- Isis-fish-devel - mailman.cloud.codelutin.com

Suppression du dossier "isis-export"
by Eric Chatellier 02 Dec '09

02 Dec '09

Bonjour, À partir de IsisFish 3.3.0.0 le dossier "isis-export" (situé a coté de isis-database-3) n'existera plus. Il ne semblait pas être utilisé pas beaucoup de monde, et fesait doublon avec les exports dans chaque simulation ce qui doublait l'espace disque utilisé. Concernant le dev, le dossier "isis-export" servait aussi a stocker les résultats : - de la seconde passe de l'analyse de sensibilité - les fichier .Rdata Peut-on les déplacer dans "isis-database-3/simulations" ? Pour la seconde passe ça fera apparaître en plus une simulation qui n'en ai pas vraiment une dans la liste des anciennes simulations. -- Éric <chatellier(a)codelutin.com> Tel: 02 40 50 29 28 http://www.codelutin.com

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Re: [Isis-fish-devel] [Rd] Bug in R evaluating a huge instruction (PR#14096)
by Jean Couteau 02 Dec '09

02 Dec '09

> FWIW the restriction is only on the console input - if you send it > directly, there is no limit (I have never heard of nuiton-j2r but if > you use rJava to interface from Java to R there is no limit - the > string you parse+evaluate can be of any length). Hi Simon, nuiton-j2r is in fact an abstraction layer to rjava or rserve so that it can switch between one or other implementation using simple configuration (http://maven-site.nuiton.org/nuiton-j2r/ sorry but this is in french). And in fact I encounter the problem using it. What is done is basically creating the R instruction from java and sending it to R using the eval method from the Rengine object (as we use jri in this specific application). The R instruction should create an object a of class morris, and I try then to get back the a$X object (the X item of the morris object) but I get back a null object without any reason, that is why I tried copying the instruction directly in R and thus getting this problem. So that is strange if you say that there is no limit using rjava/jri. Cheers, Jean > > Cheers, > Simon > > >> Duncan Murdoch wrote: >>> On 01/12/2009 12:50 AM, Jean Couteau wrote: >>>> Thanks for your time Duncan, >>>> >>>> I join here the instruction that is not correct, hoping that might >>>> help you. The file is encoded in utf-8 so you should not have any >>>> problem reading it. >>>> >>>> I doubt to that it is an R bug too, but with all my tests i am less >>>> and less sure of that. >>> >>> I have no problem sourcing that file, but I do get an error if I try >>> to cut and paste it, because it's a single line of 4890 characters, >>> and that's too long. So this is an R limitation, but it's one with >>> an easy workaround: just add some line breaks into your source. >>> >>> Duncan Murdoch >>> >>> >>>> >>>> Best regards, >>>> Jean Couteau >>>>> Your message has encoding problems, so it's not readable. Could >>>>> you put the code online somewhere where we could download it in >>>>> its original form? I doubt if this is an R bug, but I can't point >>>>> out the problem in your code (or confirm that it really is an R >>>>> bug) without an undamaged copy of the code. >>>>> >>>>> Duncan Murdoch >>>>> >>>>> >>>>> >>>> >>> >>> >> >> ______________________________________________ >> R-devel(a)r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> >> > >

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Re: [Isis-fish-devel] [Rd] Bug in R evaluating a huge instruction (PR#14096)
by Jean Couteau 02 Dec '09

02 Dec '09

Thank you very much for your input Duncan and Romain. I will try to do what you are advising. The R instruction is generated from java using jri (and an abstraction layer we built upon it : nuiton-j2r), i will try add this limitation to nuiton-j2r so that it split the instruction if it is too long. Best regards, Jean Duncan Murdoch wrote: > On 01/12/2009 12:50 AM, Jean Couteau wrote: >> Thanks for your time Duncan, >> >> I join here the instruction that is not correct, hoping that might >> help you. The file is encoded in utf-8 so you should not have any >> problem reading it. >> >> I doubt to that it is an R bug too, but with all my tests i am less >> and less sure of that. > > I have no problem sourcing that file, but I do get an error if I try > to cut and paste it, because it's a single line of 4890 characters, > and that's too long. So this is an R limitation, but it's one with an > easy workaround: just add some line breaks into your source. > > Duncan Murdoch > > >> >> Best regards, >> Jean Couteau >>> Your message has encoding problems, so it's not readable. Could you >>> put the code online somewhere where we could download it in its >>> original form? I doubt if this is an R bug, but I can't point out >>> the problem in your code (or confirm that it really is an R bug) >>> without an undamaged copy of the code. >>> >>> Duncan Murdoch >>> >>> >>> >> > >

