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 0.0009245/0.0009245, allocations: 93.06 kB / 19.65 MB, free: 280 kB / 13.93 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 0.0009275/0.0009275, allocations: 165.3 kB / 23.02 MB, free: 1.551 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 1.005/1.005, allocations: 177.1 MB / 203.4 MB, free: 5.629 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 0.04711/0.04711, allocations: 9.543 MB / 269.5 MB, free: 3.938 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 2.244e-06/2.244e-06, allocations: 0 / 342.9 MB, free: 6.734 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.687e-05/2.912e-05, allocations: 4.562 kB / 342.9 MB, free: 6.73 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.008121/0.00815, allocations: 6.606 MB / 349.5 MB, free: 104 kB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.001664/0.009813, allocations: 0.8303 MB / 350.3 MB, free: 15.27 MB / 282.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003302/0.01014, allocations: 44 kB / 350.4 MB, free: 15.22 MB / 282.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002673/0.01041, allocations: 138.8 kB / 350.5 MB, free: 15.09 MB / 282.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0005087/0.01092, allocations: 225.8 kB / 350.7 MB, free: 14.86 MB / 282.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0004089/0.01133, allocations: 195.7 kB / 350.9 MB, free: 14.67 MB / 282.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0008152/0.01214, allocations: 0.8685 MB / 351.8 MB, free: 13.8 MB / 282.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006207/0.01276, allocations: 355.1 kB / 352.1 MB, free: 13.43 MB / 282.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0005859/0.01335, allocations: 0.5692 MB / 352.7 MB, free: 12.86 MB / 282.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0004083/0.01376, allocations: 319 kB / 353 MB, free: 12.54 MB / 282.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001454/0.0139, allocations: 116 kB / 353.1 MB, free: 12.43 MB / 282.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001376/0.01404, allocations: 116 kB / 353.2 MB, free: 12.32 MB / 282.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.000151/0.01419, allocations: 235.2 kB / 353.5 MB, free: 12.09 MB / 282.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002886/0.01448, allocations: 327.2 kB / 353.8 MB, free: 11.77 MB / 282.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0007441/0.01523, allocations: 0.6616 MB / 354.5 MB, free: 11.1 MB / 282.7 MB
Notification: Performance of FrontEnd - DAE generated: time 5.18e-06/0.01523, allocations: 0 / 354.5 MB, free: 11.1 MB / 282.7 MB
Notification: Performance of FrontEnd: time 1.363e-06/0.01523, allocations: 3.938 kB / 354.5 MB, free: 11.1 MB / 282.7 MB
Notification: Performance of Transformations before backend: time 1.364e-05/0.01525, allocations: 0 / 354.5 MB, free: 11.1 MB / 282.7 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 0.001516/0.01676, allocations: 1.17 MB / 355.6 MB, free: 9.887 MB / 282.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.944e-05/0.01681, allocations: 8.031 kB / 355.6 MB, free: 9.879 MB / 282.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002351/0.01705, allocations: 184.3 kB / 355.8 MB, free: 9.699 MB / 282.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002402/0.01729, allocations: 246.8 kB / 356.1 MB, free: 9.43 MB / 282.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 6.729e-05/0.01735, allocations: 78.31 kB / 356.1 MB, free: 9.352 MB / 282.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001297/0.01748, allocations: 96.38 kB / 356.2 MB, free: 9.258 MB / 282.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001151/0.01863, allocations: 0.6788 MB / 356.9 MB, free: 8.566 MB / 282.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.717e-05/0.01866, allocations: 192 / 356.9 MB, free: 8.566 MB / 282.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.674e-05/0.01873, allocations: 40.38 kB / 357 MB, free: 8.527 MB / 282.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.516e-05/0.01875, allocations: 24.38 kB / 357 MB, free: 8.504 MB / 282.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008057/0.01956, allocations: 355.7 kB / 357.3 MB, free: 8.152 MB / 282.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.00382/0.02338, allocations: 2.446 MB / 359.8 MB, free: 5.637 MB / 282.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008395/0.02422, allocations: 456.4 kB / 360.2 MB, free: 5.168 MB / 282.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003337/0.02455, allocations: 204.9 kB / 360.4 MB, free: 4.961 MB / 282.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.982e-05/0.02458, allocations: 12.5 kB / 360.4 MB, free: 4.949 MB / 282.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.308e-05/0.02461, allocations: 37.89 kB / 360.5 MB, free: 4.902 MB / 282.7 MB
Notification: Performance of pre-optimization done (n=50): time 2.846e-06/0.02462, allocations: 0 / 360.5 MB, free: 4.902 MB / 282.7 MB
Notification: Performance of matching and sorting (n=59): time 0.003142/0.02776, allocations: 1.596 MB / 362.1 MB, free: 3.277 MB / 282.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.94e-05/0.02781, allocations: 85.61 kB / 362.1 MB, free: 3.176 MB / 282.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000373/0.02818, allocations: 414.4 kB / 362.5 MB, free: 2.75 MB / 282.7 MB
