2024-04-04 14:35:37,208 INFO [main] (IsisConfig.java:196) getEnvUserHome - Using user home : /home1/datahome/aricouar 2024-04-04 14:35:37,796 INFO [main] (IsisFish.java:135) main - Starting Isis-Fish 4.4.8.1 with args : [--option, launch.ui, false, --option, perform.vcsupdate, false, --option, perform.migration, false, --option, perform.cron, false, --option, isis.home.directory, /home1/scratch/aricouar/myISISdb, --simulateWithSimulation, SQres_equilibrium_rjc_i0001, /home1/datawork/aricouar/ISIS_Travail/equilibrium_search/prep/SQres_equilibrium_rjc.zip] 2024-04-04 14:35:39,371 INFO [main] (IsisFish.java:136) main - Date: 04/04/2024 14:35 2024-04-04 14:35:39,416 INFO [main] (IsisFish.java:137) main - Java version: 17.0.10+7, OpenJDK 64-Bit Server VM 2024-04-04 14:35:39,416 INFO [main] (IsisFish.java:138) main - Platform/arch: Linux/3.12.53-60.30-default/amd64 2024-04-04 14:35:39,416 INFO [main] (IsisFish.java:139) main - java.library.path: /appli/R/3.6.3-intel-cc-17.0.2.174/lib64/R/lib:/appli/R/3.6.3-intel-cc-17.0.2.174/notR/lib:/appli/java//jdk1.8.0_66/lib:/appli/java/jdk1.8.0_66/jre/lib/amd64/server:/appli/java/jdk1.8.0_66/lib:/appli/intel/parallel_studio/parallel_studio_xe_2017_update2/compilers_and_libraries_2017.2.174/linux/mkl/lib/intel64_lin:/appli/intel/parallel_studio/parallel_studio_xe_2017_update2/compilers_and_libraries_2017.2.174/linux/mkl/lib/intel64:/appli/intel/parallel_studio/parallel_studio_xe_2017_update2/impi/2017.2.174/intel64/lib:/usr/X11R6/lib64:/appli/java//jdk1.8.0_66/lib:/appli/intel/parallel_studio/parallel_studio_xe_2017_update2/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib:/appli/R/3.6.3-intel-cc-17.0.2.174/notR/lib:/appli/R/3.6.3-intel-cc-17.0.2.174/lib:/appli/intel/parallel_studio/parallel_studio_xe_2017_update2/compilers_and_libraries_2017.2.174/linux/mpi/intel64/lib:/appli/intel/parallel_studio/parallel_studio_xe_2017_update2/compilers_and_libraries_2017.2.174/linux/mpi/mic/lib:/usr/java/packages/lib:/usr/lib64:/lib64:/lib:/usr/lib 2024-04-04 14:35:39,417 INFO [main] (IsisFish.java:140) main - PATH: /appli/intel/parallel_studio/parallel_studio_xe_2017_update2/impi/2017.2.174/intel64/bin:/appli/java//jdk1.8.0_66/bin:/appli/intel/parallel_studio/parallel_studio_xe_2017_update2/compilers_and_libraries_2017.2.174/linux/bin/intel64:/appli/intel/parallel_studio/parallel_studio_xe_2017_update2/debugger_2017/gdb/intel64:/appli/R/3.6.3-intel-cc-17.0.2.174/bin:/opt/sgi/sbin:/opt/sgi/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/opt/c3/bin:/opt/pbs/default/bin:/opt/pbs/default/sbin:/usr/lpp/mmfs/bin:/sbin:/bin 2024-04-04 14:35:39,504 INFO [main] (IsisFish.java:165) main - after init done in 2.299. 2024-04-04 14:35:39,505 INFO [main] (SimulationAction.java:173) simulateWithSimulationAndScript - Command line action : simulateWithSimulationAndScript (SQres_equilibrium_rjc_i0001, /home1/datawork/aricouar/ISIS_Travail/equilibrium_search/prep/SQres_equilibrium_rjc.zip, null) 2024-04-04 14:35:39,558 INFO [main] (SimulationExecutor.java:87) - SimulationExecutor started with 2 thread for dans un sous processus 2024-04-04 14:35:40,253 INFO [main] (SimulationExecutor.java:87) - SimulationExecutor started with 2 thread for sur le serveur Datarmor 2024-04-04 14:35:40,254 INFO [main] (SimulationExecutor.java:87) - SimulationExecutor started with 2 thread for dans le m��me processus 