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News archive

  • New regular-sized WUs available

    After long rounds of testing of the VM checkpointing system, today we have finally released a new set of WUs. These complete one of our virus projects and are small to medium in size. Once this work bunch is completed we will move on to an overall update of the science apps which will be followed by a lot of new work.

    Nach langem Testen des VM-Checkpointingsystems haben wir heute endlich einen neuen Satz an WUs verfügbar gemacht. Diese vervollständigen eines unserer Virenprojekte und umfassen kleine bis mittlere WU-Größen. Sobald dieser Arbeitssatz durchgerechnet ist, möchten wir die Science-Apps aktualisieren und werden danach eine ganze Menge neuer Arbeit haben.

    Michael.

    22 Jul 2014, 17:54:19 UTC · Comment

  • RNA World team at Chemnitz Linux Days

    Einige Mitglieder des RNA World Teams werden am kommenden Wochenende (15.-16.3.) auf den Chemnitzer Linux-Tagen sein. Es gibt einen Stand des Rechenkraft.net e.V. wo man das Team und andere Rechenkraft.net Mitglieder treffen kann.
    Die "Chemnitzer Linux-Tage" ist eine Veranstaltung zum Thema Linux und OpenSource Software. Dort wird für jeden etwas geboten, Anfänger wie auch Fortgeschrittene.

    Some people of the RNA World team will be on the Chemnitz Linux Days 2014 from 15.-16.3. in Chemnitz, Germany. Rechenkraft.net has a booth in the main hall where you can meet the team and other Rechenkraft.net people.
    The "Chemnitz Linux Days" is a conference that deals with Linux and Open Source Software. It is open for everyone, novices and experts alike.

    14 Mar 2014, 13:38:10 UTC · Comment

  • please upgrade your BOINC installations to use VM application

    Please upgrade your BOINC installations to 7.2.33 (recommended stable release at the moment) if you want to get work for the VirtualBox enabled application. Because of a bug in versions before 7.2.24 the BOINC Client would start several Virtual Machines without checking if enough RAM is available. The RNA World Server will only issue VM-tasks to version 7.2.24 or newer. For further assistance visit our website or the forum.

    Wer Aufgaben für die VirtualBox Anwendung bekommen möchte muss auf die BOINC Version 7.2.33 aktualisieren (die empfohlene stabile Version im Moment). Wegen eines Fehlers in Versionen vor 7.2.24 wurden mehrere Virtuelle Maschinen gestartet ohne den verfügbaren Arbeitsspeicher zu überprüfen. Der RNA World Server wird VM-Aufgaben nur ab Version 7.2.24 oder neuer zuteilen. Bei weiteren Fragen bitte die Webseite oder das Forum besuchen.

    20 Dec 2013, 14:48:36 UTC · Comment

  • Latest VirtualBox version now possible

    So far you had to specifically use version 4.2.16 of VirtualBox to ensure proper function of our novel checkpointing approach. Now you may use any of the later versions - the bug is no more relevant for us.

    Bislang mußtet ihr stets Version 4.2.16 von VirtualBox installieren, damit es zu keinen Problemen mit unserem neuen Checkpointing-Ansatz kam. Ab sofort könnt ihr auch alle neueren Versionen verwenden. Der Fehler ist behoben.

    Michael.

    13 Nov 2013, 14:05:14 UTC · Comment

  • Reported bugs under examination, partly resolved

    Based on your bug reports we managed to identify and resolve a number of bugs in the virtual machine (VM) approach. A very limited set of WUs have been generated to examine the system behavior. It appears that some issues remain with the Linux version. We will keep you informed.

    Basierend auf euren Berichten konnten wir eine Reihe von Fehlern in unserer Virtuellen Maschine (VM) identifizieren und beheben. Momentan zirkuliert ein sehr begrenzter Satz von neuen WUs, um zu prüfen, ob jetzt alles sauber läuft. Es sieht so aus, dass es unter Linux noch ein Problem gibt. Wir halten euch auf dem Laufenden.

    Michael.

    10 Nov 2013, 17:05:15 UTC · Comment

  • new Applications using VirtualBox released

    We just released new application versions for Windows, Mac and Linux of the cmsearch VM app that uses VirtualBox for checkpointing. Here is how you can participate:

    1. if applicable, enable the AMD-v or VT-x capability of your CPU in your BIOS
    2. install VirtualBox on your computer (4.2.16 is required, 4.2.18 or better are not working at the moment)
    3. install BOINC 7.x (sometimes you have to reinstall after the VirtualBox installation)
    4. select the cmsearch VM application on your RNA World preferences page
    5. allow BOINC to use at least 2GB of hard disk space and 4GB of RAM on your global preferences page


    Please visit our forum or comment on this news item if you have problems.

    Deutsch/German:
    Wir haben gerade neue Versionen der cmsearch VM Anwendung für Windows, Mac und Linux veröffentlicht, welche mittels VirtualBox als Checkpointingsystem für mehr Sicherheit sorgen. Und so kann man teilnehmen:


    1. falls vorhanden, die AMD-v oder VT-x Fähigkeit der CPU im BIOS aktivieren
    2. VirtualBox auf dem Computer installieren (4.2.16 wird benötigt, 4.2.18 oder besser funktionieren im Moment nicht)
    3. BOINC 7.x installieren (manchmal muss auch erneut installiert werden nachdem VirtualBox installiert wurde)
    4. die cmsearch VM Anwendung in den RNA World Einstellungen auswählen
    5. in den Berechnungseinstellungen BOINC die Nutzung von mind. 2GB Festplattenplatz und 4GB RAM ermöglichen


    Probleme können gerne in unserem Forum oder als Kommentar zu diesem Newseintrag gemeldet werden.

    20 Oct 2013, 14:07:56 UTC · Comment

  • Results section updated

    Today I have taken some time to update the RNA World project results section - especially with respect to our initial three publications, although these three do not yet contain results of the RNA World computational efforts. We are also planning to make available several parts of our raw results, soon (open data-style).

    Heute habe ich die RNA World Projektergebnisübersicht aktualisiert - insbesondere mit Hinblick auf unsere ersten drei Fachpublikationen, auch wenn diese noch keine RNA World Rechenergebnisse beinhalten. Wir haben desweiteren vor, schon bald eine Reihe unserer Rohdaten im Stil eines OpenData Ansatzes verfügbar zu machen.

    Michael.

    8 Oct 2013, 11:25:50 UTC · Comment

  • Checkpointing coming up

    Presumably next wednesday we will install the new checkpointing system. So please do not be surprised if there is a system outage. Old WUs should be preocessed as usual - so do not worry about your long-runners. If you like to use the checkpointing system, you will have to install VirtualBox. Of course, we will first send out WUs to the beta testers.