Notification: Performance of collectPreVariables (initialization): time 3.359e-05/0.02822, allocations: 37.7 kB / 362.6 MB, free: 2.707 MB / 282.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002778/0.02849, allocations: 498.5 kB / 363.1 MB, free: 2.211 MB / 282.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001648/0.02866, allocations: 238 kB / 363.3 MB, free: 1.977 MB / 282.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001886/0.02885, allocations: 140.3 kB / 363.4 MB, free: 1.832 MB / 282.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001966/0.02904, allocations: 0.5274 MB / 364 MB, free: 1.293 MB / 282.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003048/0.02935, allocations: 167.6 kB / 364.1 MB, free: 1.129 MB / 282.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004666/0.02981, allocations: 0.4952 MB / 364.6 MB, free: 484 kB / 282.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001089/0.0309, allocations: 0.8495 MB / 365.5 MB, free: 15.45 MB / 298.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.899e-06/0.03091, allocations: 0 / 365.5 MB, free: 15.45 MB / 298.7 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001062/0.03197, allocations: 0.6686 MB / 366.1 MB, free: 14.78 MB / 298.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.696e-05/0.032, allocations: 8 kB / 366.2 MB, free: 14.77 MB / 298.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.586e-05/0.03201, allocations: 11.94 kB / 366.2 MB, free: 14.76 MB / 298.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 3.211e-05/0.03205, allocations: 19.94 kB / 366.2 MB, free: 14.74 MB / 298.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005716/0.03262, allocations: 184.4 kB / 366.4 MB, free: 14.56 MB / 298.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.209e-05/0.03264, allocations: 19.92 kB / 366.4 MB, free: 14.54 MB / 298.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002716/0.03291, allocations: 28 kB / 366.4 MB, free: 14.51 MB / 298.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.832e-05/0.03296, allocations: 40 kB / 366.5 MB, free: 14.47 MB / 298.7 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 0.0003441/0.0333, allocations: 240.8 kB / 366.7 MB, free: 14.23 MB / 298.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001143/0.03342, allocations: 67.67 kB / 366.8 MB, free: 14.16 MB / 298.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001039/0.03352, allocations: 80.83 kB / 366.8 MB, free: 14.08 MB / 298.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.881e-06/0.03353, allocations: 4 kB / 366.8 MB, free: 14.08 MB / 298.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.845e-06/0.03354, allocations: 0 / 366.8 MB, free: 14.08 MB / 298.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.233e-06/0.03354, allocations: 3.984 kB / 366.8 MB, free: 14.07 MB / 298.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.00083/0.03437, allocations: 0.4968 MB / 367.3 MB, free: 13.54 MB / 298.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.108e-06/0.03438, allocations: 0 / 367.3 MB, free: 13.54 MB / 298.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004527/0.03483, allocations: 115.8 kB / 367.4 MB, free: 13.43 MB / 298.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 5.55e-06/0.03483, allocations: 0 / 367.4 MB, free: 13.43 MB / 298.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.883e-05/0.03487, allocations: 16 kB / 367.5 MB, free: 13.41 MB / 298.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.739e-06/0.03488, allocations: 7.938 kB / 367.5 MB, free: 13.41 MB / 298.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.557e-06/0.03488, allocations: 3.984 kB / 367.5 MB, free: 13.4 MB / 298.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001015/0.0359, allocations: 0.8253 MB / 368.3 MB, free: 12.56 MB / 298.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.736e-05/0.03595, allocations: 43.7 kB / 368.3 MB, free: 12.52 MB / 298.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.612e-05/0.03601, allocations: 16 kB / 368.4 MB, free: 12.5 MB / 298.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002199/0.03623, allocations: 11.94 kB / 368.4 MB, free: 12.49 MB / 298.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.713e-05/0.0363, allocations: 44.36 kB / 368.4 MB, free: 12.45 MB / 298.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.731e-05/0.03632, allocations: 8 kB / 368.4 MB, free: 12.44 MB / 298.7 MB
Notification: Performance of sorting global known variables: time 0.0002184/0.03654, allocations: 263.1 kB / 368.7 MB, free: 12.18 MB / 298.7 MB
Notification: Performance of sort global known variables: time 8e-08/0.03654, allocations: 0 / 368.7 MB, free: 12.18 MB / 298.7 MB
Notification: Performance of remove unused functions: time 0.000611/0.03715, allocations: 156 kB / 368.8 MB, free: 12.03 MB / 298.7 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 0.0001371/0.03729, allocations: 113.6 kB / 368.9 MB, free: 11.91 MB / 298.7 MB
Notification: Performance of simCode: created initialization part: time 0.0007462/0.03804, allocations: 455 kB / 369.4 MB, free: 11.46 MB / 298.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.555e-06/0.03804, allocations: 4.125 kB / 369.4 MB, free: 11.46 MB / 298.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002951/0.03834, allocations: 199.4 kB / 369.6 MB, free: 11.26 MB / 298.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005158/0.03885, allocations: 65.41 kB / 369.6 MB, free: 11.2 MB / 298.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002473/0.04132, allocations: 1.581 MB / 371.2 MB, free: 9.57 MB / 298.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001339/0.04146, allocations: 156 kB / 371.4 MB, free: 9.398 MB / 298.7 MB
Notification: Performance of simCode: alias equations: time 0.0002235/0.04168, allocations: 60.59 kB / 371.4 MB, free: 9.34 MB / 298.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001372/0.04182, allocations: 48.48 kB / 371.5 MB, free: 9.293 MB / 298.7 MB
Notification: Performance of SimCode: time 1.232e-06/0.04182, allocations: 0 / 371.5 MB, free: 9.293 MB / 298.7 MB
Notification: Performance of Templates: time 0.00889/0.05071, allocations: 5.296 MB / 376.8 MB, free: 4.086 MB / 298.7 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: 3.1156794051639736]