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Bug in R evaluating a huge instruction
by Jean Couteau 01 Dec '09

01 Dec '09

Hello, I do not know if i am facing a bug or a mistake (and if it is a bug i do not know in which category I can put it on the bug tracker), so I post my message here. I am trying to use the Morris function from the sensitivity package (but that is not the problem). I created a (big) instruction that should generate a morris object in which there is a data.frame i am interested in. My instruction is : a<-morris(model=NULL,factors=c("PecheAmateurs décembre.proportionMetier","PechePetitMetierMer mai.proportionMetier","PecheAmateurs mai.proportionMetier","PecheChalutiere janvier.minInactivityDays","PechePetitMetierEtang octobre.minInactivityDays","PechePetitMetierEtang décembre.minInactivityDays","FiletMer.standardisationFactor","PecheAmateurs juin.minInactivityDays","PechePetitMetierEtang novembre.minInactivityDays","PechePetitMetierMer septembre.minInactivityDays","PechePetitMetierMer avril.minInactivityDays","PecheAmateurs août.proportionMetier","PecheChalutiere novembre.minInactivityDays","PechePetitMetierMer février.proportionMetier","PecheChalutiere juillet.minInactivityDays","PechePetitMetierMer octobre.proportionMetier","CSar Groupe 5.reproductionRate","PechePetitMetierMer août.proportionMetier","PechePetitMetierMer janvier.minInactivityDays","PechePetitMetierEtang mai.minInactivityDays","PecheAmateurs octobre.minInactivityDays","PecheAmateurs septembre.minInactivityDays","PecheChalutiere juin.minInactivityDays","PecheChalutiere avril.minInactivityDays","PecheAmateurs juillet.proportionMetier","PecheChalutiere mai.minInactivityDays","PechePetitMetierEtang septembre.minInactivityDays","PechePetitMetierMer janvier.proportionMetier","PecheAmateurs septembre.proportionMetier","PechePetitMetierEtang février.minInactivityDays","PechePetitMetierEtang mars.minInactivityDays","PechePetitMetierEtang juillet.minInactivityDays","PechePetitMetierMer septembre.proportionMetier","CSar.capturability","PechePetitMetierMer juin.proportionMetier","PecheChalutiere mars.minInactivityDays","PecheChalutiere septembre.minInactivityDays","PecheAmateurs janvier.minInactivityDays","PechePetitMetierMer août.minInactivityDays","PechePetitMetierMer juillet.proportionMetier","PecheChalutiere décembre.minInactivityDays","PecheAmateurs avril.minInactivityDays","PecheAmateurs mars.proportionMetier","PechePetitMetierMer novembre.minInactivityDays","PechePetitMetierEtang août.minInactivityDays","CSar.recruitmentDistribution","PecheChalutiere février.minInactivityDays","CSar.naturalDeathRate","PecheAmateurs octobre.proportionMetier","PechePetitMetierMer mai.minInactivityDays","PechePetitMetierMer mars.proportionMetier","PecheAmateurs août.minInactivityDays","FiletEtang.standardisationFactor","PecheChalutiere août.minInactivityDays","PecheAmateurs janvier.proportionMetier","PecheAmateurs décembre.minInactivityDays","PechePetitMetierEtang avril.minInactivityDays","PecheAmateurs mars.minInactivityDays","PechePetitMetierMer