December 2013 - Isis-fish-users - mailman.cloud.codelutin.com

Journées ISIS-Fish : c'est NOS journées ! ;-)
by Sigrid Lehuta Jan. 24, 2014

Jan. 24, 2014

Hello, Pour vous rappeler que ces journées, c'est l'occasion de faire remonter les questions, problèmes et demandes en live et d'obtenir des explications sur ce que vous voulez. Alors n'hésitez pas à préparer vos listes de doléances, on sera là pour ça ! A jeudi !

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Simulations arrêtées en cours
by Loic GASCHE Jan. 7, 2014

Jan. 7, 2014

Bonjour, J'ai lancé vendredi soir des simulations sur caparmor, et celles-ci semblent toutes arrêtées en cours de simulation ce matin. Je les ai lancées avec la version 4.2.1.2 d'ISIS car la méthode que je voulais utiliser (LHS) ne nous permet pas de faire d'AS sur les matrices qu' Eric à rendues accessibles dans la 4.2.1.3. J'ai recu environ un millier de messages d'erreur de caparmor concernant la "job performance" de mes simus. Dans les premiers messages reçus, cette "job performance" est de 0.72, puis elle décroit progressivement au cours du temps. Dans les derniers messages elle est au mieux à 0.05. J'ai mis en PJ l'état d'avancement des simus tel qu'on peut le voir dans l'interface ISIS. Comme elles sont sensées tourner 16 par 16 sur caparmor on voit que de nouvelles simulations ont été lancées alors que les précédentes n'étaient pas sensées être terminées. Un autre point surprenant est que toutes les simus ne s'arrêtent pas au même pas de temps. La plupart s'arrêtent à l'année 4, mais pas forcément au même mois, et certaines vont jusqu'en Décembre 11 s'arrêtent à l'export des résultats.. J'ai mis une capture d'écran de l'interface d'ISIS où on voit l'état des simus et une de la configuration pour caparmor, au cas où j'aurais encore fait une bêtise de ce côté là. Une idée de la cause du problème, et de comment le résoudre ? Loïc

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Ressources Isis-fish
by Postmaster ISIS-Fish Dec. 31, 2013

Dec. 31, 2013

Amis utilisateurs d'ISIS-Fish, Ce mail automatique, envoyé tous les 3 mois sur les listes de diffusions du projet, a pour but de vous rappeler toutes les ressources disponibles pour toutes vos éventuelles questions et problèmes. Documentation et manuel utilisateurs ------------------------------------ La documentation d'ISIS-Fish est présente sur le site à cette adresse : http://isis-fish.org/v4/index.html. N'hésitez pas à nous remonter les parties qui ne sont pas claires ou les parties qui ne sont pas à jour, le logiciel évoluant, certaines parties de la documentation sont peut-être obsolètes. Questions et FAQ ---------------- Vous pouvez poser vos questions à cette même liste de diffusion en envoyant un mail à isis-fish-users(a)list.isis-fish.org. Toutes les personnes abonnées le recevront et pourront répondre à vos éventuelles questions. N'oubliez pas, avant de poser votre question, de rechercher parmis les archives de la liste (http://list.isis-fish.org/pipermail/isis-fish-users/) votre question a peut-être déjà été posée. Les questions les plus fréquemment posées sont regroupées sur le site sur la page FAQ : http://isis-fish.org/v4/user/FAQ.html Forge, rapports de bug, suivi des évolutions -------------------------------------------- Si vous rencontrez un bug, vous pouvez vérifier sur la forge ISIS-Fish (http://forge.codelutin.com/projects/isis-fish/issues) si nous en avons déjà connaissance. Si nous n'en avons pas connaissance, vous pouvez nous rapporter le bug, nous l'intègrerons dans la liste des évolutions prévues (http://forge.codelutin.com/projects/isis-fish/roadmap) Pour rapporter un bug (ou une demande d'évolution), donnez nous le maximum de détails sur ce bug (comment vous l'avez obtenu ? votre base, vos paramètres et le fichier debug.txt). Plus nous avons d'informations, plus nous pourrons vous aider simplement. L'équipe ISIS-Fish

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Fwd: Re: Fwd: Re: Fwd: Re: HelpDesk Nv3 / n°=191007 : Re: Accès à plus de coeurs sur caparmor ?
by Loic GASCHE Dec. 17, 2013

