August 2009 - binari@psb.ugent.be - maillist.psb.ugent.be

Re: [Binari] cluster problems of last 2 days
by Michiel Van Bel 14 Aug '09

14 Aug '09

Hall of shame! (not me though, i havent used the cluster in months) Frederik Delaere wrote: > Hi Cluster people, > > As you might have noticed there where cluster problems the last two days. > The partition where the grid engine is installed was full, I cleaned > it up but it was > full again in a couple of hours, which make the complete grid engine > fail, and jobs got lost. > > It took me a while to figure out what went wrong, but I found the > problem: > > somebody submitted a couple of 1000 jobs with a 2 megabyte parameter / > job > > eg: "qsub somejob.pl <insert 2 megabytes of parameters here>" > > grid engine stores all these commands while the jobs are in the queue, > it stores it on > its own partition and not somewhere on a data partition, the partition > went from > 21% usage to 99% usage in a couple of hours. To solve this, the jobs > had to be > changed to read these parameters from a file stored somewhere on the NAS. > > So in the future, tell new people about this, or it will happen again > some day. > > frederik > -- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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[Binari] lab t-shirts
by Tine Blomme 14 Aug '09

14 Aug '09

Hi, In the mail of Nathalie, there is an announcement for a presentation of Prof. Erin O'Shea. I just visited the website of her group, and they have a "fun section", where they present the t-shirts they have made for their group each year. Shouldn't we have that too? http://golgi.harvard.edu/O'Shea/fun_stuff/tshirts/index.html Tine °°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°° Tine Blomme Bioinformatics group VIB department of Plant Systems Biology Ghent University Technologiepark 927, B-9052 Zwijnaarde Tel: +32 (0)9 331 38 22

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[Binari] [Fwd: R2.9.1 on cluster]
by Lieven Sterck 13 Aug '09

13 Aug '09

R2D2 ? -------- Original Message -------- Subject: R2.9.1 on cluster Date: Thu, 13 Aug 2009 16:28:08 +0200 From: Dany Cuyt <dacuy(a)psb.vib-ugent.be> To: r(a)psb.ugent.be, Biocomp <biocomp(a)psb.vib-ugent.be> Please be notified that R2.9.1 (which is the latest version) is now available on the cluster. wkr, Dany -- ================================================================== Dany Cuyt Tel:+32 (0)9 331 38 17 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM dacuy(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ================================================================== -- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be ============================================================== "You tried your best and you failed miserably. The lesson is: never try!" - H. Simpson

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[Binari] [Fwd: cluster problems]
by Sofie Van Landeghem 13 Aug '09

13 Aug '09

This is the second fucking time that the cluster just goes down and kills jobs that have been running for a week or longer. With only 7 days to go untill my paper submission deadline, it's impossible to run the analyses again on time. What bothers me is how lightly they deal with it, they don't even tell you that running jobs stopped, or why the fuck it happened again. Shouldn't they at least try to garantee uptime? Backup systems? It's the bloody cluster ffs, not a playground. I know I should swear less, but this really pisses me off. Sofie -------- Originele bericht -------- Onderwerp: cluster problems Datum: Thu, 13 Aug 2009 09:49:39 +0200 Van: Frederik Delaere <frlae(a)psb.vib-ugent.be> Aan: Biocomp <biocomp(a)psb.vib-ugent.be> CC: Luc Van Wiemeersch <luwie(a)psb.vib-ugent.be> you can submit jobs again to the cluster frederik -- ================================================================== Frederik Delaere Tel:+32 (0)9 331 38 14 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM frlae(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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Re: [Binari] mexican flu - mexicaanse griep
by Michiel Van Bel 13 Aug '09

13 Aug '09

Anyone else having the impression they're taking the influenza scare a bit too far? Do they honestly think people are gonna wash their hands every hour or so? Only one way out people: all hail Nurgle (http://en.wikipedia.org/wiki/Chaos_(Warhammer)#Nurgle ) Yeah yeah, I've been playing Warhammer too much lately, I admit :-) René Custers wrote: > NL version below > > > Dear, > > This is to reinforce your attention to the possibilities of preventing a widespread outbreak of the mexican flu. The most important measures are correct hand hygiene and prevention of spreading the virus by sneezing. You will find the relevant instructions summarized on the poster attached. I have also included a poster on hand hygiene from our occupational health service. Please act accordingly. > > This information will remain available on the VIB intranet under the heading 'mexican flu'. When necessary new information will be added to this folder. > > I would also like to point out to you that the UGent already has been been active in preparing for and communicating about the mexican flu. You can find relevant information at http://www.ugent.be/nl/univgent/welzijnmilieu/gezondheid/loc_index > > > Beste, > > Met dit bericht willen we uw aandacht vestigen op de mogelijkheden om een weidverspreide epidemie van de mexicaanse griep te voorkomen. De belangrijkste preventiemaatregelen zijn een goede hand hygiène en voorkomen dat je het virus verspreidt dmv niezen. De belangrijkste instructies zijn samengevat op de bijgevoegde poster. Ik heb ook een poster over correcte hand hygiène toegevoegd afkomstig van onze arbeidsgeneeskundige dienst. Volg de instructies aub op. > > Deze informatie blijft beschikbaar op het VIB intranet onder de hoofding 'mexican flu'. Indien nodig zal nieuwe informatie aan deze folder worden toegevoegd. > > Ik wil er ook nog op wijzen dat de UGent ook al actief is geweest in de voorbereiding op en communicatie rond de mexicaanse griep. U kunt informatie hierover terugvinden op http://www.ugent.be/nl/univgent/welzijnmilieu/gezondheid/loc_index > > > René Custers > regulatory & communications manager > > VIB > Rijvisschestraat 120 > BE-9052 ZWIJNAARDE, Belgium > T +32 (0)9 2446611, M +32 (0)474 521340 > F +32 (0)9 2446610 > rene.custers(a)vib.be > www.vib.be > > > -- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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Re: [Binari] VIB Intranet certificate warning.
by Thomas Abeel 10 Aug '09