2024-04-04 14:35:40,254 INFO [main] (InProcessSimulatorLauncher.java:108) simulate - simulate SQres_equilibrium_rjc_i0001 with file /home1/datawork/aricouar/ISIS_Travail/equilibrium_search/prep/SQres_equilibrium_rjc.zip 2024-04-04 14:35:41,612 INFO [main] (SimulationStorage.java:762) importAndRenameZip - Import simulation file /home1/datawork/aricouar/ISIS_Travail/equilibrium_search/prep/SQres_equilibrium_rjc.zip in directory /home1/scratch/aricouar/myISISdb/isis-database/simulations and rename from ^.*?/(.*)$ to SQres_equilibrium_rjc_i0001/$1 2024-04-04 14:35:59,023 INFO [main] (SimulationStorage.java:769) importAndRenameZip - Last entry was SQres_equilibrium_rjc_i0001/simulators/SimulatorEffortByCell.java extract name SQres_equilibrium_rjc_i0001 2024-04-04 14:35:59,024 INFO [main] (DataStorage.java:208) getStorage - Create new storage for SQres_equilibrium_rjc_i0001 2024-04-04 14:36:12,341 INFO [SimThread SQres_equilibrium_rjc_i0001] (InProcessSimulatorLauncher.java:342) localSimulateSameThread - 04/04/2024 14:36 Java version: 17.0.10+7 Isis-fish version: 4.4.8.1 2024-04-04 14:36:14,333 INFO [SimThread SQres_equilibrium_rjc_i0001] (InProcessSimulatorLauncher.java:201) message - Mise en place des aspects Cache 2024-04-04 14:36:14,334 INFO [SimThread SQres_equilibrium_rjc_i0001] (SimulationControl.java:206) setText - Mise en place des aspects Cache 2024-04-04 14:36:19,275 INFO [SimThread SQres_equilibrium_rjc_i0001] (DataStorage.java:163) getMemStorage - Create new memory storage for SQres_equilibrium_rjc_i0001 2024-04-04 14:36:20,522 INFO [SimThread SQres_equilibrium_rjc_i0001] (DataStorage.java:208) getStorage - Create new storage for SQres_equilibrium_rjc_i0001 2024-04-04 14:36:24,907 INFO [SimThread SQres_equilibrium_rjc_i0001] (InProcessSimulatorLauncher.java:201) message - Simulation execution 2024-04-04 14:36:24,908 INFO [SimThread SQres_equilibrium_rjc_i0001] (SimulationControl.java:206) setText - Simulation execution 2024-04-04 14:36:24,910 INFO [SimThread SQres_equilibrium_rjc_i0001] (SimulationContext.java:497) message - Ex��cution des scripts de Presimulation 2024-04-04 14:36:24,911 INFO [SimThread SQres_equilibrium_rjc_i0001] (SimulationControl.java:206) setText - Ex��cution des scripts de Presimulation 2024-04-04 14:36:25,696 INFO [SimThread SQres_equilibrium_rjc_i0001] (InProcessSimulatorLauncher.java:438) localSimulateSameThread - Matrix backend: org.nuiton.math.matrix.DoubleBigVector and org.nuiton.math.matrix.DoubleSparseHashVector threshold: 1000 2024-04-04 14:36:25,816 INFO [SimThread SQres_equilibrium_rjc_i0001] (IsisCacheBackendOnGuava.java:238) adjustedCache - Cache size ajusted to 1,445Go (equivalent to 0 step need) 2024-04-04 14:36:27,287 INFO [SimThread SQres_equilibrium_rjc_i0001] (SimulationControl.java:206) setText - Rules initialisation:[rules.MaccoEquilibriumRestartSim@5f1421f8, rules.ForcageEffort_SaufPropStr_2015_2022_MACCO@3dc5543a, rules.EffortReductionFromFile@3ca45a9e] nom de la simu en cours : SQres_equilibrium_rjc_i0001 file : _SQres_equilibrium_rjc/i0001/Raja_clavata_restart.csv 2024-04-04 14:36:31,893 INFO [SimThread SQres_equilibrium_rjc_i0001] (IsisCacheBackendOnGuava.java:104) weigh - Cache can't compute value size of class java.lang.String 2024-04-04 14:36:31,933 ERROR [SimThread SQres_equilibrium_rjc_i0001] (InProcessSimulatorLauncher.java:500) localSimulateSameThread - Error during simulation java.lang.NullPointerException: Cannot invoke "org.nuiton.math.matrix.MatrixND.importCSV(java.io.Reader, int[])" because "ajc$this.matNinit" is null at rules.MaccoEquilibriumRestartSim.init_aroundBody0(MaccoEquilibriumRestartSim.java:111) ~[?:?] at rules.MaccoEquilibriumRestartSim$AjcClosure1.run(MaccoEquilibriumRestartSim.java:1) ~[?:?] at org.aspectj.runtime.reflect.JoinPointImpl.proceed(JoinPointImpl.java:179) ~[aspectjweaver-1.9.21.jar:?] at fr.ifremer.isisfish.aspect.RuleAspect.makeTimedCall(RuleAspect.java:121) ~[?:?] at fr.ifremer.isisfish.aspect.RuleAspect.initCall(RuleAspect.java:70) ~[?:?] at rules.MaccoEquilibriumRestartSim.init(MaccoEquilibriumRestartSim.java:80) ~[?:?] at simulators.DefaultSimulator.simulate(DefaultSimulator.java:135) ~[?:?] at fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher.localSimulateSameThread(InProcessSimulatorLauncher.java:439) [isis-fish-4.4.8.1.jar:4.4.8.1] at fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher$SimThread.run(InProcessSimulatorLauncher.java:262) [isis-fish-4.4.8.1.jar:4.4.8.1] 2024-04-04 14:36:31,968 INFO [SimThread SQres_equilibrium_rjc_i0001] (InProcessSimulatorLauncher.java:528) localSimulateSameThread - Simulation time: 19.611 2024-04-04 14:36:31,971 INFO [SimThread SQres_equilibrium_rjc_i0001] (IsisCacheBackendOnGuava.java:238) adjustedCache - Cache size ajusted to 236o (equivalent to 2 step need) --- Cache Statistiques --- Total call: 4 Cache used: 0 Cache usage: 0% - IsisCacheBackendOnGuava initial cache size: 1,933Go, cache size reevaluated: 236o, totalCached: 118o, numberStep: 1, numberEntries: 2 Step min: 118o, max: 118o, mean: 118o, standard deviation: 0o Entry min: 58o, max: 60o, mean: 59o, standard deviation: 1o -------------------- 2024-04-04 14:36:32,059 INFO [SimThread SQres_equilibrium_rjc_i0001] (InProcessSimulatorLauncher.java:201) message - Simulation termin��e 2024-04-04 14:36:32,060 INFO [SimThread SQres_equilibrium_rjc_i0001] (SimulationControl.java:206) setText - Simulation termin��e Exception in thread "SimThread SQres_equilibrium_rjc_i0001" fr.ifremer.isisfish.simulator.SimulationException: Error during simulation at fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher.localSimulateSameThread(InProcessSimulatorLauncher.java:502) at fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher$SimThread.run(InProcessSimulatorLauncher.java:262) Caused by: java.lang.NullPointerException: Cannot invoke "org.nuiton.math.matrix.MatrixND.importCSV(java.io.Reader, int[])" because "ajc$this.matNinit" is null at rules.MaccoEquilibriumRestartSim.init_aroundBody0(MaccoEquilibriumRestartSim.java:111) at rules.MaccoEquilibriumRestartSim$AjcClosure1.run(MaccoEquilibriumRestartSim.java:1) at org.aspectj.runtime.reflect.JoinPointImpl.proceed(JoinPointImpl.java:179) at fr.ifremer.isisfish.aspect.RuleAspect.makeTimedCall(RuleAspect.java:121) at fr.ifremer.isisfish.aspect.RuleAspect.initCall(RuleAspect.java:70) at rules.MaccoEquilibriumRestartSim.init(MaccoEquilibriumRestartSim.java:80) at simulators.DefaultSimulator.simulate(DefaultSimulator.java:135) at fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher.localSimulateSameThread(InProcessSimulatorLauncher.java:439) ... 1 more 2024-04-04 14:36:32,064 INFO [main] (DataStorage.java:208) getStorage - Create new storage for SQres_equilibrium_rjc_i0001