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 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.001156/0.001156, allocations: 81.17 kB / 19.87 MB, free: 4.621 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.001856/0.001856, allocations: 169 kB / 23.27 MB, free: 1.223 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 1.007/1.007, allocations: 177.2 MB / 203.7 MB, free: 5.52 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo): time 0.04118/0.04118, allocations: 9.556 MB / 269.8 MB, free: 3.805 MB / 250.7 MB
"
[Timeout remaining time 180]
Using package BioChem with version 1.1.3 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo)
Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo)
Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo)
Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo)
Running command: translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container")
translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.415e-06/2.415e-06, allocations: 0 / 343.3 MB, free: 7.531 MB / 314.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.069e-05/3.31e-05, allocations: 2.312 kB / 343.3 MB, free: 7.527 MB / 314.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01431/0.01434, allocations: 6.488 MB / 349.8 MB, free: 1.012 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.001674/0.01601, allocations: 0.8341 MB / 350.7 MB, free: 180 kB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0004524/0.01647, allocations: 40 kB / 350.7 MB, free: 140 kB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002808/0.01675, allocations: 146.9 kB / 350.8 MB, free: 15.99 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004533/0.0172, allocations: 221.7 kB / 351.1 MB, free: 15.77 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003585/0.01756, allocations: 195.7 kB / 351.3 MB, free: 15.58 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0007111/0.01827, allocations: 0.8723 MB / 352.1 MB, free: 14.71 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0004726/0.01874, allocations: 351.1 kB / 352.5 MB, free: 14.35 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0005052/0.01925, allocations: 0.5653 MB / 353 MB, free: 13.78 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003492/0.0196, allocations: 319 kB / 353.3 MB, free: 13.47 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001042/0.0197, allocations: 116 kB / 353.5 MB, free: 13.36 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 9.479e-05/0.0198, allocations: 116 kB / 353.6 MB, free: 13.24 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001154/0.01991, allocations: 231.2 kB / 353.8 MB, free: 13.02 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002249/0.02014, allocations: 335.2 kB / 354.1 MB, free: 12.69 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0005801/0.02072, allocations: 0.6577 MB / 354.8 MB, free: 12.03 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 4.609e-06/0.02072, allocations: 3.984 kB / 354.8 MB, free: 12.02 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.503e-06/0.02072, allocations: 0 / 354.8 MB, free: 12.02 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 1.772e-05/0.02074, allocations: 0 / 354.8 MB, free: 12.02 MB / 330.7 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 252
 * Number of variables: 252
Notification: Performance of Generate backend data structure: time 0.001116/0.02186, allocations: 1.17 MB / 356 MB, free: 10.81 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.309e-05/0.0219, allocations: 8.031 kB / 356 MB, free: 10.8 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.000158/0.02206, allocations: 188.3 kB / 356.1 MB, free: 10.62 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001871/0.02225, allocations: 246.8 kB / 356.4 MB, free: 10.35 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.744e-05/0.02229, allocations: 74.38 kB / 356.5 MB, free: 10.28 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 9.139e-05/0.02238, allocations: 100.4 kB / 356.6 MB, free: 10.18 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0006273/0.02301, allocations: 0.624 MB / 357.2 MB, free: 9.539 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.198e-05/0.02303, allocations: 8.078 kB / 357.2 MB, free: 9.531 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.161e-05/0.02307, allocations: 40.38 kB / 357.2 MB, free: 9.492 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.546e-05/0.02309, allocations: 24.38 kB / 357.3 MB, free: 9.469 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003172/0.02341, allocations: 269.7 kB / 357.5 MB, free: 9.207 MB / 330.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002606/0.02601, allocations: 2.356 MB / 359.9 MB, free: 6.785 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0006422/0.02666, allocations: 419.9 kB / 360.3 MB, free: 6.352 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001982/0.02685, allocations: 188.8 kB / 360.5 MB, free: 6.16 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.463e-05/0.02688, allocations: 8.5 kB / 360.5 MB, free: 6.148 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.155e-05/0.02691, allocations: 49.77 kB / 360.5 MB, free: 6.09 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=50): time 2.846e-06/0.02691, allocations: 0 / 360.5 MB, free: 6.09 MB / 330.7 MB
Notification: Performance of matching and sorting (n=59): time 0.00176/0.02867, allocations: 1.292 MB / 361.8 MB, free: 4.773 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.267e-05/0.02871, allocations: 89.58 kB / 361.9 MB, free: 4.668 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002182/0.02892, allocations: 410.2 kB / 362.3 MB, free: 4.246 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 2.306e-05/0.02895, allocations: 33.7 kB / 362.3 MB, free: 4.207 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001916/0.02914, allocations: 0.4945 MB / 362.8 MB, free: 3.703 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001205/0.02926, allocations: 230 kB / 363.1 MB, free: 3.477 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000132/0.02939, allocations: 144.2 kB / 363.2 MB, free: 3.328 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001764/0.02957, allocations: 0.5312 MB / 363.7 MB, free: 2.785 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001555/0.02972, allocations: 143.5 kB / 363.9 MB, free: 2.645 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003061/0.03003, allocations: 483 kB / 364.3 MB, free: 2.012 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0006071/0.03064, allocations: 0.7635 MB / 365.1 MB, free: 1.082 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.421e-06/0.03064, allocations: 4 kB / 365.1 MB, free: 1.078 MB / 330.7 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0005684/0.03121, allocations: 0.5943 MB / 365.7 MB, free: 488 kB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.866e-05/0.03123, allocations: 14.03 kB / 365.7 MB, free: 476 kB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.137e-06/0.03124, allocations: 8 kB / 365.7 MB, free: 468 kB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.832e-05/0.03126, allocations: 15.94 kB / 365.7 MB, free: 452 kB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003301/0.03159, allocations: 196.4 kB / 365.9 MB, free: 256 kB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.091e-05/0.0316, allocations: 19.92 kB / 366 MB, free: 236 kB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001482/0.03175, allocations: 28 kB / 366 MB, free: 208 kB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.355e-05/0.03177, allocations: 28 kB / 366 MB, free: 180 kB / 330.7 MB