décembre.minInactivityDays","PecheAmateurs mai.minInactivityDays","PechePetitMetierEtang juin.minInactivityDays","Harpon.standardisationFactor","PecheAmateurs novembre.minInactivityDays","PecheAmateurs novembre.proportionMetier","PechePetitMetierMer mars.minInactivityDays","Ligneemb.standardisationFactor","PecheAmateurs juin.proportionMetier","PecheAmateurs avril.proportionMetier","PechePetitMetierMer juillet.minInactivityDays","PechePetitMetierMer avril.proportionMetier","PechePetitMetierMer octobre.minInactivityDays","PechePetitMetierMer février.minInactivityDays","PecheAmateurs juillet.minInactivityDays","PechePetitMetierMer décembre.proportionMetier","PecheAmateurs février.proportionMetier","PecheChalutiere octobre.minInactivityDays","CSar Groupe 4.reproductionRate","CSar Groupe 7.reproductionRate","Lignecote.standardisationFactor","CSar.meanWeight","CSar Groupe 6.reproductionRate","PechePetitMetierMer juin.minInactivityDays","PechePetitMetierMer novembre.proportionMetier","PechePetitMetierEtang janvier.minInactivityDays","PecheAmateurs février.minInactivityDays","CSar.growth"),r=10,design=list(type="oat",levels=c(5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5),grid.jump=c(2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2)),binf=c(0.0,0.0,0.0,11.0,10.0,12.0,0.06,10.0,11.0,0.0,0.0,0.0,10.0,0.0,11.0,0.0,1120.0,0.0,10.0,22.0,12.0,10.0,10.0,11.0,0.0,11.0,15.0,0.0,0.0,23.0,16.0,22.0,0.0,0.0,0.0,11.0,10.0,18.0,0.0,0.0,11.0,11.0,0.0,3.0,22.0,0.0,8.0,0.0,0.0,0.0,0.0,8.0,0.1456,11.0,0.0,18.0,17.0,11.0,7.0,11.0,20.0,0.0464,16.0,0.0,1.0,0.1515,0.0,0.0,0.0,0.0,1.0,11.0,9.0,0.0,0.0,11.0,1120.0,1120.0,0.0749,0.0,1120.0,0.0,0.0,13.0,16.0,0.0),bsup=c(1.0,1.0,1.0,15.0,14.0,16.0,0.09,14.0,15.0,2.0,2.0,1.0,14.0,1.0,15.0,1.0,1680.0,1.0,14.0,26.0,16.0,14.0,14.0,14.0,1.0,15.0,19.0,1.0,1.0,27.0,20.0,26.0,1.0,1.0,1.0,15.0,14.0,22.0,2.0,1.0,15.0,15.0,1.0,7.0,26.0,1.0,12.0,1.0,1.0,2.0,1.0,12.0,0.2184,15.0,1.0,22.0,21.0,15.0,11.0,15.0,24.0,0.0696,20.0,1.0,5.0,0.22,1.0,1.0,2.0,1.0,5.0,15.0,13.0,1.0,1.0,15.0,1680.0,1680.0,0.11244,1.0,1680.0,2.0,1.0,17.0,20.0,1.0)) I checked several times and this intruction seams to have the right syntax but R asks me to finish my instruction (I need to add two parenthesis at the end so that it can be evaluated, but do not give me the right results). I replaced the factors vector by its size (the morris method allows that) and the evaluation is ok (with right results). I tryed also replacing the binf and bsup vectors by a single value (authorized by the morris function also), leaving the factors vector, and the evaluation is also ok (so it is not the factors vector that is creating the problem). This seems really odd to me and I cannot see where is the problem so I am thinking about a R bug (even if the sensitivity package is not loaded, i cannot enter the instruction, thus it is not a sensitivity problem). Did somebody already encountered such a bug (if it is a bug) ? I am using R 2.9.2 under linux/Xubuntu 9.10 and this has also been tried on R 2.9.0 on Windows 7. I can provide more info if needed. Jean Couteau Code Lutin