Dec. 17, 2013

Bonjour, Il apparait qu'il y a eu une mauvaise compréhension entre l'assistance de l'IFREMER et nous concernant les queues qui peuvent être utilisées par ISIS sur caparmor : - On ne peut toujours pas utiliser les queues "parallel" avec ISIS. - Il existe bien une queue spéciale pour ISIS "isisfish" qui permet de faire tourner ses simus sur plus de 16 coeurs à la fois, MAIS chaque simu sur cette queue doit durer moins de dix minutes. - Donc la seule solution pour le moment pour les grosses simus est d'utiliser la queue par défaut "sequentiel" qui a 16 coeurs. Tina a jeté un coup d'oeil à mes simus sur cette queue et trouve qu'on n'utilise pas toute la puissance du processeur. En particulier, elle trouve des "futex wait" et demande si c'est normal. Voici son message : -------- Message original -------- Sujet: Re: Fwd: Re: [Isis-fish-users] Fwd: Re: HelpDesk Nv3 / n°=191007 : Re: Accès à plus de coeurs sur caparmor ? Date : Tue, 17 Dec 2013 11:08:40 +0100 De : Tina ODAKA <Tina.Odaka(a)ifremer.fr> Organisation : IFREMER Pour : Loic GASCHE <Loic.Gasche(a)ifremer.fr> hi, i checked your jobid "0" you have 56 min of walltime where as CPU was only used for 43 minutes; i.e. it only use about 75% of cpu power. I tried to to strace on your java process, and i do not know what it is waiting, but i saw a lot of "futex wait" can you ask code-lutin if it is normal?? what i did is checking your java process's system call. lgasche 29123 29100 78 09:08 ? 00:45:56 /home3/caparmor/poussin/jdk64/bin/java -Djava.library.path=jri64 -DR.type=jni -Xmx3000M -jar isis-fish-4.2.1.2.jar --option launch.ui false --option perform.vcsupdate false --option perform.migration false --option perform.cron false --simulateRemotellyWithPreScript as_7DV10_toutesRegles_SansCantonnements_ParamsPrincipaux_2013-12-17-10-08_1 /home1/caparmor/lgasche/isis-tmp/simulation-as_7DV10_toutesRegles_SansCantonnements_ParamsPrincipaux_2013-12-17-10-08-preparation.zip /home1/caparmor/lgasche/isis-tmp/simulation-as_7DV10_toutesRegles_SansCantonnements_ParamsPrincipaux_2013-12-17-10-08_1-result.zip /home1/caparmor/lgasche/isis-tmp/simulation-as_7DV10_toutesRegles_SansCantonnements_ParamsPrincipaux_2013-12-17-10-08_1-prescript.bsh r5i0n0:~ # strace -p 29123 -f [pid 29249] sched_yield( <unfinished ...> [pid 29243] futex(0x4012ed28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29236] sched_yield( <unfinished ...> [pid 29228] <... sched_yield resumed> ) = 0 [pid 29249] <... sched_yield resumed> ) = 0 [pid 29243] <... futex resumed> ) = 0 [pid 29240] <... sched_yield resumed> ) = 0 [pid 29236] <... sched_yield resumed> ) = 0 [pid 29233] sched_yield( <unfinished ...> [pid 29228] sched_yield( <unfinished ...> [pid 29222] sched_yield( <unfinished ...> [pid 29249] sched_yield( <unfinished ...> [pid 29243] futex(0x2afb140008b4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x2afb140008b0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29249] <... sched_yield resumed> ) = 0 [pid 29245] <... futex resumed> ) = 0 [pid 29243] <... futex resumed> ) = 1 [pid 29245] futex(0x40130a28, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29240] sched_yield( <unfinished ...> [pid 29236] sched_yield( <unfinished ...> [pid 29240] <... sched_yield resumed> ) = 0 [pid 29233] <... sched_yield resumed> ) = 0 [pid 29228] <... sched_yield resumed> ) = 0 [pid 29222] <... sched_yield resumed> ) = 0 [pid 29249] sched_yield( <unfinished ...> [pid 29243] futex(0x40130a28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29240] sched_yield( <unfinished ...> [pid 29249] <... sched_yield resumed> ) = 0 [pid 29236] <... sched_yield resumed> ) = 0 [pid 29228] sched_yield( <unfinished ...> [pid 29222] sched_yield( <unfinished ...> [pid 29249] sched_yield( <unfinished ...> [pid 29245] <... futex resumed> ) = 0 [pid 29249] <... sched_yield resumed> ) = 0 [pid 29245] futex(0x40130a28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29243] <... futex resumed> ) = 1 [pid 29245] <... futex resumed> ) = 0 [pid 29240] <... sched_yield resumed> ) = 0 [pid 29236] sched_yield( <unfinished ...> [pid 29233] sched_yield( <unfinished ...> [pid 29228] <... sched_yield resumed> ) = 0 [pid 29222] <... sched_yield resumed> ) = 0 [pid 29249] futex(0x40132d24, FUTEX_WAIT_PRIVATE, 50941, NULL <unfinished ...> [pid 29243] futex(0x40130fb4, FUTEX_WAIT_PRIVATE, 50909, NULL <unfinished ...> [pid 29245] futex(0x2afb140008b4, FUTEX_WAIT_PRIVATE, 50671, NULL <unfinished ...> [pid 29240] futex(0x4012f244, FUTEX_WAIT_PRIVATE, 50727, NULL <unfinished ...> [pid 29236] <... sched_yield resumed> ) = 0 [pid 29233] <... sched_yield resumed> ) = 0 [pid 29228] futex(0x401299f4, FUTEX_WAIT_PRIVATE, 51249, NULL <unfinished ...> [pid 29233] futex(0x4012b764, FUTEX_WAIT_PRIVATE, 50907, NULL <unfinished ...> [pid 29222] futex(0x40132d24, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x40132d20, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29249] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29222] <... futex resumed> ) = 0 [pid 29249] futex(0x40132728, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29222] futex(0x40127c84, FUTEX_WAIT_PRIVATE, 50875, NULL <unfinished ...> [pid 29249] <... futex resumed> ) = 0 [pid 29249] futex(0x40130fb4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x40130fb0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29243] <... futex resumed> ) = 0 [pid 29249] futex(0x4012ed28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29243] futex(0x4012ed28, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29249] <... futex resumed> ) = 0 [pid 29243] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29249] futex(0x40132d24, FUTEX_WAIT_PRIVATE, 50943, NULL <unfinished ...> [pid 29243] futex(0x4012ed28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29243] futex(0x4012f244, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4012f240, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29240] <... futex resumed> ) = 0 [pid 29236] futex(0x4012b7a4, FUTEX_WAIT_PRIVATE, 51125, NULL <unfinished ...> [pid 29243] <... futex resumed> ) = 1 [pid 29240] futex(0x4012cf28, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29243] futex(0x4012cf28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29240] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29243] futex(0x40130fb4, FUTEX_WAIT_PRIVATE, 50911, NULL <unfinished ...