10 Aug '09

And exactly what's the point of this certificate? Learn people to ignore broken, outdated, and plain wrong certificates What about getting a proper one and using it for what it is meant to be used: security. -Thomas Helpdesk PSB wrote: > Dear All, > > If you encounter any problems accessing the VIB HQ Intranet site warning > about an expired certificate, please //follow the steps below to accept > a new certificate. > > 1. Click *Add Exception...* > 2. In the following dialog, click *Get Certificate*. > 3. Click *Confirm Security Exception*. > > A more detailes explenation will be provided on the IT & Help General Faq > > Kind regards, > > IT Support

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[Binari] psbmysql02 rip
by Joost Van Den Cruyce 10 Aug '09

10 Aug '09

Someone killed, or rather choked to death, psbsql2 by filling up it's hd. Prepare the wall in the hall? Joost -- ================================================================== Joost Van Den Cruyce Tel:+32 (0)9 331 38 92 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM jocru(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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Re: [Binari] Software.FastTree 2.0.0 for inferring large any experience?
by Sofie Van Landeghem 07 Aug '09

07 Aug '09

Who the fuck? Joris Meys wrote: > Dear all, > > I'm currently writing my master dissertation under the supervision of > Jens. I read the announcement of FastTree 2 in the mail this week, and > it would greatly help me, as I have to build a few thousand trees in a > rather short time frame. I'm not afraid of figuring out how it works > myself, but if anybody has some tips, they are greatly appreciated. > Thank you in advance > > Joris > > ------------------------------------------------------------------------ > > Subject: > [Fwd: Other: Software.FastTree 2.0.0 for inferring large] > From: > Yves Van de Peer <yves.vandepeer(a)psb.vib-ugent.be> > Date: > Sat, 01 Aug 2009 08:52:31 +0200 > To: > Bioinformatics & Evolutionary Genomics <beg(a)psb.ugent.be> > > To: > Bioinformatics & Evolutionary Genomics <beg(a)psb.ugent.be> > > > > > -------- Original Message -------- > Subject: Other: Software.FastTree 2.0.0 for inferring large > Date: Sat, 1 Aug 2009 02:40:28 -0400 (EDT) > From: evoldir(a)evol.biology.mcmaster.ca > Reply-To: brian(a)helix.biology.mcmaster.ca > To: yves.vandepeer(a)psb.ugent.be > > > > We announce FastTree 2, a tool for inferring approximately > maximum-likelihood trees for large alignments. FastTree is more > accurate than PhyML 3's default settings and 100-1,000 times faster > than PhyML or RAxML. FastTree analyzed an alignment of >200,000 16S > ribosomal RNAs in a day on a desktop computer. > > Models: Jukes-Cantor or GTR (nucleotide) or JTT (amino acid) > Rate variation across sites: the CAT approximation (1 rate per site) > Support values: local SH-like supports (or global bootstrap) > > FastTree 2 is available at > http://www.microbesonline.org/fasttree/ > > Morgan N. Price & Paramvir S. Dehal > Physical Biosciences Division > Lawrence Berkeley National Lab > fasttree(a)microbesonline.org > > > morgannprice(a)yahoo.com > > > -- Sofie Van Landeghem PhD Student VIB Department of Plant Systems Biology, Ghent University Bioinformatics and Evolutionary Genomics Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 36 95 fax:+32 (0)9 3313809 Website: http://bioinformatics.psb.ugent.be

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[Binari] Translator
by Thomas Van Parys 07 Aug '09

07 Aug '09

Ok, this is funny. The script translates a sentence back and forth between English and Japanese, until an equilibrium is found. I suggest you try at least "May the force be with you". T. -- ================================================================== Thomas Van Parys Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM thomas.vanparys(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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[Binari] today's poll on the redactie.be
by Tine Blomme 07 Aug '09

07 Aug '09

De socialenetwerksite Facebook trekt steeds meer 55-plussers aan. Een reden voor heel wat jongeren -kinderen of kleinkinderen van de "nieuwe" Facebook-leden- om de site de rug toe te keren. Bent u Facebook ontvlucht omdat uw (groot)ouders erop zitten? -- ================================================================== Tine Blomme Tel:+32 (0)9 331 38 22 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM tiblo(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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