    Kommenden Mittwoch werden wir voraussichtlich das neue Checkpointingsystem installieren. Es kann dadurch vorübergehend zu Serverausfällen kommen - also wundert euch nicht. Die alten WUs sollten ganz normal weiter prozessiert werden, also einfach laufen lassen. Um das neue Checkpointingsystem zukünftig nutzen zu können, muss lediglich VirtualBox installiert werden. Aber wir werden am Anfang natürlich erstmal nur die Betatester mit den neuen WUs bestücken.

    Michael.

    7 Sep 2013, 17:38:43 UTC · Comment

  • 3rd place in Thomas Krenn Open Source Contest

    Hi guys - we did it. The RNA World team / Rechenkraft.net received the 3rd place in this year's Thomas Krenn Open Source Contest. This means, we will get server hardware worth 1000,- € in support of our project. It was a spontaneous application while we presented RNA World and Rechenkraft.net e.V. at the Berlin LinuxTag 2013 and therefore is worth double to us! Thanks to all participants.

    Das RNA World Team / Rechenkraft.net hat den 3. Platz des diesjährigen Thomas Krenn Open Source Contests bekommen und wir erhalten somit Server Hardware im Wert von 1000,- €. Da dies eine ganz spontane Bewerbung auf dem Berliner LinuxTag 2013 war, bedeutet uns das Ergebnis umso mehr. Vielen Dank an alle Unterstützer!

    Michael.

    30 Aug 2013, 9:36:34 UTC · Comment

  • LinuxTag 2013

    First of all thanks to all the hard working participants and visitors at our booth at the Berlin LinuxTag 2013 - we had a great time. Spontaneously, the RNA World team paticipated at the Thomas Krenn Open Source Contest in order to acquire sophisticated server hardware. We will know how well we performed in a couple of weeks.
    Moreover, during the 2nd RNA World Workshop / 1st Rechenkraft.net Hackathon which we put into practice as announced at the back space desk during the LinuxTag, we managed to achieve significant progress regarding RNA World's VM-based checkpointing and job submission interfaces.
    Of course, we also took a couple of pictures which you can view here:

    https://www.dropbox.com/sh/pix5w5se7ycfdk2/00h4utbYfH
    https://www.dropbox.com/sh/bj2gq56imp3671j/5ITZiUqoAC

    On top of that, our server administrator Yoyo presented a talk on BOINC's wrapper technology - you can find the slides here:

    http://www.rechenkraft.net/wiki/images/c/c3/BoincYoYoWrapper.pdf

    Vielen Dank an alle Helfer und Besucher unseres Standes auf dem Berliner LinuxTag 2013 - wir hatten eine Menge Spass und Erfolg bei unseree Präsentation. Das RNA World Projekt-Team nahm spontan an dem diesjährigen Thomas Krenn Open Source Contest teil, in der Hoffnung unsere Serverhardware weiter ergänzen zu können. In einigen Wochen werden wir wissen, ob wir unter den Auserwählten sind.
    Desweiteren konnten wir im Rahmen des angekündigten 2. RNA World Workshops bzw. 1. Rechenkraft.net Hackathon nennenswerte Fortschritte im Hinblick auf ein VM basiertes Checkpointing und die Job Submission Interfaces von RNA World erarbeiten. Dazu nutzten wir die Arbeitsbank im hinteren Teil unseres Standes auf dem LinuxTag.
    Ein paar Bilder von unserem Stand auf dem LinuxTag 2013 findet ihr hier:

    https://www.dropbox.com/sh/pix5w5se7ycfdk2/00h4utbYfH
    https://www.dropbox.com/sh/bj2gq56imp3671j/5ITZiUqoAC

    Als krönenden Abschluss präsentierte unser RNA World Server Administrator Yoyo einen Vortrag über den praktischen Einsatz von BOINCs Wrapper Technologie - die PowerPoint-Folien findet ihr hier:

    http://www.rechenkraft.net/wiki/images/c/c3/BoincYoYoWrapper.pdf

    Michael.

    21 Jun 2013, 10:09:42 UTC · Comment

  • RNA World & Rechenkraft.net: LinuxTag 2013 in Berlin

    This one is just in German, because there will barely be anybody who will join us at a conference in Berlin.

    Ein fröhliches Hallo an alle Interessierten im Bereich "Distributed Computing",
    der seit 2005 in Deutschland operierende gemeinnützige Verein Rechenkraft.net e.V. wird dieses Jahr einen Stand auf dem Berliner LinuxTag präsentieren und Du kannst daran teilhaben:

    Termin & Ort:
    22.-25. Mai 2013,
    Messehalle 7.1c unter dem Berliner Funkturm, Berlin

    Wir waren dieses Jahr bereits auf den Chemnitzer Linux-Tagen vertreten und hatten dort eine Menge Spass und positive Rückmeldungen für unsere Distributed Computing Leidenschaft erhalten. Als man uns dann auch noch seitens des Berliner LinuxTags angesprochen hatte, ob wir nicht auch in Berlin teilnehmen möchten, haben wir spontan zugesagt. Die Planungen haben nun das Endstadium erreicht und deshalb senden wir euch heute diese Informationen.

    Offizielle Infos im Web zum Berliner LinuxTag 2013:
    http://www.linuxtag.org/2013/

    Wir werden an unserem Stand neben allerlei Distrbuted Computing Projekten, die wir per Beamer auf eine Leinwand projizierend erklären werden, dieses Jahr vor allem die beiden Projekte Quake Catecher Network und (QCN) Radioactive@home (RAH) vorstellen. Und zwar selbstversändlich mit komplettem Sensoren-Satz, sodass man am Stand live sehen kann, wie diese Projekte arbeiten. Worum geht es dabei überhaupt? QCN ist ein weltweites Sensornetzwerk für Erdbeben und RAH mißt in einem weltweiten Netzwerk die Gammahintergrundstrahlung.
    Zusätzlich werden wir am Stand allerlei ARM-basierte Hardware haben, da wir uns aktuell mit der Portierung von DC-Projekten auf den Smartphonebereich befassen.

    Planung & Diskussionsforum für den Berliner LinuxTag auf Rechenkraft.net:
    http://www.rechenkraft.net/phpBB/viewtopic.php?f=12&t=12761

    Wer bei uns am Stand mitarbeiten will, der trägt sich einfach für den gewünschten Termin in unserem unten stehenden Organisationsplan (Doodle) ein. Natürlich erhalten alle Helfer freien Zutritt zur Messe. Bei uns läuft das üblicherweise sehr locker ab, sodass eigentlich jeder, der ein wenig von Distributed Computing versteht, dabei sein kann. Und keine Sorge, Du wirst nicht alleine dort stehen: 8 Leute haben schon verbindlich zugesagt. Ich selbst bin natürlich auch da.

