sein, als was wir bisher mit CMCALIBRATE berechnet hatten, allerdings könnte es ein paar Ausnahmen geben.
Michael.
13 Jul 2010 19:16:58 UTC
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Bilingual NEWS messages
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.
11 Jul 2010 11:49:46 UTC
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Searching for translators
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 many languages as possible. Please contact us if you want to help.
yoyo
25 Jun 2010 21:19:08 UTC
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Brief conference update
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.
Michael.
25 Jun 2010 20:50:02 UTC
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RNA World conference presentation
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.
17 Jun 2010 22:45:26 UTC
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Problems solved
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. ;-)
Michael.
30 Apr 2010 12:21:04 UTC
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WU generator transiently stopped...
...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-occur 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.
Michael.
28 Apr 2010 6:36:30 UTC
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Genome annotations running
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.
26 Apr 2010 8:20:14 UTC
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Tuberculosis project
The first set of WUs dealing with our tuberculosis project (please see the previous thread and the scientific project objectives on our website) is now ready for processing. These WUs should have quite heterogeneous run times of up to a maximum of 10 hrs (on an Intel i7 920 2,66 GHz Quad-Core CPU) and should be devoid of RAM or traffic problems. I hope that even those that had problems with our last set of huge CMS WUs will consider participating again since I believe this is a very interesting research project.
Michael.
7 Apr 2010 12:50:59 UTC
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CMS RAM issue, current WUs and novel project
You may have noticed that I am a bit less responsive during the past two weeks concerning user support. This in fact has good reason since I am currently travelling around in India to meet our cooperation partners and discuss a set of very interesting projects I have planned from long hand since quite some time now. The outcome is this: While we are currently working on resolving the RAM issue with the large eukaryotic work units, as of today, I have replaced the remaining WUs of this batch by a novel, highly exciting project dealing with tuberculosis that is actually based on our very promising results obtained for the Lin64 CMC WU series we completed successfully a few weeks ago. I have meanwhile tested these Lin64 CMC results and they seem perfect as all testings could be completed to my full satisfaction.
If all works as expected, you can expect the first WUs of the tuberculosis type to pour in on your machines by tomorrow or maybe even tonight. We just have to finish up the latest large WU batch that has been processed and fed in by the server. For a few more details on that project, just take a look at our constantly improving scientific objectives page.
Michael.
5 Apr 2010 17:46:08 UTC
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no multiple screensaver starts anymore
With cmcalibrate 0.22 for win32/64 and cmsearch 0.11 for win32/64 the screensaver shouldn't start multiple times anymore.
yoyo
18 Mar 2010 20:59:27 UTC
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New work
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. Also, please watch the RAM requirements since a few WUs might end up taking up to 2.3 GB of memory.
Michael.
6 Mar 2010 18:56:29 UTC
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Problem solved
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.
Michael.
5 Mar 2010 22:49:05 UTC
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last 2 cmsearch archives
With the last 2 cmsearch runs we send and received round about 900.000 results and transfered 1 TByte of data.
yoyo
4 Mar 2010 21:32:03 UTC
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Current status
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.
4 Mar 2010 15:09:40 UTC
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Run-time filter required
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.
Michael.
23 Feb 2010 5:42:23 UTC
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Transitioner and validator transiently disabled
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.
22 Feb 2010 8:21:53 UTC
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Application priorities and server responsiveness
We have tweaked a bit server-side on the application priorities such that CMC WUs will go out preferentially compared to CMS WUs. This should help to avoid displacing CMC WUs that are already in progress by CMS WUs which have much shorter deadlines. Moreover, it should help those of you running many machines that differ in OS to make sure all systems are being served without having to disable the one or the other application manually anymore (as e.g. CMS on Linux x64). Additionally, it should reduce the need for setting up complex profiles for individual machines. Please note that CMC WU completion always is of major importance to us since this process represents the bottle neck for all of our current downstream analyses.
Also, due to the floods of rather short WUs our server is having a hard time on the MySQL side. In response to this, we have altered the scheme by which work is fed into the RNA World system such that in the future the run time distribution can be controlled much better. At present, the server has some sort of a protection setting that simply reduces the server responsiveness if too many clients ask for communication in a very short period of time. At your end it might therefore look as if no work was there or as if the server is down. But be assured, both should not be the case, so just keep on crunching.
Michael.
21 Feb 2010 16:30:06 UTC
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New work prepared
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!
Michael.
20 Feb 2010 22:06:39 UTC
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HD checkup complete, new CMS WUs ahead
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.
19 Feb 2010 8:11:07 UTC
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CMC only, for a while...
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.
15 Feb 2010 16:40:32 UTC
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Some unexpected anomalies
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.
Michael.
14 Feb 2010 14:05:24 UTC
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CMC work units available for Linux x64 systems
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.
