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 0.001393/0.001393, allocations: 92.22 kB / 19.65 MB, free: 276 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 0.001654/0.001654, allocations: 173 kB / 23.02 MB, free: 1.547 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 0.9515/0.9515, allocations: 177.1 MB / 203.4 MB, free: 5.633 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 0.03921/0.03921, allocations: 9.545 MB / 269.5 MB, free: 3.945 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 2.134e-06/2.134e-06, allocations: 0 / 342.9 MB, free: 6.746 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.51e-05/2.723e-05, allocations: 2.312 kB / 342.9 MB, free: 6.742 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.007531/0.007558, allocations: 6.612 MB / 349.5 MB, free: 112 kB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.001483/0.009041, allocations: 0.8225 MB / 350.3 MB, free: 15.28 MB / 282.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003504/0.009392, allocations: 40 kB / 350.4 MB, free: 15.24 MB / 282.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002841/0.009676, allocations: 142.8 kB / 350.5 MB, free: 15.1 MB / 282.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0005159/0.01019, allocations: 225.8 kB / 350.7 MB, free: 14.88 MB / 282.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0004134/0.01061, allocations: 203.8 kB / 350.9 MB, free: 14.68 MB / 282.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0008038/0.01141, allocations: 0.8645 MB / 351.8 MB, free: 13.81 MB / 282.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005462/0.01196, allocations: 355.1 kB / 352.1 MB, free: 13.44 MB / 282.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0005311/0.01249, allocations: 0.5692 MB / 352.7 MB, free: 12.87 MB / 282.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003803/0.01287, allocations: 319 kB / 353 MB, free: 12.55 MB / 282.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001397/0.01301, allocations: 116 kB / 353.1 MB, free: 12.44 MB / 282.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001347/0.01314, allocations: 116 kB / 353.2 MB, free: 12.33 MB / 282.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001462/0.01329, allocations: 227.2 kB / 353.5 MB, free: 12.11 MB / 282.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002882/0.01358, allocations: 331.2 kB / 353.8 MB, free: 11.78 MB / 282.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0007117/0.01429, allocations: 0.6577 MB / 354.5 MB, free: 11.12 MB / 282.7 MB
Notification: Performance of FrontEnd - DAE generated: time 4.028e-06/0.01429, allocations: 3.984 kB / 354.5 MB, free: 11.12 MB / 282.7 MB
Notification: Performance of FrontEnd: time 7.31e-07/0.01429, allocations: 7.938 kB / 354.5 MB, free: 11.11 MB / 282.7 MB
Notification: Performance of Transformations before backend: time 1.009e-05/0.0143, allocations: 0 / 354.5 MB, free: 11.11 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 0.00148/0.01578, allocations: 1.162 MB / 355.6 MB, free: 9.906 MB / 282.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.17e-05/0.01582, allocations: 8.031 kB / 355.6 MB, free: 9.898 MB / 282.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002355/0.01606, allocations: 188.3 kB / 355.8 MB, free: 9.715 MB / 282.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002378/0.0163, allocations: 250.8 kB / 356.1 MB, free: 9.441 MB / 282.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 6.47e-05/0.01636, allocations: 78.31 kB / 356.1 MB, free: 9.363 MB / 282.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001263/0.01649, allocations: 96.38 kB / 356.2 MB, free: 9.27 MB / 282.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.00113/0.01762, allocations: 0.6788 MB / 356.9 MB, free: 8.578 MB / 282.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.958e-05/0.01765, allocations: 192 / 356.9 MB, free: 8.578 MB / 282.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.403e-05/0.01772, allocations: 40.38 kB / 357 MB, free: 8.539 MB / 282.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.758e-05/0.01775, allocations: 24.38 kB / 357 MB, free: 8.516 MB / 282.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0007806/0.01853, allocations: 355.7 kB / 357.3 MB, free: 8.164 MB / 282.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003726/0.02226, allocations: 2.45 MB / 359.8 MB, free: 5.645 MB / 282.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.000859/0.02311, allocations: 456.4 kB / 360.2 MB, free: 5.176 MB / 282.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003508/0.02347, allocations: 208.8 kB / 360.4 MB, free: 4.965 MB / 282.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.636e-05/0.02349, allocations: 8.5 kB / 360.4 MB, free: 4.957 MB / 282.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.207e-05/0.02352, allocations: 41.89 kB / 360.5 MB, free: 4.906 MB / 282.7 MB
Notification: Performance of pre-optimization done (n=50): time 2.445e-06/0.02353, allocations: 0 / 360.5 MB, free: 4.906 MB / 282.7 MB
Notification: Performance of matching and sorting (n=59): time 0.003185/0.02671, allocations: 1.585 MB / 362.1 MB, free: 3.293 MB / 282.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.133e-05/0.02676, allocations: 85.61 kB / 362.1 MB, free: 3.191 MB / 282.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003868/0.02715, allocations: 406.4 kB / 362.5 MB, free: 2.773 MB / 282.7 MB
