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/BioChem 1.1.2-master/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/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/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 BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/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/BioChem 1.1.2-master/package.mo): time 0.1646/0.1646, allocations: 12.25 MB / 27.21 MB, free: 0.9531 MB / 18.57 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001677/0.001677, allocations: 177 kB / 30.74 MB, free: 3.973 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 2.58/2.58, allocations: 223.1 MB / 257.3 MB, free: 9.398 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001725/0.001725, allocations: 96.25 kB / 311.1 MB, free: 10.95 MB / 250.7 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0004732/0.0004733, allocations: 12.66 kB / 374.7 MB, free: 53.1 MB / 298.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1056/0.1061, allocations: 53.08 MB / 427.7 MB, free: 12.52 MB / 298.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01341/0.1196, allocations: 7.264 MB / 435 MB, free: 5.223 MB / 298.7 MB
Notification: Performance of NFInst.instExpressions: time 0.002052/0.1217, allocations: 0.8576 MB / 435.9 MB, free: 4.363 MB / 298.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0007327/0.1225, allocations: 40 kB / 435.9 MB, free: 4.324 MB / 298.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0003994/0.1229, allocations: 107.3 kB / 436 MB, free: 4.219 MB / 298.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0007923/0.1237, allocations: 199.4 kB / 436.2 MB, free: 4.023 MB / 298.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0005647/0.1243, allocations: 111.9 kB / 436.3 MB, free: 3.914 MB / 298.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001227/0.1256, allocations: 0.5467 MB / 436.9 MB, free: 3.367 MB / 298.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0008234/0.1264, allocations: 406.3 kB / 437.3 MB, free: 2.949 MB / 298.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003462/0.1268, allocations: 250.9 kB / 437.5 MB, free: 2.703 MB / 298.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0004264/0.1272, allocations: 310.4 kB / 437.8 MB, free: 2.398 MB / 298.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001069/0.1274, allocations: 40 kB / 437.8 MB, free: 2.359 MB / 298.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001358/0.1275, allocations: 44 kB / 437.9 MB, free: 2.316 MB / 298.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001143/0.1276, allocations: 131.4 kB / 438 MB, free: 2.188 MB / 298.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001727/0.1278, allocations: 177.3 kB / 438.2 MB, free: 2.008 MB / 298.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.001035/0.1289, allocations: 0.8651 MB / 439.1 MB, free: 1.141 MB / 298.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.977e-06/0.1289, allocations: 11.94 kB / 439.1 MB, free: 1.129 MB / 298.7 MB
Notification: Performance of FrontEnd: time 2.234e-06/0.1289, allocations: 0 / 439.1 MB, free: 1.129 MB / 298.7 MB
Notification: Performance of Transformations before backend: time 3.312e-05/0.1289, allocations: 0 / 439.1 MB, free: 1.129 MB / 298.7 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 0.002246/0.1312, allocations: 0.9552 MB / 440 MB, free: 128 kB / 298.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.692e-05/0.1313, allocations: 8.031 kB / 440 MB, free: 120 kB / 298.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002947/0.1316, allocations: 94.88 kB / 440.1 MB, free: 24 kB / 298.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0005043/0.1321, allocations: 297.7 kB / 440.4 MB, free: 15.69 MB / 314.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001076/0.1322, allocations: 81.94 kB / 440.5 MB, free: 15.61 MB / 314.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002868/0.1325, allocations: 99.98 kB / 440.6 MB, free: 15.51 MB / 314.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002593/0.1351, allocations: 0.8563 MB / 441.4 MB, free: 14.64 MB / 314.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 5.899e-05/0.1352, allocations: 4 kB / 441.5 MB, free: 14.64 MB / 314.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001361/0.1354, allocations: 36 kB / 441.5 MB, free: 14.61 MB / 314.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.391e-05/0.1354, allocations: 27.95 kB / 441.5 MB, free: 14.58 MB / 314.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.00204/0.1375, allocations: 0.6208 MB / 442.1 MB, free: 13.96 MB / 314.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.008459/0.146, allocations: 2.847 MB / 445 MB, free: 11.03 MB / 314.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.001841/0.1479, allocations: 0.5144 MB / 445.5 MB, free: 10.5 MB / 314.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 6.084e-05/0.148, allocations: 4.5 kB / 445.5 MB, free: 10.49 MB / 314.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.513e-05/0.148, allocations: 46.94 kB / 445.5 MB, free: 10.44 MB / 314.7 MB
Notification: Performance of pre-optimization done (n=50): time 3.566e-06/0.148, allocations: 0 / 445.5 MB, free: 10.44 MB / 314.7 MB
Notification: Performance of matching and sorting (n=59): time 0.009445/0.1575, allocations: 2.158 MB / 447.7 MB, free: 8.234 MB / 314.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.38e-05/0.1576, allocations: 85.67 kB / 447.8 MB, free: 8.133 MB / 314.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0006496/0.1583, allocations: 369.4 kB / 448.2 MB, free: 7.766 MB / 314.7 MB