Warning: Assuming fixed start value for the following 12 variables:
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         nucleus.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         cytoplasm.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         cytoplasm.ambientSubstance.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytoplasm.y5.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytoplasm.y4.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytoplasm.y2.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytoplasm.y1.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         nucleus.ambientSubstance.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         nucleus.y7.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         nucleus.y6.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         nucleus.y3.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 39
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (107):
 * Single equations (assignments): 107
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0002481/0.03202, allocations: 252.2 kB / 366.3 MB, free: 15.92 MB / 346.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 6.634e-05/0.03208, allocations: 67.66 kB / 366.3 MB, free: 15.85 MB / 346.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.991e-05/0.03215, allocations: 68.91 kB / 366.4 MB, free: 15.79 MB / 346.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.671e-06/0.03216, allocations: 11.94 kB / 366.4 MB, free: 15.77 MB / 346.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.867e-06/0.03216, allocations: 0 / 366.4 MB, free: 15.77 MB / 346.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.374e-06/0.03217, allocations: 3.984 kB / 366.4 MB, free: 15.77 MB / 346.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005851/0.03276, allocations: 433.2 kB / 366.8 MB, free: 15.32 MB / 346.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.078e-06/0.03276, allocations: 0 / 366.8 MB, free: 15.32 MB / 346.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002601/0.03302, allocations: 107.9 kB / 366.9 MB, free: 15.21 MB / 346.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.615e-06/0.03302, allocations: 0 / 366.9 MB, free: 15.21 MB / 346.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.491e-05/0.03305, allocations: 15.98 kB / 366.9 MB, free: 15.2 MB / 346.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.324e-06/0.03305, allocations: 4 kB / 367 MB, free: 15.2 MB / 346.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.122e-06/0.03305, allocations: 0 / 367 MB, free: 15.2 MB / 346.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005512/0.0336, allocations: 0.7781 MB / 367.7 MB, free: 14.4 MB / 346.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.747e-05/0.03364, allocations: 43.66 kB / 367.8 MB, free: 14.36 MB / 346.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.71e-05/0.03368, allocations: 12 kB / 367.8 MB, free: 14.35 MB / 346.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001218/0.0338, allocations: 12 kB / 367.8 MB, free: 14.34 MB / 346.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.756e-05/0.03384, allocations: 40.36 kB / 367.8 MB, free: 14.3 MB / 346.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.574e-05/0.03385, allocations: 12 kB / 367.8 MB, free: 14.29 MB / 346.7 MB
Notification: Performance of sorting global known variables: time 0.0001103/0.03396, allocations: 251 kB / 368.1 MB, free: 14.04 MB / 346.7 MB
Notification: Performance of sort global known variables: time 1.41e-07/0.03396, allocations: 0 / 368.1 MB, free: 14.04 MB / 346.7 MB
Notification: Performance of remove unused functions: time 0.0003532/0.03432, allocations: 156 kB / 368.2 MB, free: 13.89 MB / 346.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 2
 * Number of states: 12 (nucleus.V,nucleus.y3.n,nucleus.y6.n,nucleus.y7.n,nucleus.ambientSubstance.n,cytoplasm.V,cytoplasm.y1.n,cytoplasm.y2.n,cytoplasm.y4.n,cytoplasm.y5.n,cytoplasm.ambientSubstance.n,V)
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (59):
 * Single equations (assignments): 59
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.0002863/0.0346, allocations: 118.2 kB / 368.4 MB, free: 13.76 MB / 346.7 MB
Notification: Performance of simCode: created initialization part: time 0.0003744/0.03498, allocations: 399 kB / 368.7 MB, free: 13.37 MB / 346.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.794e-06/0.03498, allocations: 4.062 kB / 368.8 MB, free: 13.36 MB / 346.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001404/0.03512, allocations: 175.4 kB / 368.9 MB, free: 13.19 MB / 346.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003233/0.03544, allocations: 66.81 kB / 369 MB, free: 13.12 MB / 346.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001631/0.03707, allocations: 1.561 MB / 370.5 MB, free: 11.52 MB / 346.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 9.689e-05/0.03717, allocations: 156 kB / 370.7 MB, free: 11.34 MB / 346.7 MB
Notification: Performance of simCode: alias equations: time 0.0002089/0.03738, allocations: 64.59 kB / 370.8 MB, free: 11.28 MB / 346.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001909/0.03757, allocations: 170.1 kB / 370.9 MB, free: 11.11 MB / 346.7 MB
Notification: Performance of SimCode: time 6.01e-07/0.03757, allocations: 0 / 370.9 MB, free: 11.11 MB / 346.7 MB
Notification: Performance of Templates: time 0.00873/0.0463, allocations: 5.806 MB / 376.7 MB, free: 5.41 MB / 346.7 MB
"
[Timeout remaining time 660]
make -j1 -f BioChem_BioChem.Examples.CircadianOscillator.Container.makefile [Timeout 660]
(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=240  -lv LOG_STATS > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 2.848453911021352]