Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr BioChem_BioChem.Examples.CircadianOscillator.Container.conf.json loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false) loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false) loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false) loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo", uses=false) Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo) Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo) Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo) Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo) Running command: translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container") translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container") Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.00107/0.00107, allocations: 104.3 kB / 16.37 MB, free: 6.367 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001016/0.001016, allocations: 195.4 kB / 17.31 MB, free: 5.91 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.121/1.121, allocations: 222.9 MB / 241 MB, free: 15.17 MB / 206.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.05514/0.05514, allocations: 12.28 MB / 303.4 MB, free: 3.246 MB / 238.1 MB Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl" Notification: Performance of FrontEnd - Absyn->SCode: time 1.664e-05/1.667e-05, allocations: 2.281 kB / 367.1 MB, free: 3.441 MB / 302.1 MB Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.1054/0.1054, allocations: 8.478 MB / 375.6 MB, free: 49.64 MB / 302.1 MB Notification: Performance of NFInst.instExpressions: time 0.000653/0.1061, allocations: 0.8195 MB / 376.4 MB, free: 49.48 MB / 302.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001988/0.1063, allocations: 42.97 kB / 376.5 MB, free: 49.48 MB / 302.1 MB Notification: Performance of NFTyping.typeComponents: time 0.0001737/0.1065, allocations: 141.7 kB / 376.6 MB, free: 49.48 MB / 302.1 MB Notification: Performance of NFTyping.typeBindings: time 0.0003021/0.1068, allocations: 204.6 kB / 376.8 MB, free: 49.45 MB / 302.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.0002483/0.1071, allocations: 198.7 kB / 377 MB, free: 49.44 MB / 302.1 MB Notification: Performance of NFFlatten.flatten: time 0.0005173/0.1076, allocations: 0.9823 MB / 378 MB, free: 49.41 MB / 302.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.0005159/0.1081, allocations: 0.5692 MB / 378.6 MB, free: 49.33 MB / 302.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.0001785/0.1083, allocations: 371.3 kB / 378.9 MB, free: 49.25 MB / 302.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.0002152/0.1086, allocations: 424.6 kB / 379.3 MB, free: 49.16 MB / 302.1 MB Notification: Performance of NFPackage.collectConstants: time 9.135e-05/0.1087, allocations: 117.6 kB / 379.5 MB, free: 49.16 MB / 302.1 MB Notification: Performance of NFFlatten.collectFunctions: time 9.41e-05/0.1088, allocations: 115.5 kB / 379.6 MB, free: 49.16 MB / 302.1 MB Notification: Performance of combineBinaries: time 0.0005137/0.1093, allocations: 1.419 MB / 381 MB, free: 48.38 MB / 302.1 MB Notification: Performance of replaceArrayConstructors: time 0.0002383/0.1095, allocations: 0.8884 MB / 381.9 MB, free: 47.76 MB / 302.1 MB Notification: Performance of NFVerifyModel.verify: time 0.0001007/0.1096, allocations: 166.3 kB / 382 MB, free: 47.73 MB / 302.1 MB Notification: Performance of FrontEnd: time 5.158e-05/0.1097, allocations: 32.06 kB / 382.1 MB, free: 47.72 MB / 302.1 MB Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 252 (252) * Number of variables: 252 (252) Notification: Performance of Bindings: time 0.002405/0.1121, allocations: 4.587 MB / 386.7 MB, free: 46.01 MB / 302.1 MB Notification: Performance of FunctionAlias: time 0.0001097/0.1122, allocations: 216.6 kB / 386.9 MB, free: 46 MB / 302.1 MB Notification: Performance of Early Inline: time 0.001643/0.1139, allocations: 2.564 MB / 389.4 MB, free: 45.61 MB / 302.1 MB Notification: Performance of simplify1: time 0.0001191/0.114, allocations: 200.8 kB / 389.6 MB, free: 45.5 MB / 302.1 MB Notification: Performance of Alias: time 0.004122/0.1181, allocations: 5.652 MB / 395.3 MB, free: 42.12 MB / 302.1 MB Notification: Performance of simplify2: time 6.022e-05/0.1182, allocations: 92.95 kB / 395.4 MB, free: 42.09 MB / 302.1 MB Notification: Performance of Events: time 4.901e-05/0.1182, allocations: 97.2 kB / 395.5 