> [pid 29240] futex(0x4012cf28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29240] futex(0x2afb140008b4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x2afb140008b0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29245] <... futex resumed> ) = 0 [pid 29240] <... futex resumed> ) = 1 [pid 29245] futex(0x40130a28, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29240] futex(0x40130a28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29245] <... futex resumed> ) = 0 [pid 29240] <... futex resumed> ) = 1 [pid 29245] futex(0x40130a28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29245] futex(0x401299f4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x401299f0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29228] <... futex resumed> ) = 0 [pid 29245] futex(0x2afb140008b4, FUTEX_WAIT_PRIVATE, 50673, NULL <unfinished ...> [pid 29228] futex(0x40127728, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29240] futex(0x4012f244, FUTEX_WAIT_PRIVATE, 50729, NULL <unfinished ...> [pid 29228] <... futex resumed> ) = 0 [pid 29228] futex(0x4012b764, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4012b760, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29233] <... futex resumed> ) = 0 [pid 29228] <... futex resumed> ) = 1 [pid 29233] futex(0x40129428, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29228] futex(0x40129428, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29233] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29228] <... futex resumed> ) = 0 [pid 29233] futex(0x40129428, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29228] futex(0x401299f4, FUTEX_WAIT_PRIVATE, 51251, NULL <unfinished ...> [pid 29233] <... futex resumed> ) = 0 [pid 29233] futex(0x40127c84, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x40127c80, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29222] <... futex resumed> ) = 0 [pid 29233] futex(0x4012b764, FUTEX_WAIT_PRIVATE, 50909, NULL <unfinished ...> [pid 29222] futex(0x40125928, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29222] futex(0x40132d24, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x40132d20, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29249] <... futex resumed> ) = 0 [pid 29222] <... futex resumed> ) = 1 [pid 29249] futex(0x40132728, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29222] futex(0x40132728, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29249] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29222] <... futex resumed> ) = 0 [pid 29249] futex(0x40132728, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29222] futex(0x40127c84, FUTEX_WAIT_PRIVATE, 50877, NULL <unfinished ...> [pid 29249] <... futex resumed> ) = 0 [pid 29249] futex(0x40130fb4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x40130fb0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29243] <... futex resumed> ) = 0 [pid 29249] futex(0x4019f884, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4019f880, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29243] futex(0x4012ed28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29256] <... futex resumed> ) = 0 [pid 29249] <... futex resumed> ) = 1 [pid 29256] futex(0x4019f128, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29249] futex(0x4019f128, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29256] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29249] <... futex resumed> ) = 0 [pid 29256] futex(0x4019f128, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29249] futex(0x40132d24, FUTEX_WAIT_PRIVATE, 50945, NULL <unfinished ...> [pid 29256] <... futex resumed> ) = 0 [pid 29243] <... futex resumed> ) = 0 [pid 29243] futex(0x4012b7a4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4012b7a0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29236] <... futex resumed> ) = 0 [pid 29243] futex(0x40130fb4, FUTEX_WAIT_PRIVATE, 50913, NULL <unfinished ...> [pid 29236] futex(0x4012b228, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29236] futex(0x4012f244, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4012f240, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29240] <... futex resumed> ) = 0 [pid 29236] <... futex resumed> ) = 1 [pid 29240] futex(0x4012cf28, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29236] futex(0x4012cf28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29240] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29236] <... futex resumed> ) = 0 [pid 29240] futex(0x4012cf28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29236] futex(0x4012b7a4, FUTEX_WAIT_PRIVATE, 51127, NULL <unfinished ...> [pid 29240] <... futex resumed> ) = 0 [pid 29240] futex(0x2afb140008b4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x2afb140008b0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29245] <... futex resumed> ) = 0 [pid 29240] <... futex resumed> ) = 1 [pid 29245] futex(0x40130a28, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29240] futex(0x40130a28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29245] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29240] <... futex resumed> ) = 0 [pid 29245] futex(0x40130a28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29240] futex(0x4012f244, FUTEX_WAIT_PRIVATE, 50731, NULL <unfinished ...> [pid 29245] <... futex resumed> ) = 0 [pid 29245] futex(0x401299f4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x401299f0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29228] <... futex resumed> ) = 0 [pid 29245] futex(0x2afb140008b4, FUTEX_WAIT_PRIVATE, 50675, NULL <unfinished ...> [pid 29228] futex(0x40127728, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29228] futex(0x4012b764, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4012b760, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29233] <... futex resumed> ) = 0 [pid 29228] futex(0x401299f4, FUTEX_WAIT_PRIVATE, 51253, NULL <unfinished ...> [pid 29233] futex(0x40129428, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29233] futex(0x40127c84, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x40127c80, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29222] <... futex resumed> ) = 0 [pid 29233] futex(0x4012b764, FUTEX_WAIT_PRIVATE, 50911, NULL <unfinished ...> [pid 29222] futex(0x40125928, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29222] futex(0x40127c84, FUTEX_WAIT_PRIVATE, 50879, NULL <unfinished ...> [pid 29296] <... futex resumed> ) = -1 ETIMEDOUT (Connection timed out) [pid 29296] futex(0x2afb1402ee28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29296] futex(0x4179ee94, 0x189 /* FUTEX_??? */, 1, {1387274027, 162380000}, ffffffff) = -1 ETIMEDOUT (Connection timed out) [pid 29296] futex(0x2afb1402ee28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29296] futex(0x4179ee94, 0x189 /* FUTEX_??? */, 1, {1387274027, 212506000}, ffffffff) = -1 ETIMEDOUT (Connection timed out) [pid 29296] futex(0x2afb1402ee28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29296] futex(0x4179ee94, 0x189 /* FUTEX_??? */, 1, {1387274027, 262659000}, ffffffff) = -1 ETIMEDOUT (Connection timed out) [pid 29296] futex(0x2afb1402ee28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29296] futex(0x4179ee94, 0x189 /* FUTEX_??? */, 1, {1387274027, 312820000}, ffffffff <unfinished ...