    Doodle-Umfrage zur Planung unsere Standbesetzung:
    http://www.doodle.com/x9edtedn35tw5hp5

    Natürlich müssen wir ein bischen planen, wer was mitbringt. Und das passiert in folgedenm Forenbereich.

    Wer bringt was mit zum LinuxTag:
    http://www.rechenkraft.net/phpBB/viewtopic.php?f=12&t=12830

    Da wir dieses Jahr am Stand parallel zur regulären Präsentation diverser Distributed Computing Projekte das erste Rechenkraft.net Hackathon bzw. (je nach Ausgestaltung) den 2. RNA World Workshop durchführen möchten, sammeln wir in folgendem Forenbereich Ideen für das anzugehende Programmierprojekt.

    Ideen für das Projekt des 1. Rechenkraft.net Hackathon / 2. RNA World Workshops:
    http://www.rechenkraft.net/phpBB/viewtopic.php?f=76&t=12829

    Wir hoffen, zahlreiche Interessierte und Unterstützung unter bzw. durch euch zu finden!
    Da wir bei den Veranstaltern SCHNELLSTMÖGLICH die Mitarbeiternamen angeben müssen, bitten wir euch dringend, euch möglichst heute noch im oben verlinkten Doodle einzutragen, wenn ihr uns beistehen möchtet.Wie gesagt: Man muss nicht jeden Tag teilnehmen, es ist also auch möglich, NUR am Samstag oder so zu kommen.

    Beste Grüße,
    Michael.
    - - - - -
    Dr. Michael Weber
    Vorstandsvorsitzender
    Rechenkraft.net e.V. - Verein zur Förderung von Bildung, Forschung & Wissenschaft durch Einsatz vernetzter Computer
    Chemnitzer Str. 33
    D-35039 Marburg
    Germany

    Web: http://www.rechenkraft.net
    Mail: kontakt ät Rechenkraft.net

    Unsere Distributed Computing Projekte:
    RNA World: http://www.rnaworld.de
    Yoyo@home: http://www.rechenkraft.net/yoyo/

    .
    EDIT :
    .

    Nochmal: Wenn jemand von euch Lust hat, bei uns am Stand dabei zu helfen, anderen das Thema DC schmackhaft zu machen, dann tragt euch im Doodle ein. Wir werden dem Betreffenden ein 4-Tagesticket besorgen. Dasselbe gilt für Leute, die am Stand beim RKN Hackathon teilnehmen wollen. Wir planen, für alle aktiven im Doodle registrierten Teilnehmer in Berlin eine gemeinsame FeWo zu mieten. RKN wird dort höchstwahrscheinlich finanzierend einspringen. Also ran an die Bouletten!

    15 May 2013, 10:06:47 UTC · Comment

  • ARM developer hardware

    Thanks to JagDoc the RNA World team has received an ODROID-U2 developer board plus some additional equipment which will now allow us to port RNA World code to ARM systems.

    Vielen Dank an JacDoc für die grosszüggige Bereitstellung eines ODROID-U2 Entwicklerboards inkl. einiger zusätzlicher Hardware zwecks Portierung von RNA World Code auf ARM Systeme.

    Michael.

    22 Mar 2013, 11:36:45 UTC · Comment

  • Moved XXL workunits (< 72h) to S

    Since we are running out of S (short) workunits I moved some shorter XXL workunits to S workunits. This means, that S workunits run now up to 3 days.
    yoyo

    1 Jan 2013, 19:37:16 UTC · Comment

  • version 0.32 for cmsearch

    The new version for cmsearch XXL and S for Windows32 and Windows64 has the following new feature:
    - disabled heartbeat to avoid missing heartbeat errors
    - writes not every time, that check pointing isn't working on Windows. Instead this is written only once.

    yoyo

    1 Jan 2013, 19:03:05 UTC · Comment

  • Moved XXL workunits to S

    Since we are running out of S (short) workunits I moved some shorter XXL workunits to S workunits. This means, that S workunits run now up to 2 days.
    yoyo

    20 Dec 2012, 16:38:46 UTC · Comment

  • Only few small WUs available

    We are currently running a bit short on small WUs. Soon, new WUs of this type will be generated.

    Die Zahl der im System verbliebenen kurzen WUs ist momentan gering, aber wir werden bald neue einstellen.

    Michael.

    5 Oct 2012, 8:44:39 UTC · Comment

  • Back online

    The server is back online. The disc was replaced and the raid syncs now.

    21 Sep 2012, 21:59:40 UTC · Comment

  • Short outage for disc replacement

    A disc of our server raid finished the cooperation and is no more working. For replacement the server must be switched off. We hope that this will be a short outage.

    - yoyo -

    21 Sep 2012, 18:13:01 UTC · Comment

  • New work available

    We have again added several new work unit archives to the server - all with short runtimes and pseudo-checkpointing (i.e. these WUs contain multiple small genomes to be checked for ncRNAs in a single file).

    Es sind wieder etliche neue Arbeitspakete mit vergleichsweise kurzen Laufzeiten auf dem Server verfügbar.

    Michael.

    8 Aug 2012, 8:01:05 UTC · Comment

  • small workunits

    The wu-generator is running and creates now also cmsearch S (short running) workunits. If you were waiting for them, now it is time to fetch them.
    yoyo

    23 Jun 2012, 6:49:51 UTC · Comment

  • 1. RNA World Workshop successful

    Now that the 1st RNA World Workshop is over, I thought it might be nice to drop a brief note on what we have achieved. In short, enjoying a wonderful relaxing work environment, we managed to install Linux on the BeagleBoard-xM which harbors an ARM Cortex-A8 CPU and we successfully compiled and tested the RNA World science applications on that system. Moreover, we now also have a client for the ARM Cortex-A9 CPU which is found in some of the latest tablet and smartphone hardware. The test results obtained so far are encouraging us to further follow up the idea of making RNA World universally available on ARM-based hardware.

    Nachdem nun der 1. RNA World Workshop vorüber ist, möchte ich hier kurz ein paar Zeilen zu den erreichten Ergebnissen präsentieren. Es ist uns in einer wunderbar entspannten Arbeitsumgebung gelungen, Linux auf dem BeagleBoard-xM zu installieren. Dieser Einplatinencomputer enthält einen ARM Cortex-A8 Prozessor, für den es uns gelang, die RNA World Quellcodes zu kompilieren und erste Tests mit den resultierenden Binaries durchzuführen. Auch für den ARM Cortex-A9, den man in neuerer Tablet- und Smartphone-Hardware findet, konnten wir einen Client erzeugen. Die bisherigen Testergebnisse sind ermutigend genug, um die Idee weiterzuverfolgen RNA World auf ARM-basierter Hardware verfügbar zu machen.