Notification: Performance of collectPreVariables (initialization): time 3.501e-05/0.02718, allocations: 37.7 kB / 362.6 MB, free: 2.73 MB / 282.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002766/0.02746, allocations: 0.4985 MB / 363.1 MB, free: 2.223 MB / 282.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001636/0.02762, allocations: 234 kB / 363.3 MB, free: 1.992 MB / 282.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001867/0.02781, allocations: 144.3 kB / 363.4 MB, free: 1.844 MB / 282.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001804/0.02799, allocations: 0.5235 MB / 364 MB, free: 1.309 MB / 282.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003124/0.0283, allocations: 171.6 kB / 364.1 MB, free: 1.141 MB / 282.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004847/0.02879, allocations: 0.4913 MB / 364.6 MB, free: 500 kB / 282.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001297/0.03009, allocations: 0.8456 MB / 365.5 MB, free: 15.47 MB / 298.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.94e-06/0.03009, allocations: 0 / 365.5 MB, free: 15.47 MB / 298.7 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001088/0.03118, allocations: 0.669 MB / 366.1 MB, free: 14.8 MB / 298.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.228e-05/0.0312, allocations: 8 kB / 366.1 MB, free: 14.79 MB / 298.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.538e-05/0.03122, allocations: 15.94 kB / 366.2 MB, free: 14.77 MB / 298.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.591e-05/0.03124, allocations: 15.94 kB / 366.2 MB, free: 14.76 MB / 298.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005952/0.03184, allocations: 183.7 kB / 366.4 MB, free: 14.58 MB / 298.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.084e-05/0.03186, allocations: 23.92 kB / 366.4 MB, free: 14.55 MB / 298.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002664/0.03213, allocations: 20 kB / 366.4 MB, free: 14.54 MB / 298.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.961e-05/0.03219, allocations: 40 kB / 366.4 MB, free: 14.5 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 0.0003037/0.03249, allocations: 243.7 kB / 366.7 MB, free: 14.25 MB / 298.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001193/0.03261, allocations: 67.67 kB / 366.7 MB, free: 14.18 MB / 298.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001045/0.03271, allocations: 80.83 kB / 366.8 MB, free: 14.1 MB / 298.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.889e-06/0.03272, allocations: 4 kB / 366.8 MB, free: 14.1 MB / 298.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.931e-06/0.03272, allocations: 3.984 kB / 366.8 MB, free: 14.09 MB / 298.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.913e-06/0.03273, allocations: 4 kB / 366.8 MB, free: 14.09 MB / 298.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007874/0.03352, allocations: 0.5007 MB / 367.3 MB, free: 13.55 MB / 298.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.946e-06/0.03352, allocations: 0 / 367.3 MB, free: 13.55 MB / 298.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004649/0.03399, allocations: 115.8 kB / 367.4 MB, free: 13.44 MB / 298.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.987e-06/0.03399, allocations: 0 / 367.4 MB, free: 13.44 MB / 298.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.351e-05/0.03403, allocations: 16 kB / 367.5 MB, free: 13.43 MB / 298.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.729e-06/0.03404, allocations: 3.938 kB / 367.5 MB, free: 13.42 MB / 298.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.704e-06/0.03404, allocations: 0 / 367.5 MB, free: 13.42 MB / 298.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009946/0.03503, allocations: 0.8253 MB / 368.3 MB, free: 12.58 MB / 298.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 4.988e-05/0.03508, allocations: 43.7 kB / 368.3 MB, free: 12.54 MB / 298.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.444e-05/0.03514, allocations: 12 kB / 368.3 MB, free: 12.52 MB / 298.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002039/0.03534, allocations: 19.94 kB / 368.4 MB, free: 12.5 MB / 298.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.545e-05/0.03541, allocations: 40.36 kB / 368.4 MB, free: 12.46 MB / 298.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.574e-05/0.03543, allocations: 12 kB / 368.4 MB, free: 12.45 MB / 298.7 MB
Notification: Performance of sorting global known variables: time 0.0001861/0.03562, allocations: 255.1 kB / 368.7 MB, free: 12.2 MB / 298.7 MB
Notification: Performance of sort global known variables: time 1e-07/0.03562, allocations: 0 / 368.7 MB, free: 12.2 MB / 298.7 MB
Notification: Performance of remove unused functions: time 0.0005984/0.03622, allocations: 156 kB / 368.8 MB, free: 12.05 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 0.0001302/0.03635, allocations: 113.6 kB / 368.9 MB, free: 11.93 MB / 298.7 MB
Notification: Performance of simCode: created initialization part: time 0.0007142/0.03706, allocations: 454.7 kB / 369.4 MB, free: 11.49 MB / 298.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.024e-06/0.03707, allocations: 0 / 369.4 MB, free: 11.49 MB / 298.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002976/0.03736, allocations: 203.4 kB / 369.6 MB, free: 11.28 MB / 298.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005567/0.03792, allocations: 73.91 kB / 369.6 MB, free: 11.21 MB / 298.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002126/0.04004, allocations: 1.581 MB / 371.2 MB, free: 9.586 MB / 298.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 9.495e-05/0.04014, allocations: 156 kB / 371.4 MB, free: 9.414 MB / 298.7 MB
Notification: Performance of simCode: alias equations: time 0.0001511/0.04029, allocations: 60.59 kB / 371.4 MB, free: 9.355 MB / 298.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001073/0.0404, allocations: 48.48 kB / 371.5 MB, free: 9.309 MB / 298.7 MB
Notification: Performance of SimCode: time 1.072e-06/0.0404, allocations: 0 / 371.5 MB, free: 9.309 MB / 298.7 MB
Notification: Performance of Templates: time 0.007774/0.04817, allocations: 5.52 MB / 377 MB, free: 3.879 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: 2.928794118575752]