> [pid 29256] mprotect(0x2afb0bbe0000, 4096, PROT_READ) = 0 [pid 29256] futex(0x401ec634, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x401ec630, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29411] <... futex resumed> ) = 0 [pid 29411] futex(0x41b25828, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29256] futex(0x4019f884, 0x189 /* FUTEX_??? */, 25587, {1387274028, 305424000}, ffffffff <unfinished ...> [pid 29411] <... futex resumed> ) = 0 [pid 29411] futex(0x401ae004, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x401ae000, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29262] <... futex resumed> ) = 0 [pid 29411] futex(0x2afb2357b984, 0x189 /* FUTEX_??? */, 1, {1387274027, 405532000}, ffffffff <unfinished ...> [pid 29262] futex(0x401a5e28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29262] futex(0x401ae004, FUTEX_WAIT_PRIVATE, 77, NULL <unfinished ...> [pid 29296] <... futex resumed> ) = -1 ETIMEDOUT (Connection timed out) [pid 29296] futex(0x2afb1402ee28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29296] futex(0x4179ee94, 0x189 /* FUTEX_??? */, 1, {1387274027, 362969000}, ffffffff) = -1 ETIMEDOUT (Connection timed out) [pid 29296] futex(0x2afb1402ee28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29296] futex(0x4179ee94, 0x189 /* FUTEX_??? */, 1, {1387274027, 413120000}, ffffffff <unfinished ...> [pid 29411] <... futex resumed> ) = -1 ETIMEDOUT (Connection timed out) [pid 29411] futex(0x4229a828, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29411] futex(0x4019f884, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4019f880, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29411] futex(0x401ec634, FUTEX_WAIT_PRIVATE, 8799, NULL <unfinished ...> [pid 29256] <... futex resumed> ) = 0 [pid 29256] futex(0x4019f128, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29256] mprotect(0x2afb0bbe1000, 4096, PROT_READ) = 0 [pid 29256] mprotect(0x2afb0bbe1000, 4096, PROT_READ|PROT_WRITE) = 0 [pid 29256] mprotect(0x2afb0bbe0000, 4096, PROT_NONE) = 0 [pid 29256] futex(0x40132d24, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x40132d20, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29249] <... futex resumed> ) = 0 [pid 29256] futex(0x4019f884, FUTEX_WAIT_PRIVATE, 25589, NULL <unfinished ...> [pid 29249] futex(0x40132728, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29249] futex(0x40130fb4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x40130fb0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29243] <... futex resumed> ) = 0 [pid 29243] futex(0x4012ed28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29243] futex(0x4012b7a4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4012b7a0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29236] <... futex resumed> ) = 0 [pid 29243] futex(0x4012b228, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29236] futex(0x4012b228, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29243] <... futex resumed> ) = 0 [pid 29236] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29249] sched_yield( <unfinished ...> [pid 29243] sched_yield( <unfinished ...> [pid 29249] <... sched_yield resumed> ) = 0 [pid 29236] futex(0x4012b228, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29236] futex(0x4012f244, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4012f240, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29240] <... futex resumed> ) = 0 [pid 29236] <... futex resumed> ) = 1 [pid 29240] futex(0x4012cf28, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29236] futex(0x4012cf28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29240] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29236] <... futex resumed> ) = 0 [pid 29249] sched_yield() = 0 [pid 29240] futex(0x4012cf28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29236] sched_yield( <unfinished ...> [pid 29240] <... futex resumed> ) = 0 [pid 29236] <... sched_yield resumed> ) = 0 [pid 29249] sched_yield( <unfinished ...> [pid 29240] futex(0x2afb140008b4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x2afb140008b0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29249] <... sched_yield resumed> ) = 0 [pid 29236] sched_yield( <unfinished ...> [pid 29245] <... futex resumed> ) = 0 [pid 29240] <... futex resumed> ) = 1 [pid 29236] <... sched_yield resumed> ) = 0 [pid 29249] sched_yield( <unfinished ...> [pid 29245] futex(0x40130a28, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29240] futex(0x40130a28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29236] sched_yield( <unfinished ...> [pid 29245] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29240] <... futex resumed> ) = 0 [pid 29236] <... sched_yield resumed> ) = 0 [pid 29249] <... sched_yield resumed> ) = 0 [pid 29245] futex(0x40130a28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29240] sched_yield( <unfinished ...> [pid 29236] sched_yield( <unfinished ...> [pid 29245] <... futex resumed> ) = 0 [pid 29240] <... sched_yield resumed> ) = 0 [pid 29236] <... sched_yield resumed> ) = 0 [pid 29249] sched_yield( <unfinished ...> [pid 29245] futex(0x401299f4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x401299f0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29249] <... sched_yield resumed> ) = 0 [pid 29240] sched_yield( <unfinished ...> [pid 29236] sched_yield( <unfinished ...> [pid 29245] <... futex resumed> ) = 1 [pid 29240] <... sched_yield resumed> ) = 0 [pid 29236] <... sched_yield resumed> ) = 0 [pid 29228] <... futex resumed> ) = 0 [pid 29228] futex(0x40127728, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29249] sched_yield() = 0 [pid 29228] <... futex resumed> ) = 0 [pid 29249] sched_yield( <unfinished ...> [pid 29245] sched_yield( <unfinished ...> [pid 29240] sched_yield( <unfinished ...> [pid 29228] futex(0x4012b764, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4012b760, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29249] <... sched_yield resumed> ) = 0 [pid 29233] <... futex resumed> ) = 0 [pid 29228] <... futex resumed> ) = 1 [pid 29233] futex(0x40129428, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29228] futex(0x40129428, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29233] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29228] <... futex resumed> ) = 0 [pid 29245] <... sched_yield resumed> ) = 0 [pid 29243] <... sched_yield resumed> ) = 0 [pid 29240] <... sched_yield resumed> ) = 0 [pid 29236] sched_yield( <unfinished ...> [pid 29233] futex(0x40129428, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29249] sched_yield( <unfinished ...> [pid 29245] sched_yield( <unfinished ...> [pid 29233] <... futex resumed> ) = 0 [pid 29228] sched_yield( <unfinished ...