    23 May 2012, 7:42:14 UTC · Comment

  • 1. RNA World Workshop in Wieda (Harz/Germany)

    Vom 17. bis zum 20. Mai findet in Wieda im Harz der 1. RNA World Workshop statt. Hintergrund des Ganzen ist unser Bestreben, möglichst viele Projektinteressierte so aktiv wie möglich in RNA World einzubinden. Wir möchten deshalb dieses Jahr die Gelegenheit nutzen, RNA World Interessierte zum 1. RNA World Workshop im Rahmen des seit Jahren stattfindenden teamübergreifenden BOINC Treffens zusammenzubringen. Dieses Jahr wollen wir unter anderem gemeinsam probieren, ob wir ARM-basierte Systeme für RNA World nutzbar machen können. Alles weitere kann im Forum besprochen werden.
    Interessenten laden sich bitte das Anmeldeformular mit weiteren Informationen herunter.

    The 1st RNA World Workshop will be held from 17th-20th May in Wieda (Harz/Gemany). The idea behind this workshop is our aim to integrate as many RNA World-interested people as possible in a more active manner. For this reason, this year we would like to take advantage of the opportunity to bring RNA World-interested people together at the 1. RNA World Workshop which will be held together with the team-independent BOINC Meeting which takes place in Germany since many years. In this year's RNA World workshop, we would like to see whether we can get ARM-based machines to run with RNA World. Further details can be discussed in the RNA World forum.
    People interested in participation may download the registration form with further information (e.g. on accomodation, etc.). For our foreign supporters we are aware that this announcement comes on short notice, but this year we would just like to first take a look at how much interest there is for such a gathering before we go ahead with plannings for an internationally suitable meeting.
    Michael.

    23 Apr 2012, 8:57:24 UTC · Comment

  • Results, presentations, publications summary section updated

    We just updated our results, presentations and publications section on the project website to give a more complete overview of the project achievements so far.

    Wir haben heute den Projektwebseitenbereich Ergebnisse, Präsentationen und Publikationen aktualisiert, um das bisher Erreichte vollständiger zu dokumentieren.

    Michael.

    13 Apr 2012, 18:04:15 UTC · Comment

  • RNA World at the 2nd Heidelberg Forum for Young Life Scientists

    The 2nd Citizen Cyberscience Summit in London is barely over while I am almost on the road again to head for the next RNA World project presentation - this time at the 2nd Heidelberg Forum for Young Life Scientists which takes place from 23rd to 24th of February in Heidelberg/Germany. I think it is worth to note that besides the RNA World presentation, Rechenkraft.net e.V. will additionally show up with their own booth to celebrate its premiere as an official sponsor of a scientific event.

    Der zweite Citizen Cyberscience Kongress in London ist kaum vorüber, da befinde ich mich auch schon auf dem Weg zur nächsten RNA World Projektpräsentation - diesmal vom 23.-24. Februar in Heidelberg auf dem 2nd Heidelberg Forum for Young Life Scientists. Bei der Gelegenheit wird Rechenkraft.net e.V. übrigens zusätzlich zur RNA World Präsentation mit einem eigenen Stand sein Debüt als offizieller Sponsor einer wissenschaftlichen Veranstaltung feiern.

    Michael.

    22 Feb 2012, 10:23:48 UTC · Comment

  • RNA World at the 2nd Citizen Cyberscience Summit in London

    Tomorrow I will present a talk on the RNA World Project at the 2nd Citizen Cyberscience Summit in London. The focus will be on a novel type of user participation system which I term the 'RNA World Advanced User Participation Kit'. More details will follow soon. ;-)

    Morgen werde ich das RNA World Projekt auf dem 2nd Citizen Cyberscience Summit in London präsentieren. Im Fokus wird ein neues System zu erweiterten Beteiligungsmöglichkeiten unserer Unterstützer am RNA World Projekt stehen. Einzelheiten werden bald bekannt gegeben. ;-)

    Michael.

    16 Feb 2012, 13:04:49 UTC · Comment

  • Thanks to the charity race participants

    Now that the 2012 charity race is over we would like to thank all the participants for crunching away an amazing pile of work units! You guys are just terrific! ;-)

    Michael.

    3 Feb 2012, 12:08:40 UTC · Comment

  • Small WU archives up and running as announced

    The test runs were completed successfully and the server has been charged with a number of additional small WU archives as announced before. Enjoy! And thanks for your great support! ;-)

    Michael.

    16 Jan 2012, 8:26:02 UTC · Comment

  • Additional WUs for the charity race...

    ...are in preparation. We hope to have these ready for delivery during this weekend. A lot of small WUs should be there as well to complement the remaining long runners.

    Michael.

    14 Jan 2012, 0:27:42 UTC · Comment

  • Merry christmas and a happy new year

    The RNA World team wishes a merry christmas and a happy new year to all of our volunteers. Thank you very much for all your valuable contributions.

    Michael.

    23 Dec 2011, 7:47:42 UTC · Comment

  • Thanks to Ton for generous hardware donation

    The RNA World team would like to thank Ton van Born for the generous donation of valuable server hardware. Among the three donated machines is a dual Opteron board equipped with two Dual-Core AMD Opteron processors (Opteron 2218 @ 2.6GHz), 32 GB of RAM, 8 TB HDs in a RAID6 array, 2x GigaBit network adapters and a dual power supply. This equipment will certainly help us to overcome a number of performance issues we experienced in the past. Thanks a lot Ton!

    Das RNA World Team möchte sich ganz herzlich bei Ton van Born für die grosszügige Spende wertvoller Hardware bedanken. Unter den drei gespendeten Maschinen befindet sich auch ein Dual-Opteron-Board ausgestattet mit zwei Dual-Core AMD Opteron Prozessoren (Opteron 2218 @ 2.6GHz), 32 GB RAM, 8 TB Festplatten in einem RAID6-Array, 2x GigaBit Netzwerkadaptern und zwei Netzteilen zur Eröhung der Ausfallsicherheit. Diese Hardware wird uns sehr nützlich sein, einige der Leistungsengpässe der Vergangenheit in den Griff zu bekommen. Vielen Dank, Ton!

    Michael.

    28 Nov 2011, 22:36:25 UTC · Comment

  • Thanks a lot for your support in the voting competition

    The voting is over and we would like to thank all participants who supported our organization. Unfortunately, we did not make it among the top 1000 in Germany as the final result is 6.459 votings, rank 1.216. But that's how it sometimes goes. ;-)

    Vielen Dank an alle Unterstützer, die für uns ihre Stimme in die Waagschale geworfen haben. Der Endstand ist 6.459 Stimmen, Platz 1.216, d.h. wir haben es trotz aller Bemühungen leider nicht unter die ersten 1000 Vereine geschafft. Vielleicht beim nächsten Mal... ;-)

    Michael.