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Unable to connect to Caparmor
by Jean Couteau 30 Nov '09

30 Nov '09

Tina, I am at Ifremer now and I am trying to connect to Caparmor, but the connection is closed right after login and i cannot do anything. Is there a problem with Caparmor or is this my computer or something ? Here is the reponse of my ssh command : ssh poussin@caparmor Last login: Mon Nov 30 09:07:08 2009 from na54-126.ifremer.fr Connection to caparmor closed. Thanks in advance for your help Jean Couteau Code Lutin

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Fw: croquis poue isis fish
by Benjamin POUSSIN 20 Nov '09

20 Nov '09

Salut, voila quelques proposition d'emilie. A vos remarques je lui ferais suivre. ----- Message Transféré ----- Date: Wed, 18 Nov 2009 23:19:03 +0100 (CET) De: Emilie MAISONHAUTE À: poussin(a)codelutin.com Sujet: croquis poue isis fish voila des petites recherches pour vendredi tout peut être modifié compo, mélange avec les 4 propositions, couleurs... je commençais d'autres recherches avec des pélicans..mais j'ai pas le temps de les travailler pour vendredi . bonne journée milie -- Benjamin -------------------- tél: +33 (0) 2 40 50 29 28 email: poussin(a)codelutin.com () campagne du ruban ascii http://www.codelutin.com /\ pour les mails en ascii

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Re: [Isis-fish-devel] question: java
by Eric Chatellier 17 Nov '09

17 Nov '09

Le 12/11/2009 09:49, Tina ODAKA a écrit : > hello eric jean benjamin, Hi, Sorry for the long response delay :-( > i was talking with sgi about that your code is slow. > they asked me one thing >> JAVA : >> Ce language se base sur une machine virtuelle qui fait la génération >> des instruction à la volée. Les langages interprétés ne sont pas >> performant par définition. Il doit être possible de générer une >> version "compilée" du code Java qui doit apporter de meilleurs >> performances. > i guess your code is 'version "compilée"', isn't it? IsisFish code is "pre-compiled" into java bytecode [1]. This bytecode is interpreted by the Java virtual machine at runtime. Next, Java use JIT compilation [2], to improve runtime performance. So, Java isn't slow, and run as fast as native compiled programs, or maybe even faster ;-) > tina [1] : http://en.wikipedia.org/wiki/Bytecode [2] : http://en.wikipedia.org/wiki/Just-in-time_compilation -- Éric <chatellier(a)codelutin.com> Tel: 02 40 50 29 28 http://www.codelutin.com

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Utilisation des jobs multiples caparmor par IsisFish
by Eric Chatellier 16 Nov '09

16 Nov '09

Bonjour, Si les tests sur l'utilisation des multijobs caparmor vous semble satisfaisant, je suis près à faire la modification dans IsisFish. La modification n'est cependant pas évidente. Au niveau du lanceur de simulations caparmor, différent cas sont à prévoir : - simulation simple (envoi d'un script unique) - simulation issue d'un plan indépendant (pas d'envoi de script) - dernière simulation issue d'un plan indépendant (envoi d'un script multiple) - simulation issue d'un plan dépendant (envoi d'un script unique) - simulation issue d'une AS (pas d'envoi de script) - dernière simulation issue d'une AS (envoi d'un script multiple) Ou peut-être que le "plan" peut jouer un rôle en envoyant des infos supplémentaire au lanceur de simulation. -- Éric <chatellier(a)codelutin.com> Tel: 02 40 50 29 28 http://www.codelutin.com

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Ajout de nouveaux formats de cartes
by Eric Chatellier 13 Nov '09

13 Nov '09

Bonjour, Je suis en train d'ajouter les nouveaux formats de cartes dans isis-fish, cependant, je ne trouve pas facilement des cartes pour tester ces formats. Auriez vous des cartes de tests dans les formats suivants : - "Digital Chart of the World (.dcw)" - "Vector Product Format (.vpf)" - "Vector Map (.vmap)" - "Compressed ARC Digitized Raster Graphics (.cadrg)" - "Controlled Image Base (.cib)" - "Raster Product Format (.rpf)" - "Digital Terrain Elevation Data (levels 0, 1, 2) (.dt0, .dt0, .dt2)" - "MapInfo (.mif)" - "ArcInfo (.e00)" Ou plus généralement, des sites de références pour trouver des cartes. Merci. -- Éric <chatellier(a)codelutin.com> Tel: 02 40 50 29 28 http://www.codelutin.com

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Isis-Fish 3.2.0.10 est disponible.
by Eric Chatellier 12 Nov '09

12 Nov '09

Bonjour, Une nouvelle version d'Isis-Fish est disponible au téléchargement à l'adresse : http://isis-fish.labs.libre-entreprise.org/wiki-moin/instance/cgi-bin/moin.… Cette version - corrige un problème dans la génération des plans dépendants pour les lanceurs caparmor et sous processus - augmente la mémoire utilisée par les jobs sur caparmor (2Go) Le changelog complet est disponible à l'adresse : http://isis-fish.labs.libre-entreprise.org/wiki-moin/instance/cgi-bin/moin.… -- Éric <chatellier(a)codelutin.com> Tel: 02 40 50 29 28 http://www.codelutin.com

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