> [pid 29233] futex(0x40127c84, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x40127c80, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29228] <... sched_yield resumed> ) = 0 [pid 29233] <... futex resumed> ) = 1 [pid 29222] <... futex resumed> ) = 0 [pid 29249] <... sched_yield resumed> ) = 0 [pid 29245] <... sched_yield resumed> ) = 0 [pid 29240] sched_yield( <unfinished ...> [pid 29236] <... sched_yield resumed> ) = 0 [pid 29249] sched_yield( <unfinished ...> [pid 29243] sched_yield( <unfinished ...> [pid 29233] futex(0x40125928, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29228] sched_yield( <unfinished ...> [pid 29233] <... futex resumed> ) = 0 [pid 29228] <... sched_yield resumed> ) = 0 [pid 29222] futex(0x40125928, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29249] <... sched_yield resumed> ) = 0 [pid 29249] sched_yield( <unfinished ...> [pid 29245] sched_yield( <unfinished ...> [pid 29243] <... sched_yield resumed> ) = 0 [pid 29245] <... sched_yield resumed> ) = 0 [pid 29240] <... sched_yield resumed> ) = 0 [pid 29236] sched_yield( <unfinished ...> [pid 29233] sched_yield( <unfinished ...> [pid 29222] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29228] sched_yield( <unfinished ...> [pid 29233] <... sched_yield resumed> ) = 0 [pid 29228] <... sched_yield resumed> ) = 0 [pid 29222] futex(0x40125928, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29249] <... sched_yield resumed> ) = 0 [pid 29249] sched_yield( <unfinished ...> [pid 29243] sched_yield( <unfinished ...> [pid 29233] sched_yield( <unfinished ...> [pid 29245] sched_yield( <unfinished ...> [pid 29222] <... futex resumed> ) = 0 [pid 29249] <... sched_yield resumed> ) = 0 [pid 29249] futex(0x40127c84, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x40127c80, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29245] <... sched_yield resumed> ) = 0 [pid 29243] <... sched_yield resumed> ) = 0 [pid 29245] futex(0x2afb140008b4, FUTEX_WAIT_PRIVATE, 50677, NULL <unfinished ...> [pid 29243] futex(0x40130fb4, FUTEX_WAIT_PRIVATE, 50915, NULL <unfinished ...> [pid 29240] futex(0x4012f244, FUTEX_WAIT_PRIVATE, 50733, NULL <unfinished ...> [pid 29236] <... sched_yield resumed> ) = 0 [pid 29233] <... sched_yield resumed> ) = 0 [pid 29236] futex(0x4012b7a4, FUTEX_WAIT_PRIVATE, 51129, NULL <unfinished ...> [pid 29233] futex(0x4012b764, FUTEX_WAIT_PRIVATE, 50913, NULL <unfinished ...> [pid 29228] sched_yield( <unfinished ...> [pid 29222] futex(0x40127c84, FUTEX_WAIT_PRIVATE, 50881, NULL <unfinished ...> [pid 29228] <... sched_yield resumed> ) = 0 [pid 29222] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29228] futex(0x401299f4, FUTEX_WAIT_PRIVATE, 51255, NULL <unfinished ...> [pid 29222] futex(0x40127c80, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29249] <... futex resumed> ) = 1 [pid 29222] <... futex resumed> ) = 0 [pid 29249] futex(0x40132d24, FUTEX_WAIT_PRIVATE, 50947, NULL <unfinished ...> [pid 29222] futex(0x40127c80, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29222] futex(0x40125928, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29222] futex(0x4012b764, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4012b760, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29233] <... futex resumed> ) = 0 [pid 29222] <... futex resumed> ) = 1 [pid 29233] futex(0x40129428, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29222] futex(0x4019f884, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4019f880, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29233] <... futex resumed> ) = 0 [pid 29222] <... futex resumed> ) = 1 [pid 29256] <... futex resumed> ) = 0 [pid 29233] futex(0x4012b7a4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4012b7a0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29222] futex(0x40127c84, FUTEX_WAIT_PRIVATE, 50883, NULL <unfinished ...> [pid 29256] futex(0x4019f128, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29236] <... futex resumed> ) = 0 [pid 29233] <... futex resumed> ) = 1 [pid 29236] futex(0x4012b228, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29256] <... futex resumed> ) = 0 [pid 29233] futex(0x4012b228, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29296] <... futex resumed> ) = -1 ETIMEDOUT (Connection timed out) [pid 29236] <... futex resumed> ) = 0 [pid 29233] <... futex resumed> ) = 1 [pid 29296] futex(0x2afb1402ee28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29236] futex(0x4012b228, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29233] futex(0x4012b764, FUTEX_WAIT_PRIVATE, 50915, NULL <unfinished ...> [pid 29236] <... futex resumed> ) = 0 [pid 29236] futex(0x40130fb4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x40130fb0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29243] <... futex resumed> ) = 0 [pid 29236] <... futex resumed> ) = 1 [pid 29243] futex(0x4012ed28, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29236] futex(0x4012ed28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29243] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29236] <... futex resumed> ) = 0 [pid 29243] futex(0x4012ed28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29236] futex(0x4012b7a4, FUTEX_WAIT_PRIVATE, 51131, NULL <unfinished ...> [pid 29243] <... futex resumed> ) = 0 [pid 29243] futex(0x2afb140008b4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x2afb140008b0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29245] <... futex resumed> ) = 0 [pid 29243] <... futex resumed> ) = 1 [pid 29245] futex(0x40130a28, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29243] futex(0x40130a28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29245] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29243] <... futex resumed> ) = 0 [pid 29245] futex(0x40130a28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29243] futex(0x40130fb4, FUTEX_WAIT_PRIVATE, 50917, NULL <unfinished ...> [pid 29245] <... futex resumed> ) = 0 [pid 29245] futex(0x4012f244, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x4012f240, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29240] <... futex resumed> ) = 0 [pid 29245] futex(0x4012cf28, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29240] futex(0x4012cf28, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29245] <... futex resumed> ) = 0 [pid 29240] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29245] futex(0x2afb140008b4, FUTEX_WAIT_PRIVATE, 50679, NULL <unfinished ...> [pid 29240] futex(0x4012cf28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29240] futex(0x401299f4, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x401299f0, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1}) = 1 [pid 29228] <... futex resumed> ) = 0 [pid 29240] futex(0x4012f244, FUTEX_WAIT_PRIVATE, 50735, NULL <unfinished ...