    20 Nov 2011, 2:02:05 UTC · Comment

  • Internet voting to support RNA World

    Liebe RNA World Unterstützer,
    wie ihr ja wisst, wird RNA World von Rechenkraft.net e.V. unterstützt. Derzeit haben wir die einmalige Gelegenheit eine zweckungebundene Spende von 1.000€ zu erhalten. Doch dafür braucht es ein wenig Hilfe.

    Eine bekannte deutsche Bank hat eine Aktion gestartet, an dessen Ende die Bank 1.000€ an die ersten 1.000 gemeinnützigen Vereine spendet, die die meisten Stimmen bekommen haben.

    Mit deiner Stimme kann es Rechenkraft.net e.V. unter eben diese 1.000 Vereine schaffen. Somit könnte auch das RNA World Serverhosting unterstützt werden.

    Du brauchst lediglich auf dem unten genannten Link deine E-Mail-Adresse angeben und in der dann erhaltenen E-Mail auf den Bestätigungslink klicken. Pro E-Mail-Adresse sind drei Stimmen möglich, die auch alle an den gleichen Verein gehen können.

    https://verein.ing-diba.de/sonstiges/35039/rechenkraftnet-ev

    Es wäre schön, wenn ihr uns unterstützen könntet.


    Dear RNA World supporters,
    as you know RNA World is supported by Rechenkraft.net e.V. At present, the German non-profit society Rechenkraft.net e.V. has the unique opportunity to receive a donation of €1.000. For this purpose, your help would be appreciated.

    A well-known German bank as launched a campain, where 1.000 non-profit societies can win a single donation of €1.000 each. The criterion to receive the price is to rank among the top 1000 non-profit societies, so the total number of votes collected from the internet users is of importance.

    With your vote Rechenkraft.net e.V. might be able to rank among the first 1.000 societies which would help to fund the RNA World server hosting.

    The only thing you need to do is to register yourself with one of your email addresses on the website linked below. By clicking on the confirmation link subsequently sent by email by the bank to you, you confirm your vote. That's all. There are three votes allowed per email address of which all three can go to the same society.

    https://verein.ing-diba.de/sonstiges/35039/rechenkraftnet-ev

    We would be happy if you would consider supporting us in this campaign.

    Best wishes,
    Michael.

    2 Nov 2011, 17:52:14 UTC · Comment

  • WU generator transiently halted

    Unfortunately, we have only little workspace left on the server hard drives such that we needed to halt the WU generator once again. Presumably, the problem will be resolved sometime tomorrow evening. At present, we cannot afford increasing our HD capacities due to lack of funding.

    Wir mussten wegen Plattenplatzmangel erneut den WU-Generator anhalten. Das Problem sollte aber voraussichtlich im Laufe des morgigen Abends wieder behoben sein. Leider können wir aus Finanzierungsgründen momentan nicht dafür sorgen, dass der Server mit mehr Speicherkapazitäten ausgestattet wird.

    Michael.

    14 Sep 2011, 18:44:50 UTC · Comment

  • WU shortage issue resolved

    Due to critical space limitations on the server HDs caused by the massive results inflow, we transiently had to halt the work generator and assimilator. This issue has now been resolved such that WU generation will resume shortly.

    Wegen des hohen Aufkommens angelieferter Ergebnisarchive hatten wir vorübergehend ein Speicherplatzproblem auf den Serverfestplatten, so dass wir den WU-Generator und -Assimilator anhalten mussten. Dieses Problem ist nun behoben, sodass die WU-Generierung in Kürze wieder durchstarten wird.

    Michael.

    7 Sep 2011, 16:35:21 UTC · Comment

  • Annual server costs

    Please help us to cover our annual server costs by donating on our donation page which can be found here:
    http://www.rnaworld.de/rnaworld//donations.php

    Bitte helft uns, unsere jährlichen Serverkosten zu decken, indem ihr falls möglich auf folgender Webseite eine kleine Spende für das Projekt leistet.
    http://www.rnaworld.de/rnaworld//donations.php

    In der BRD sind diese Spenden steuerbegünstigt, d.h. wir dürfen euch als gemeinnütziger Verein eine Spendenquittung auststellen.

    Michael.

    1 Jul 2011, 16:04:30 UTC · Comment

  • Database crash resolved

    You might have noticed a recent problem with our server. We have fixed it.
    Now we are in the process of moving on to a whole new bunch of projects as announced earlier.

    Die kürzlich aufgetretenen Probleme mit dem Server konnten behoben werden und wir sind nun dabei, auf die bereits angekündigten neuen Projekte umzustellen.

    Michael.

    31 May 2011, 16:50:50 UTC · Comment

  • New projects coming up

    First of all, we wish all our participants a happy Easter season. ;-)

    While we are in the middle of full transition to the earlier announced specialized CMSEARCH S and XXL applications, a set of very interesting new projects is being prepared for which we did a number of promising tests in advance. Among these are projects that deal with (1) RNA-based thermosensors (extension of a project which we performed around February/March 2010), (2) the identification of non-coding RNAs in metagenomic data sets (i.e., environmental nucleic acid samples, e.g. from seawater or hydrothermal vents) and (3) a very important project of potential medical relevance that aims at analyzing RNA-based mechanisms by which viruses perturb regulatory processes of their target cells. More information will follow soon.

    Zunächst einmal wünschen wir all unseren Unterstützern ein fröhliches Osterfest. ;-)

    Während wir mitten in der Umstellung auf die beiden neuen, spezialisierten CMSEARCH S und XXL Applikationen sind, bereiten wir eine Serie sehr interessanter, neuer Projekte vor, für die wir bereits im Vorfeld eine Reihe vielversprechender Tests durchgeführt haben. Im Rahmen dieser Projekte befassen wir uns (1) mit RNA-basierten Thermosensoren (Erweiterung eines Projekts, das wir bereits im Februar/März 2010 durchgeführt hatten), (2) der Identifizierung nicht-kodierender RNAs in Metagenomdatensätzen (das sind der Umwelt entnommene Nukleinsäureproben, z.B. aus Meerwasser oder Thermalquellen) und (3) einem sehr wichtigen Projekt mit potentiell medizinischer Relevanz, das darauf abzielt, RNA-basierte Mechanismen zu untersuchen, die von Viren eingesetzt werden, um regulatorische Prozesse ihrer Zielzellen nach Belieben umzuprogrammieren. Nähere Informationen werden bald folgen.

    Michael.

    23 Apr 2011, 1:26:45 UTC · Comment

  • Long running Intron WUs removed

    Today we have removed the remaining 10 very long running Intron_gpI WUs from the system to accelerate the transition to a split CMSEARCH application as described earlier. Do not worry, credits have been granted to all of these that were cancelled. In fact, the granted credits were double the claimed credits. We will re-deliver these WUs at a later time to a subset of users once the transition is complete.