Michael.
13 Feb 2010 16:19:28 UTC
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Some server beating...
The current sets 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.
12 Feb 2010 15:48:57 UTC
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New work
As announced, the server is currently getting fed with new work.
Michael.
10 Feb 2010 4:34:11 UTC
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WU shortage will be resolved by tomorrow
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.
9 Feb 2010 14:07:32 UTC
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New work units ahead
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.
8 Feb 2010 12:31:42 UTC
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Account registration open
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.
6 Feb 2010 14:15:11 UTC
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Work unit shortage ahead
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.
4 Feb 2010 7:59:40 UTC
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Participants using W2K wanted
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.
2 Feb 2010 12:49:38 UTC
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Server migration completed
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.
31 Jan 2010 12:44:06 UTC
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Maintenance break and server move
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 possible!
26 Jan 2010 20:30:25 UTC
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Work available and preliminary server info
The server is currently delivering another set of approx. 25.000 work units. After that, we will have to do some in-depth analysis of the results acquired so far and maybe use the idle time to migrate the server to a new machine which, hopefully, will be an Intel i7-based quad core with 12 GB of RAM and a dual 1.5 TB HD RAID system. ;-)
Michael.
25 Jan 2010 10:39:31 UTC
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New work units...
...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.
22 Jan 2010 18:26:49 UTC
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ready to translate
RNA World is now 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
18 Jan 2010 18:42:03 UTC
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Again more work
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.
18 Jan 2010 9:48:52 UTC
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Donators, Sponsors needed
Last night our server was total overloaded. Also the disc is now nearly full. We need now to rent a much more powerfull 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.
16 Jan 2010 21:06:50 UTC
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A set of novel CMSEARCH work units...
...will be available today. After changing the HR class for this application, we need to conduct a set of further tests. We will combine that by searching the entire set of 958 completely sequenced bacterial genomes (as stored in EMBL database) for the presence of a small RNA. So, with this (1) we combine the HR test with a scientific project we would also perform assuming the system works perfect (which, of course, we actually do) and (2) we expect to have a few more work units this time. ;-)
Michael.
13 Jan 2010 10:24:02 UTC
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RNA World in deutsch
Die RNA World Seite gibts jetzt auch in deutsch. Fehler, Probleme und Inkonsistenzen bitte im Forum melden.
9 Jan 2010 21:31:19 UTC
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cmsearch HR class
We changed HR class for cmsearch to coarse grain to see if there are any problems with validating results.
9 Jan 2010 12:23:03 UTC
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Additional work units loaded...
...today.
Michael.
7 Jan 2010 14:56:17 UTC
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Again new work units for CMSEARCH
For additional test purposes, I will again release around 2000 work units today. Stay tuned... ;-)
Michael.
4 Jan 2010 10:28:54 UTC
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Coming up today: new work units for CMSEARCH.
The results from the previous CMCALIBRATE test round came in today and look quite promising, so we will use these to release another few hundred work units today to check the performance of CMSEARCH. If we are lucky, the results of these may already form the basis for our first scientific publication.
Michael.
31 Dec 2009 11:40:20 UTC
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MERRY CHRISTMAS AND HAPPY NEW YEAR!
I would like to wish all participants and early testers of RNA World a very Merry Christmas and a happy New Year!
yoyo
24 Dec 2009 10:04:01 UTC
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Import of Boinc wide teams
I imported all Boinc wide registered teams. Now we should have more than 600 additional testers.
21 Dec 2009 22:47:00 UTC
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WUs aborted
I aborted the last set of cmsearch wus. They were generated with a to low max result size boundary. Additionally the assimilator on the server was doing some strange things. I fixed both and generated a new batch of cmsearch wus.
21 Dec 2009 22:44:52 UTC
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wus wrong
I aborted the last round of work units. They were generated using a wrong cmbuild version. This is now fixed and they are generated again.
18 Dec 2009 22:32:30 UTC
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science
Applications are update to the newest Infernal version. We released also some workunits.
18 Dec 2009 19:44:00 UTC
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science
Update of project description.
3 Dec 2009 17:44:00 UTC
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server update
I used the stable_server version for the server update. But the feeder crashed and I needed some hours to debug the feeder and find the problem. There is an bug in the source which happens if HR us used.
6 Nov 2009 21:16:00 UTC
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server update
Server updated, will now create some test wus for all apps.
6 Nov 2009 18:16:00 UTC
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server update
Updating the Boinc server to the lates server_stable branch.
6 Nov 2009 16:20:00 UTC
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app testing
Testing the first application.
29 May 2009 13:50:00 UTC
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Server setup
Welcome to RNA World! The server is now setup and runs upperCASE.
21 May 2009 11:50:00 UTC
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