> [pid 29228] futex(0x40127728, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29228] futex(0x40132d24, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x40132d20, {FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...> [pid 29249] <... futex resumed> ) = 0 [pid 29228] <... futex resumed> ) = 1 [pid 29249] futex(0x40132728, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> [pid 29228] futex(0x40132728, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29249] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable) [pid 29228] <... futex resumed> ) = 0 [pid 29249] futex(0x40132728, FUTEX_WAKE_PRIVATE, 1 <unfinished ...> [pid 29228] futex(0x401299f4, FUTEX_WAIT_PRIVATE, 51257, NULL <unfinished ...> [pid 29249] <... futex resumed> ) = 0 [pid 29249] futex(0x40132d24, FUTEX_WAIT_PRIVATE, 50949, NULL <unfinished ...> [pid 29296] <... futex resumed> ) = 0 [pid 29296] futex(0x4179ee94, 0x189 /* FUTEX_??? */, 1, {1387274027, 481023000}, ffffffff) = -1 ETIMEDOUT (Connection timed out) [pid 29296] futex(0x2afb1402ee28, FUTEX_WAKE_PRIVATE, 1) = 0 [pid 29296] futex(0x4179ee94, 0x189 /* FUTEX_??? */, 1, {1387274027, 531188000}, ffffffff^C <unfinished ...> Process 29123 detached Process 29203 detached Process 29222 detached Process 29228 detached Process 29233 detached Process 29236 detached Process 29240 detached Process 29243 detached Process 29245 detached Process 29249 detached Process 29256 detached Process 29262 detached Process 29263 detached Process 29281 detached Process 29285 detached Process 29289 detached Process 29293 detached Process 29296 detached Process 29305 detached Process 29307 detached Process 29312 detached Process 29313 detached Process 29315 detached Process 29326 detached Process 29328 detached Process 29329 detached Process 29341 detached Process 29343 detached Process 29356 detached Process 29409 detached Process 29411 detached r5i0n0:~ # Le 17/12/2013 10:11, Loic GASCHE a écrit : > I have submitted it already with sequentiel. > > Le 17/12/2013 10:10, Tina ODAKA a écrit : >> anyway, try to submit it with sequentiel, >> and mail me when you submit? >> i try to check how the job is running to see if anything can be speed up >> tina >> >> >> >> Le 17/12/2013 09:55, Tina ODAKA a écrit : >>> If one simulation need 5 hours to run, you need to use the >>> default queue, which is sequentiel (you do not need to put -q >>> sequentiel, as it is a defalut queue) >>> >>> tina >>> >>> Le 17/12/2013 09:49, Loic GASCHE a écrit : >>>> Hi Tina, >>>> >>>> Thanks a lot. >>>> >>>> Does "each job can run max 10 minutes" mean that one simulation can >>>> take no longer than 10 minutes to run, or it will be killed ? >>>> >>>> We use a pretty complex model this time and run it for twelve years, >>>> so one simulation needs about 5 hours to run... >>>> >>>> Loïc >>>> >>>> Le 16/12/2013 21:34, todaka a écrit : >>>>> hi loic, >>>>> >>>>> yes, there was a misunderstanding. >>>>> so, i put you in the users who can use 'isisfish' >>>>> instead of '-q parallel32' >>>>> plz use >>>>> '-q isisfish' >>>>> >>>>> you can then run more than 16 job, but each job can run max 10 >>>>> minutes. >>>>> >>>>> Tina >>>>> >>>>> >>>>> Le 2013-12-16 16:55, Loic GASCHE a écrit : >>>>>> re-bonjour tina, >>>>>> >>>>>> Voici mon dernier échange avec les gens de code lutin concernant >>>>>> l'utilisation des queues "parallel" avec ISIS. >>>>>> >>>>>> Apparemment ils avaient réussi à faire tourner des simus en >>>>>> parallel8 >>>>>> et avaient tenté en parallel32. >>>>>> >>>>>> Ils savaient qu'ISIS ne fonctionnait pas sur ces queues mais avaient >>>>>> supposé que Denis nous orientait vers les queues parallel car des >>>>>> changements de caparmor nous permettaient d'y accéder... mais en >>>>>> fait >>>>>> non. >>>>>> >>>>>> Donc tout ceci est en fait un gros malentendu entre Denis, moi et >>>>>> les >>>>>> lutins. >>>>>> >>>>>> Loïc >>>>>> >>>>>> -------- Message original -------- >>>>>> Sujet: Re: [Isis-fish-users] Fwd: Re: HelpDesk Nv3 / n°=191007 : Re: >>>>>> Accès à plus de coeurs sur caparmor ? >>>>>> Date : Thu, 21 Nov 2013 09:46:01 +0100 >>>>>> De : Eric Chatellier <chatellier(a)codelutin.com> >>>>>> Répondre à : isis-fish-users(a)list.isis-fish.org >>>>>> Organisation : Codelutin >>>>>> Pour : isis-fish-users(a)list.isis-fish.org >>>>>> >>>>>> Le 21/11/2013 08:44, Loic GASCHE a écrit : >>>>>>> >>>>>>> >>>>>>> J'ai recu toute la nuit des messages d'erreur de caparmor : >>>>>>> >>>>>>> Hello lgasche, your job 5931603.service0, jobname simulation-sim_ >>>>>>> using 33 >>>>>>> cores have >>>>>>> performance ratio as 0.00. Your real time (wall time) is 03:39 >>>>>>> where as >>>>>>> your CPU time is 00:00. This job blocks 33 cores, thus your cpu >>>>>>> time >>>>>>> should >>>>>>> get closer to 33 * your real time (wall time). If you can >>>>>>> improve the >>>>>>> performance of your job, your calculation runs faster (and you can >>>>>>> make >>>>>>> economy of computational resource). >>>>>>> Please check your code, and see if you do not do unnecessary io >>>>>>> access or bad >>>>>>> usage of MPI or OpenMP, or running non optimised paralleljob. >>>>>>> This is an automatic e-mail from caparmor. >>>>>>> >>>>>>> Apparemment il n'est pas content car le job 5931603 ne tourne pas. >>>>>>> >>>>>>> Ce qui est marrant c'est qu'il dit que ce job tourne sur 33 >>>>>>> coeurs... >>>>>> C'est moi qui ai lancé deux fois le même jobs sur deux files >>>>>> différentes. >>>>>>> >>>>>>> Est-ce que je mets fin à ce job ? >>>>>> Oui. >>>>>>> >>>>>>> Le jour ou j'ai besoin de plus de 8 coeurs il me suffit donc de >>>>>>> taper -q >>>>>>> parallel nbCoeurs pour utiliser une des queues jusqu'à 256 ? >>>>>> Non, c'est "parallel8", ou "parallel256" (sans espace) >>>>>> Il n'y a que 5 ou six file spécifiquement disponibles. >>>>>>> Dans son mail Denis indique que les queue ont un temps limité. Par >>>>>>> exemple 18 >>>>>>> heures pour la 256 coeurs. Qu'est-ce que cela signifie ? Que se >>>>>>> passe-t-il si >>>>>>> mon AS n'a pas fini de tourner après 18 heures ? >>>>>> C'est une contraintes de caparmor et plus spécifiquement de la >>>>>> politique >>>>>> d'allocation des ressources sur les super calculateurs. >>>>>> Ils veulent bien que tu prennes plus de coeurs, mais à condition >>>>>> que tu les "monopolise" moins longtemps. >>>>>> >>>>>> C'est à toi de voir suivant ta région. Si tu pense que l'AS prend >>>>>> plus >>>>>> de 18 >>>>>> heures, il faut que >>>>>> tu utilises moins de coeurs. Sinon caparmor tuera les jobs trop >>>>>> longs. >>>> >>> >> > -- =================================================== Tina Odaka RIC - IDM - IMN - IFREMER Pôle de Calcul Intensif pour la Mer (PCIM) Tel: +33 (0)2 98 22 41 85 Fax: +33 (0)2 98 22 45 46 email: Tina.Odaka(a)ifremer.fr http://www.ifremer.fr/pcim ==================================================