    Wir haben heute die verbliebenen 10 sehr lang laufenden Intron_gpI WUs aus dem System herausgenommen, um den Übergang zu unserem neuen Ansatz mit zwei CMSEARCH Varianten zu beschleunigen. Keine Sorge, die Credits für alle von uns abgebrochenen WUs wurden an euch vergeben und zwar so, dass die angeforderten Credits sogar verdoppelt wurden. Wir werden diese WUs zu einem späteren Zeitpunkt an geeignete User neu ausgeben, um unsere Ergebnisse zu komplettieren.

    Michael.

    7 Apr 2011, 22:16:24 UTC · Comment

  • Reorganization of the CMSEARCH application

    We are currently working on reorganizing the CMSEARCH application into two variants of which one will run a combined package of many very small WUs while the other runs the rest (the default CMSEARCH) WUs. With this we intend to achieve three goals. First, the combination of many tiny WUs into one package tremendously reduces the client-server communication load: a big relieve for our server which will make it significantly more stable even during team challenges and races. Second, the packaged WUs will write a checkpoint after each completed sub-WU. Third, because the users will be allowed to opt in or out for each of these two CMSEARCH variants there will be much more flexibility at the user's end to control maximum CMSEARCH runtimes.

    Momentan arbeiten wir daran, die CMSEARCH Anwendung in zwei neue Varianten umzuorganisieren. Eine davon wird viele sehr kleine WUs in einem größeren Paket zur Verfügung stellen, während die andere die verbleibenden WUs enthalten wird. Damit wollen wir drei Ziele erreichen. Erstens wird die Kombination vieler kleiner WUs in einem Paket die Client-Server-Kommunikation dramatisch reduzieren und damit generell unseren Server entlasten und diesen insbesondere während Wettbewerben stabilisieren. Zweitens wird nach Abarbeitung jeder der kleinen WUs innerhalb eines Pakets ein Checkpoint geschrieben. Drittens können die Projektteilnehmer die beiden CMSEARCH-Varianten in ihren RNA World Projekteinstellungen individuell aktivieren oder abschalten. Auf diese Weise geben wir mehr Freiraum zur Auswahl der maximal zulässigen WU-Laufzeit. Anvisiert ist im Moment, dass die CMSEARCH XXL-Variante alles an WUs mit Laufzeiten länger als 20 Stunden bedienen wird, während alle kürzeren WUs mit der CMSEARCH S Applikation bearbeitet werden. Genauere Details werden wir noch mitteilen.

    Michael.

    14 Mar 2011, 21:48:03 UTC · Comment

  • Race Voting

    There is a Charity Race Voting ongoing. Would be nice to get more votings for RNA World.

    14 Jan 2011, 17:03:14 UTC · Comment

  • Happy New Year!

    We wish a healthy, happy and successful new year to all our participants.

    Michael.

    2 Jan 2011, 17:40:39 UTC · Comment

  • Merry Christmas

    The RNA World team likes to wish a merry christmas to all of our volunteers. Thank you very much for all your valuable contributions and please have a nice couple of hopefully very relaxing days.

    Michael.

    24 Dec 2010, 21:57:12 UTC · Comment

  • Bonus credits for monster wus

    We now give up to twice as much credit for work units that run very long. To be concrete, for work units which would get more than 2200 credits in conventional calculation.

    ---

    Wir geben jetzt bis zu doppelt soviel Credits für workunits die sehr lange laufen. Um konkret zu sein, für workunits, die mehr als 2200 credits nach herkömmlicher Berechnung ergeben würden.

    ---

    yoyo

    14 Nov 2010, 11:43:09 UTC · Comment

  • Mac OS X 10.4 and 10.5 testers wanted (64 bit CPUs)

    We are currently looking for some volunteers that can help us testing improvements of our RNA World Mac OS X 10.4 and 10.5 applications. If you have a system with an Intel 64-bit CPU, know how to use the terminal and are ready to help us in improving our clients, please contact us.
    Wir suchen momentan ein paar Freiwillige, die uns beim Testen unserer verbesserten Clientversionen für Mac OS X 10.4 and 10.5 helfen möchten. Wer ein System mit einer 64-Bit Intel CPU hat, in der Lage ist auch über das Terminal Befehle einzugeben und uns helfen möchte, möge uns bitte kontaktieren.

    Michael.

    31 Oct 2010, 18:16:08 UTC · Comment

  • OSX client released

    Those of you who have a MAC might want to try our new OSX client. In case you observe any unexpected problems, please report these in our forum.

    Wir haben seit heute OSX-Unterstützung im Programm. Wer möchte, kann ja seinen Mac mal auf RNA World ansetzen. Sollte es unerwarteter Weise Probleme geben, bitte berichtet diese in unserem Forum.

    Michael.

    14 Oct 2010, 20:00:07 UTC · Comment

  • Neue Binaries für Linux

    Auch die Linux x32/64 Binaries für CMSEARCH sind inzwischen durch verbesserte, neue ersetzt worden. In einigen Tagen werden wir ein weiteres Mal die Binaries tauschen, um eine weitere ca. 10%ige Geschwindigkeitsverbesserung nutzbar zu machen, die wir durch Einsatz des Intel C++ Compilers herauskitzeln konnten (auch AMD CPUs werden genau wie Intel CPUs von diesen Verbesserungen profitieren).

    Michael.

    10 Oct 2010, 19:09:47 UTC · Comment

  • New binaries for Linux

    In the meantime we have also replaced the Linux CMSEARCH x32/64 binaries. In a few days, we intend to again change all binaries to add another approx. 10% performance improvement by usage of the Intel C++ Compiler (yes, AMD CPUs will profit the same way as Intel CPUs do).

    Michael.

    9 Oct 2010, 16:33:44 UTC · Comment

  • New binaries for Windows machines

    As of today, new binaries for CMSEARCH have been released for Windows 32/64 bit systems. These should solve a bug which was identified with a very demanding subset of WUs. Our tests have shown that this bug should no longer occur. New binaries for Linux machines will be released soon as well. We are currently testing some additional speed improvements for Linux using the Intel compiler.

    Seit heute gibt es neue CMSEARCH Binaries für Windows 32/64-Bit Maschinen, die einen Fehler beheben, der bei einigen sehr anspruchsvollen WUs auftrat. Unsere Tests zeigen, dass dieser Fehler nun nicht mehr vorkommt. Auch für Linux werden wir schon sehr bald neue Binaries anbieten können. Hier testen wir gerade noch die Möglichkeit einer zusätzlichen Geschwindigkeitsverbesserung durch Nutzung eines Intel-Compilers.

    Michael.