MB, free: 42.02 MB / 302.1 MB Notification: Performance of Detect States: time 0.0003047/0.1185, allocations: 442.4 kB / 395.9 MB, free: 41.71 MB / 302.1 MB Notification: Performance of Partitioning: time 0.0004218/0.119, allocations: 0.5565 MB / 396.5 MB, free: 41.41 MB / 302.1 MB Notification: Performance of Causalize: time 0.002029/0.121, allocations: 2.94 MB / 399.4 MB, free: 40.12 MB / 302.1 MB Notification: Performance of After Index Reduction Inline: time 0.0006276/0.1216, allocations: 1.039 MB / 400.4 MB, free: 39.25 MB / 302.1 MB Notification: Performance of Inline: time 0.001112/0.1228, allocations: 1.859 MB / 402.3 MB, free: 37.55 MB / 302.1 MB Notification: Performance of Partitioning: time 9.451e-05/0.1229, allocations: 131.6 kB / 402.4 MB, free: 37.41 MB / 302.1 MB Notification: Performance of Cleanup: time 4.357e-05/0.1229, allocations: 81.05 kB / 402.5 MB, free: 37.35 MB / 302.1 MB Notification: Performance of Causalize: time 0.003791/0.1267, allocations: 6.374 MB / 408.9 MB, free: 31.52 MB / 302.1 MB Notification: Performance of Tearing: time 6.782e-06/0.1267, allocations: 4 kB / 408.9 MB, free: 31.52 MB / 302.1 MB Notification: Performance of Initialization: time 8.42e-07/0.1267, allocations: 0 / 408.9 MB, free: 31.52 MB / 302.1 MB Notification: Performance of Tearing: time 4.478e-06/0.1267, allocations: 11.08 kB / 408.9 MB, free: 31.51 MB / 302.1 MB Notification: Performance of Categorize: time 9.107e-06/0.1268, allocations: 4 kB / 408.9 MB, free: 31.51 MB / 302.1 MB Notification: Performance of Solve: time 0.001097/0.1279, allocations: 2.886 MB / 411.8 MB, free: 28.3 MB / 302.1 MB Notification: Performance of Jacobian: time 0.0006213/0.1285, allocations: 1.124 MB / 412.9 MB, free: 27.13 MB / 302.1 MB Notification: Partition statistics after passing the back-end: * Number of ODE partitions: ..................... 0 * Number of algebraic partitions: ............... 0 * Number of ODE event partitions: ............... 2 * Number of algebraic event partitions: ......... 0 * Number of clocked partitions: ................. 0 * Number of initial partitions: ................. 1 * Number of initial(lambda=0) partitions: ....... 0 Notification: Variable statistics after passing the back-end: * Number of states: ............................. 12 (12) {nucleus.y3.n, nucleus.y6.n, nucleus.y7.n, nucleus.ambientSubstance.n, nucleus.Nucleus_V, cytoplasm.y1.n, cytoplasm.y2.n, cytoplasm.y4.n, cytoplasm.y5.n, cytoplasm.ambientSubstance.n, cytoplasm.Cytoplasm_V, Container_V} * Number of discrete states: .................... 0 (0) {} * Number of clocked states: ..................... 0 (0) {NOT YET AVAILABLE} * Number of discrete variables: ................. 0 (0) {} * Number of top-level inputs: ................... 0 (0) {} Notification: [Simulation] Strong Component statistics after passing the back-end: * Number of single strong components: ........... 84 (scalar:84, array:0, record:0) * Number of multi strong components: ............ 0 (algorithm:0, when:0, if:0, tuple:0) * Number of for-loop strong components: ......... 0 (generic: 0, entwined:0) * Number of algebraic-loop strong components: ... 0 (linear: 0, nonlinear:0) Notification: [Initialization] Strong Component statistics after passing the back-end: * Number of single strong components: ........... 119 (scalar:119, array:0, record:0) * Number of multi strong components: ............ 0 (algorithm:0, when:0, if:0, tuple:0) * Number of for-loop strong components: ......... 0 (generic: 0, entwined:0) * Number of algebraic-loop strong components: ... 9 (linear: 0, nonlinear:9) Notification: Performance of backend: time 3.548e-05/0.1285, allocations: 51.38 kB / 413 MB, free: 27.09 MB / 302.1 MB Notification: Performance of SimCode: time 0.002057/0.1306, allocations: 3.6 MB / 416.6 MB, free: 24.13 MB / 302.1 MB Notification: Performance of Templates: time 0.006208/0.1368, allocations: 4.627 MB / 421.2 MB, free: 19.93 MB / 302.1 MB make -j1 -f BioChem_BioChem.Examples.CircadianOscillator.Container.makefile (rm -f BioChem_BioChem.Examples.CircadianOscillator.Container.pipe ; mkfifo BioChem_BioChem.Examples.CircadianOscillator.Container.pipe ; head -c 1048576 < BioChem_BioChem.Examples.CircadianOscillator.Container.pipe >> ../files/BioChem_BioChem.Examples.CircadianOscillator.Container.sim & ./BioChem_BioChem.Examples.CircadianOscillator.Container -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1)