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Fwd: Your job performance on caparmor= 0.10, please check how your job runs on caparmor
by Loic GASCHE Dec. 13, 2013

Dec. 13, 2013

Ah tiens je reçois les mêmes messages d'erreur qu'Eric lorsqu'il a fait le test de parallel 32 sur caparmor : -------- Message original -------- Sujet: Your job performance on caparmor= 0.10, please check how your job runs on caparmor Date : Fri, 13 Dec 2013 13:05:01 +0000 De : assistance(a)ifremer.fr Pour : lgasche(a)ifremer.fr Copie à : dcroizef(a)ifremer.fr, pcim(a)ifremer.fr Hello lgasche, your job 5977880[4].servic, jobname simulation-as_t using 9 cores have performance ratio as 0.10. Your real time (wall time) is 00:47 where as your CPU time is 00:41. This job blocks 9 cores, thus your cpu time should get closer to 9 * your real time (wall time). If you can improve the performance of your job, your calculation runs faster (and you can make economy of computational resource). Please check your code, and see if you do not do unnecessary io access or bad usage of MPI or OpenMP, or running non optimised paralleljob. This is an automatic e-mail from caparmor. Ce qui est marrant c'est que d'un côté il me dit que ma simu ne tourne pas à la vitesse où elle devrait tourner et de l'autre qu'elle n'a même pas commencé : estimated.start_time = Sun Dec 15 12:16:56 2013. Ca veut dire que mon job a été mis en pause ?

1 0

R sur serveur linux ?
by Loic GASCHE Dec. 13, 2013

Dec. 13, 2013

Bonjour, Après une tentative infructueuse de lancement d'une As depuis le serveur linux, il apparait que celui-ci n'arrive pas à accéder à R. Donc deux questions: - Est-ce que R est installé sur le serveur de Steph ? - Comment sais où trouver le R_Home et le Path sous linux, pour pouvoir dire à ISIS où chercher (ou comment je les définis s'il faut le faire) ? Loïc

4 10

[ANN] - IsisFish 4.2.1.2 released
by Eric Chatellier Dec. 12, 2013

Dec. 12, 2013

The IsisFish team is pleased to announce the isis-fish-4.2.1.2 release! Simulateur de pecherie complexe. Documentation of the project can be found here: http://www.isis-fish.org Changes ------- Changes in this version include: New features: o New cache implementation for better performance Issue: 3952. Thanks to Benjamin Poussin. Resolved by bpoussin. Downloads --------- For a manual installation, you can download files here: http://forge.codelutin.com/projects/isis-fish/files * http://forge.codelutin.com/attachments/download/1296/isis-fish-4.2.1.2-bin.… Have fun! -IsisFish team -- Éric Chatellier - Code Lutin Tel: 02.40.50.29.28 - http://www.codelutin.com

1 1

Can't evaluate rule condition for: rules.TACpoidsPop_PourHCR@9039da
by Loic GASCHE Dec. 12, 2013

Dec. 12, 2013

Bonjour, En réponse à une question qu'on s'est posés ce matin avec Benjamin sur un WARN dans le log d'une simu. En fait ce n'est pas vraiment un problème. En effet, cette règle (TACpoidsPop_PourHCR) n'avait pas vraiment de beginStep et de endStep (elle utilise ceux de l'HCR) et donc cherchait à s'appliquer même avant le début de l'HCR (ce qu'elle ne pouvait pas faire car il lui manquait les paramètres dont elle avait besoin). Mais a partir du début de l'HCR elle s'appliquait bien. D'ailleurs ce WARN disparaissait pour les pas de temps après le début de l'HCR. J'ai quand même rajouté dans la règle TACpoidsPop_PourHCR un beginRule et un endRule qui font que la règle ne va s'appliquer et aller chercher ses paramètres qu'entre ces pas de temps. Les F obtenus sont strictement identiques mais les WARN ont disparus (sauf pour le premier pas de temps de l'HCR), ça a le mérite de faire perdre 1Mo au log. Loïc

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AS sur Correspondance entre les zones de reproduction et de recrutement
by Loic GASCHE Dec. 11, 2013