    7 Oct 2010, 21:19:37 UTC · Comment

  • RNA World conference presentation

    After the RNA World project presentation at the RNA 2010 conference in June in Seattle/USA and a seminar talk given at the Massachusetts Institute of Technology in Cambridge/USA on 9th of September, the RNA World project team currently presents the RNA World distributed supercomputer project outline and some of the acquired results at the 126th conference of the Gesellschaft Deutscher Naturforscher und Ärzte e. V. (GDNÄ) in Dresden/Germany (Twitter tweets).

    Nach der Präsentation des RNA World Projekts im Juni auf der RNA 2010 Konferenz in Seattle/USA und einem Seminarvortrag am Massachusetts Institute of Technology in Cambridge/USA am 9. September, präsentiert das RNA World Projektteam das RNA World Supercomputerkonzept und einige wissenschaftliche Ergebnisse aktuell auf der 126.Versammlung der Gesellschaft Deutscher Naturforscher und Ärzte e. V. (GDNÄ) in Dresden/BRD (Twitter tweets).

    Michael.

    19 Sep 2010, 0:15:34 UTC · Comment

  • WU reload

    As a consequence of the recently experienced WU shortage we have spent the past week processing much more work. A series of CMC WU archives has been uploaded to the server and is currently pouring into the hooked-up Linux-x64 machines (Windows will be served with CMC thereafter). Due to the longer runtimes, these WUs should in the first place keep the Linux-x64 boxes busy for a while. In parallel to that, we have decided to again close in on the large eukaryotic genomes (but this time limited to 5-50 MB in size if uncompressed to avoid RAM issues on your machines). Therefore, a large set of CMSEARCH WUs containing these genomes has now been deposited on the server as well and will be delivered to the remaining systems. We expect these to also cause extended runtimes. These two procedures should help reduce your client machine's WU requests and give our server some time to generate progressingly more work for you. Of course, additionally we have significantly increased the number of WUs the server will have to have ready in store for future requests. During this attempt of refilling our machine, it would be helpful if you guys could try not to bunker work, so that all machines can be saturated for a while with 'long runners'. We are considering hooking up additional servers to RNA World as soon as possible to increase our capacity of WU preparation. Irrespective of the trouble caused due to the massive WU requests from your side over the past two weeks, I would like to thank you for your massive support which allowed for the completion of a really amazing amount of work in a very short period of time.

    Angesichts der Tatsache, dass unser Server mit der WU Produktion trotz ausreichender Arbeitsarchive nicht mehr nachkam, haben wir die letzte Woche damit verbracht, Lösungen für das Problem zu finden. Es wurden massiv neue Archive für CMC und CMS erzeugt und auf dem Server bereitgestellt. Die Laufzeiten dieser Archive sind länger, als was wir bislang im Angebot hatten. Zuerst werden CMCs an Linux-x64 ausgegeben, um diesen Typ von Maschinen abzusättigen (Windows wird danach bedient). Parallel dazu werden wir einen zweiten CMSEARCH Versuch starten, die grossen Eukaryonten Genome zu bearbeiten. Diesmal haben wir die Genomgrößen allerdings auf 5-50 MB (unkomprimiert) limitiert, um nicht erneut auf euren Maschinen einen radikalen RAM-Mangel hervorzurufen. Damit sollten jetzt die Laufzeiten, der ab sofort ausgegebenen WUs erst einmal merklich ansteigen, was unserem Server Zeit verschafft, ausreichend Arbeit nachzuproduzieren. Wir haben zudem die Zahl der vorzuhaltendern WUs dramatisch hochgesetzt (bislang hatten wir dort 150k eingestellt, was für 2,5 TFLOPS Peakleistung ausreichend war; anvisiert sind nun über eine Million unter die der Server dann nach einmaligem Erreichen nie mehr kommen darf). Es wäre sehr hilfreich, wenn ihr das Bunkern von Arbeit in dieser WU Auffüllphase vermeiden könntet. Je breiter lang laufende WUs verteilt werden, desto eher kommt der Server wieder auf die Beine und desto kontinuierlicher werdet ihr mit Arbeit beliefert. Wir bemühen uns übrigens, baldmöglichst RNA World mit weiteren Servern ergänzen zu können, damit in Zukunft kein WU-Mangel mehr auftritt und solche Rennen ohne Probleme auch unangekündigt stattfinden können. Trotz der Probleme, die wir diesmal mit dem Nachproduzieren von WUs hatten, möchte ich an dieser Stelle die Gelegenheit nicht auslassen, euch für die massive Unterstützung zu danken. Was ihr da in den letzten Tagen an Aufgaben 'weggeknackt' habt, ist mehr als beeindruckend.

    Michael.

    10 Sep 2010, 19:19:54 UTC · Comment

  • WU shortage

    Due to an excellent, but unfortunately unannounced race with tremendous throughput (increase of compute power from approx. 2.5 TFLOPS to above 4.5 TFLOPS within only two days), our WU buffer has been sucked dry. Although we have more than enough work for even more participants, RNA World WU production is computationally expensive (for each WU that can be delivered, a mini simulation has to be carried out on the server), so our server currently can't keep up with the demand. Whatever is produced is downloaded almost instantly. On top of that the current WUs appear rather short (WU runtimes can not be deduced without the results from the mini simulations). We now try to feed in some longer running tasks over the weekend but still it may take quite some time to refill the buffers although the server works on refilling constantly.

    Aufgrund eines hervorragenden, aber leider unangekündigten Rennens, bei dem die Rechenleistung von RNA World von 2,5 TFLOPS innerhalb von nur zwei Tagen auf über 4,5 TFLOPS anstieg, ist unser WU Vorrat sozusagen abgegrast. Obwohl wir mehr als genug Arbeit für noch wesentlich mehr Teilnehmer haben, kommen wir momentan mit der WU-Produktion nicht nach, da diese im Gegensatz zu vielen anderen Projekten äusserst rechenintensiv ist (für jede WU muss auf dem Server eine kleine Minisimulation durchgeführt werden). Was immer an WUs produziert wird, laden die vielen Clients nahezu sofort wieder herunter und leider sind die momentan produzierten WUs etwas kurz (was wir ohne die Minisimulation auch nicht vorhersehen können). Wir probieren jetzt über das Wochenende selektiv längere Tasks einzuspeisen, um dem Server Zeit zu geben, den Arbeitspuffer wieder hochzufahren. Dieser war bislang auf 100k WUs gesetzt, die immer auf Vorrat sein müssen und wurde gestern angesichts der aktuellen Verdopplung der Projektleistung erst mal verdreifacht.
    Michael.

    3 Sep 2010, 12:25:22 UTC · Comment

  • New WU information panels available

    We have developed a small script that generates a graphical overview of a given CMCALIBRATE WU set regarding expected runtime requirements. See below for links to the figures (SEED, FULL, COMBINED). We plan to implement this in a fully automated manner for CMSEARCH as well. A central display URL will be selected soon (probably on the server status page).

