RNA World

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ashlynnjem
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Re: RNA World

Post by ashlynnjem » Tue Jul 13, 2010 1:15 pm

I just ran it for a week on both linux and windows machine.Work units vary from small to huge,while some taking 0.5-1.5 gig of ram.May finish in minutes,but some take 2 weeks with a 1 week deadline.Works lately has finished in seconds.I don't read German but its uses the same forums as Yoyo.

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Gavin Shaw
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Re: RNA World

Post by Gavin Shaw » Wed Jul 14, 2010 12:46 am

13 Jul 2010:

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.
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Gavin Shaw
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Re: RNA World

Post by Gavin Shaw » Mon Jul 26, 2010 3:47 am

25 Jul 2010:

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.
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Gavin Shaw
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Re: RNA World

Post by Gavin Shaw » Tue Jul 27, 2010 1:54 am

26 Jul 2010:

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.
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Re: RNA World

Post by Gavin Shaw » Sun Aug 01, 2010 1:04 am

30 Jul 2010:

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.
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Re: RNA World

Post by Gavin Shaw » Wed Aug 18, 2010 3:51 am

13 Aug 2010:

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.
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Re: RNA World

Post by Gavin Shaw » Wed Aug 18, 2010 3:51 am

15 Aug 2010:

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.
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Re: RNA World

Post by Gavin Shaw » Sat Aug 21, 2010 3:47 am

21 Aug 2010:

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.
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