Dec. 11, 2013

Bonjour, A priori dans l'interface ISIS on n'a pas la possibilité de faire d'AS sur la matrice "Correspondance entre les zones de reproduction et de recrutement" qui se trouve dans l'ongle zone pour chaque pop. Comme on se base sur des données de connectivité venant d'un autre modèle pour définir ces correspondances il serait vraiment très intéressant pour nous de pouvoir faire une AS dessus. Est-ce que cela peut être corrigé ? Loïc

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La regle TailleMin fait planter les simus ?
by Loic GASCHE Dec. 10, 2013

Dec. 10, 2013

Bonjour, C'est probablement une boulette de ma part, mais j'ai lancé plusieurs simus très simples avec la règle TailleMin et ces simus plantent. J'ai essayé avec un TAC en poids avant, et avec la règle TACPoidsTailleMin, dans les deux cas ça plante, mais pas au même pas de temps. J'ai aussi essayé en ajoutant la matrice de discards dans les résultats et les exports, ça ne change rien. Une idée ? Loïc

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bug sur caparmor
by Sigrid Lehuta Dec. 10, 2013

Dec. 10, 2013

voila l explication! -------- Message original -------- Sujet: caparmor down Date : Tue, 10 Dec 2013 09:31:29 +0100 De : Tina ODAKA <Tina.Odaka(a)ifremer.fr> Organisation : IFREMER Pour : caparmor <caparmor(a)listes.ifremer.fr> Dear caparmor user, we have problem on caparmor, you can access to data from vbannec or machine in linux only for NFS part; but not on lustre. regards, Tina

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bug simu sur caparmor
by Sigrid Lehuta Dec. 10, 2013

Dec. 10, 2013

hello mon plan sequentiel sur caparmor s'est arrété apres 6 simulations avec ce message. (relancé immediatement en local il tourne toujours 47 e simu) INFO [monitor-thread] (SimulationStorage.java:525) getSimulation - Try to open simulation sim_CalSolV2_q2_2013-12-09-15-55_5(C:\Users\slehuta\isis-fish-4\isis-database\simulations\sim_CalSolV2_q2_2013-12-09-15-55_5) ERROR [monitor-thread] (SimulationMonitor.java:428) run - An exception occurs durring monitoring fr.ifremer.isisfish.IsisFishRuntimeException: Can't read simulation parameters from file C:\Users\slehuta\isis-fish-4\isis-database\simulations\sim_CalSolV2_q2_2013-12-09-15-55_5\parameters.properties at fr.ifremer.isisfish.datastore.SimulationStorage.getParameter(SimulationStorage.java:397) at fr.ifremer.isisfish.simulator.launcher.SimulationMonitor.analyzeSensitivityResult(SimulationMonitor.java:675) at fr.ifremer.isisfish.simulator.launcher.SimulationMonitor.doPostSimulationOperation(SimulationMonitor.java:627) at fr.ifremer.isisfish.simulator.launcher.SimulationMonitor.waitAndCheckProgression(SimulationMonitor.java:480) at fr.ifremer.isisfish.simulator.launcher.SimulationMonitor.run(SimulationMonitor.java:425) Caused by: java.io.FileNotFoundException: C:\Users\slehuta\isis-fish-4\isis-database\simulations\sim_CalSolV2_q2_2013-12-09-15-55_5\parameters.properties (Le fichier spécifié est introuvable) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.<init>(Unknown Source) at fr.ifremer.isisfish.datastore.SimulationStorage.getParameter(SimulationStorage.java:392) ... 4 more INFO [pool-3-thread-1] (CalibrationSPV2qMixChannel.java:375) afterSimulation - after simulation ERROR [pool-3-thread-1] (SimulationService.java:1073) finished - Stop simulation plan, because can't call afterSimulation correctly on plan simulationplans.CalibrationSPV2qMixChannel fr.ifremer.isisfish.IsisFishRuntimeException: Can't read simulation parameters from file C:\Users\slehuta\isis-fish-4\isis-database\simulations\sim_CalSolV2_q2_2013-12-09-15-55_5\parameters.properties at fr.ifremer.isisfish.datastore.SimulationStorage.getParameter(SimulationStorage.java:397) at simulationplans.CalibrationSPV2qMixChannel.afterSimulation(CalibrationSPV2qMixChannel.java:376) at fr.ifremer.isisfish.simulator.launcher.SimulationService$PrepareSimulationJob.finished(SimulationService.java:1070) at fr.ifremer.isisfish.simulator.launcher.SimulationJob.run(SimulationJob.java:252) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Caused by: java.io.FileNotFoundException: C:\Users\slehuta\isis-fish-4\isis-database\simulations\sim_CalSolV2_q2_2013-12-09-15-55_5\parameters.properties (Le fichier spécifié est introuvable) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.<init>(Unknown Source) at fr.ifremer.isisfish.datastore.SimulationStorage.getParameter(SimulationStorage.java:392) ... 6 more

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Programme 5-6 decembre 2013
by Stephanie MAHEVAS Dec. 3, 2013

Dec. 3, 2013

Bonjour voici un programme provisoire des journées utilisateurs ISIS-Fish de décembre prochain. J'espère n'avoir oublié personne et mis les points essentiels à l'odj. Si vous souhaitez ajouter/modifier un point à l'ordre du jour, n'hésitez pas à m'en informer. Pour faciliter l'organisation (pause, repas and co), merci de vous inscrire en remplissant le formulaire *inscription 2013* sur http://www.isis-fish.org/news.html Merci de diffuser aux personnes intéressées que j'aurais pu oublier. Amitiés, Stéphanie -- ...................................................................... Stephanie MAHEVAS (Stephanie.Mahevas(a)ifremer.fr) IFREMER/EMH (Ecologie et Modèles pour l'Halieutique) Tel: (33) 2 40 37 41 81 Fax: (33) 2 40 37 40 75 o \ o / _ o __| \ / |__ o _ \ o / o /|\ | /\ ___\o \o | o/ o/__ /\ | /|\ / \ / \ | \ /) | ( \ /o\ / ) | (\ / | / \ / \ ......................................................................

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