    Wir haben ein kleines Skript entwickelt, welches euch einen grafischen Überblick über die zu erwartenden Laufzeiten der aktuellen CMCALIBRATE WU-Archive gibt. Dieses wollen wir bald voll automatisiert an zentraler Stelle (wahrscheinlich auf der Server-Satusseite) auch für jedes ausgelieferte CMSEARCH WU-Archiv verfügbar machen.

    SEED: http://www.rnaworld.de/rnaworld/cmc_rfam10_seed.png
    FULL: http://www.rnaworld.de/rnaworld/cmc_rfam10_full.png
    COMBINED: http://www.rnaworld.de/rnaworld/cmc_rfam10_both.png

    Michael.

    24 Aug 2010, 2:15:03 UTC · Comment

  • Virusscanner issues - all false positives

    Since a few days, some of the current virus scanners, as e.g. AntiVir, report a virus threat for the RNA World-associated file graphics_0.06_windows_intelx86.exe. This is a false positive detection that relates to the imperfect heuristics of these types of software. We have already informed the the antivirus scanner company AntiVir and they confirmed that this file is NOT a virus (we have that in writing!). As a consequence, the false-positive detection will be fixed in one of the next scanner updates. However, you need to take immediate action to prevent your machines from trashing one RNA World WU after the other if your system is Windows-based. You need to exclude the RNA World work directory from being scanned as long as the company has not fixed that issue. Please note, that RNA World will NEVER distribute malware! Thanks to the people who came to our forum and brought this issue to our attention such that we could inspect it in detail and solve the problem.

    Seit einigen Tagen melden einige Virenscanner (u.a. z.B. AntiVir) für die RNA World assoziierte Datei graphics_0.06_windows_intelx86.exe einen Virus (WORM/Autorun.blot). Hierbei handelt es sich um eine Falschmeldung, wie uns die Firma AntiVir schriftlich bestätigte. Das Problem wird zumindest von AntiVir in einer der nächsten Versionen behoben sein. Dennoch ist ein sofortiges Eingreifen unter Windows erforderlich, indem einfach das RNA World Arbeitsverzeichnis in der Virenscannerkonfiguration von der Virensuche ausgenommen wird - zumindest solange, bis das Problem vom Hersteller behoben wurde. Hintergrund ist die ärgerliche Tatsache, dass sonst u.U. eine WU nach der anderen geschrottet werden kann. Generell gilt: RNA World versendet NIEMALS Malware. Vielen Dank an die Leute, die uns dieses Problem in unserem Forum gemeldet und somit dazu beigetragen haben, dass wir es aufklären und eine Lösung finden konnten.

    Michael.

    21 Aug 2010, 1:17:07 UTC · Comment

  • CMCALIBRATE WUs uploaded

    As announced, the second Rfam 10.0-based CMCALIBRATE WU set has been uploaded to the server and will be processed as soon as the current WU archive generation (CMSEARCH) has completed.

    Wie angekündigt wurde das zweite Rfam 10.0 basierte CMCALIBRATE WU Archiv auf den Server hochgeladen und wird ausgeliefert, sobald der Server die aktuelle WU-Generierung (CMSEARCH-Archiv) fertiggestellt hat.

    Michael.

    15 Aug 2010, 20:22:32 UTC · Comment

  • Final round of Rfam 10.0 CMCALIBRATE WUs

    The CMCALIBRATE WUs containing the Rfam 10.0 seed alignments have been almost finished, so we are planning to feed in the full alignments some time this weekend. Again, Linux x64 machines will be challenged. This time, the maximum run time (Intel P8600 CPU, 2.4 GHz) is an impressive 285 hours job - but as usual this one is an exception out of a total of 1445 tasks.

    Die "seed" Alignments der aktuellen Rfam 10.0 Version sind in recht kurzer Zeit nahezu komplettiert worden, sodass wir dieses Wochenende das Einspeisen der "full" Aligments angehen möchten. Auch dieses Mal werden angesichts des Rechenanspruchs nur Linux x64 Maschinen bedient. Wir rechnen mit einer maximalen Laufzeit von beeindruckenden 285 Stunden auf einem Intel P8600 Prozessor (2,4 GHz) - allerdings nur für eine von insgesamt 1445 WUs.
    Michael.

    13 Aug 2010, 0:55:01 UTC · Comment

  • Rfam 10.0 issue resolved, seed WUs released

    After resolving a small uncertainty with the latest Rfam database release, we have now prepared and uploaded novel work to the RNA World server for those who run Linux x64 machines. The maximum CMCALIBRATE run time of the current set of Rfam 10.0-based work units as estimated on an Intel P8600 CPU at 2.4 GHz is 72:50 (hh:mm). The vast majority of WUs, however, will take only around one hour (approx. 10 WUs out of a total of 1446 require run times above 20 hrs). I hope this is acceptable even without checkpointing.

    Nachdem die Unklarheit bezueglich eines Alignments in der 'seed' Version der neusten Rfam 10.0 Datenbank geklaert werden konnte, haben wir nun den angekuendigten Satz neuer CMACLIBRATE WUs auf den Server geladen. Die maximale Laufzeit - gemessen auf einem Intel P8600 Prozessor (2,4 GHz) - sollte 72:50 Stunden (ss:mm) dauern. Die Mehrheit der WUs liegt allerdings deutlich darunter und zwar bei ca. 1 Stunde Rechenzeit (ca. 10 WUs von genau 1446 liegen oberhalb von 20 Std.). Ich hoffe, das ist selbst ohne Checkpointing akzeptabel.

    Michael.

    30 Jul 2010, 21:44:27 UTC · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • New work

    As announced, the server is currently getting fed with new work.
    Michael.

    10 Feb 2010, 4:34:11 UTC · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • Additional work units loaded...

    ...today.
    Michael.

    7 Jan 2010, 14:56:17 UTC · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • 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 · Comment

  • science

    Applications are update to the newest Infernal version. We released also some workunits.

    18 Dec 2009, 19:44:00 UTC · Comment

  • science

    Update of project description.

    3 Dec 2009, 17:44:00 UTC · Comment

  • 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 · Comment

  • server update

    Server updated, will now create some test wus for all apps.

    6 Nov 2009, 18:16:00 UTC · Comment

  • server update

    Updating the Boinc server to the lates server_stable branch.

    6 Nov 2009, 16:20:00 UTC · Comment

  • app testing

    Testing the first application.

    29 May 2009, 13:50:00 UTC · Comment

  • Server setup

    Welcome to RNA World! The server is now setup and runs upperCASE.

    21 May 2009, 11:50:00 UTC · Comment



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