Notification: Performance of collectPreVariables (initialization): time 8.5e-05/0.1584, allocations: 33.7 kB / 448.2 MB, free: 7.727 MB / 314.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003918/0.1588, allocations: 454.2 kB / 448.6 MB, free: 7.273 MB / 314.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002695/0.1591, allocations: 216.8 kB / 448.8 MB, free: 7.059 MB / 314.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.41e-05/0.1591, allocations: 16 kB / 448.9 MB, free: 7.043 MB / 314.7 MB
Notification: Performance of setup shared object (initialization): time 0.0002098/0.1594, allocations: 358.8 kB / 449.2 MB, free: 6.684 MB / 314.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000656/0.16, allocations: 242.7 kB / 449.4 MB, free: 6.445 MB / 314.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0008424/0.1609, allocations: 480.9 kB / 449.9 MB, free: 5.855 MB / 314.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0007969/0.1617, allocations: 300.1 kB / 450.2 MB, free: 5.562 MB / 314.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.051e-05/0.1618, allocations: 4 kB / 450.2 MB, free: 5.559 MB / 314.7 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.002087/0.1639, allocations: 0.7995 MB / 451 MB, free: 4.75 MB / 314.7 MB
Notification: Performance of prepare postOptimizeDAE: time 3.39e-05/0.1639, allocations: 8 kB / 451 MB, free: 4.742 MB / 314.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.987e-05/0.164, allocations: 8 kB / 451 MB, free: 4.734 MB / 314.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 4.551e-05/0.164, allocations: 16 kB / 451 MB, free: 4.719 MB / 314.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001351/0.1654, allocations: 187.7 kB / 451.2 MB, free: 4.535 MB / 314.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 3.191e-05/0.1654, allocations: 15.94 kB / 451.2 MB, free: 4.52 MB / 314.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0007282/0.1662, allocations: 55.94 kB / 451.3 MB, free: 4.465 MB / 314.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.947e-05/0.1663, allocations: 36 kB / 451.3 MB, free: 4.43 MB / 314.7 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
         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
         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.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" 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
         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.ambientSubstance.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         cytoplasm.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" 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
         cytoplasm.y2.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 (linear and non-linear blocks): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0007695/0.167, allocations: 285 kB / 451.6 MB, free: 4.152 MB / 314.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001554/0.1672, allocations: 55.38 kB / 451.7 MB, free: 4.098 MB / 314.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002022/0.1674, allocations: 64.91 kB / 451.7 MB, free: 4.031 MB / 314.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.262e-05/0.1675, allocations: 11.98 kB / 451.7 MB, free: 4.02 MB / 314.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 9.408e-06/0.1675, allocations: 0 / 451.7 MB, free: 4.02 MB / 314.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.897e-06/0.1675, allocations: 0 / 451.7 MB, free: 4.02 MB / 314.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001923/0.1694, allocations: 0.7632 MB / 452.5 MB, free: 3.207 MB / 314.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 8.587e-06/0.1695, allocations: 0 / 452.5 MB, free: 3.207 MB / 314.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001243/0.1707, allocations: 103.9 kB / 452.6 MB, free: 3.105 MB / 314.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 1.72e-05/0.1708, allocations: 7.984 kB / 452.6 MB, free: 3.098 MB / 314.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.855e-05/0.1709, allocations: 16 kB / 452.6 MB, free: 3.082 MB / 314.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 9.839e-06/0.1709, allocations: 8 kB / 452.6 MB, free: 3.074 MB / 314.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.465e-06/0.1709, allocations: 0 / 452.6 MB, free: 3.074 MB / 314.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.002101/0.173, allocations: 0.9494 MB / 453.6 MB, free: 2.102 MB / 314.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001897/0.1732, allocations: 116.5 kB / 453.7 MB, free: 1.969 MB / 314.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.000105/0.1734, allocations: 12 kB / 453.7 MB, free: 1.957 MB / 314.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005893/0.174, allocations: 31.89 kB / 453.7 MB, free: 1.926 MB / 314.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001099/0.1741, allocations: 36.47 kB / 453.8 MB, free: 1.891 MB / 314.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.769e-05/0.1742, allocations: 19.98 kB / 453.8 MB, free: 1.871 MB / 314.7 MB
Notification: Performance of sorting global known variables: time 0.0003791/0.1745, allocations: 239.2 kB / 454 MB, free: 1.641 MB / 314.7 MB
Notification: Performance of sort global known variables: time 2.475e-06/0.1746, allocations: 112 / 454 MB, free: 1.641 MB / 314.7 MB
Notification: Performance of remove unused functions: time 0.0009038/0.1755, allocations: 159.9 kB / 454.2 MB, free: 1.484 MB / 314.7 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 (linear and non-linear blocks): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.0001757/0.1757, allocations: 118 kB / 454.3 MB, free: 1.363 MB / 314.7 MB
Notification: Performance of simCode: created initialization part: time 0.001545/0.1772, allocations: 0.5952 MB / 454.9 MB, free: 0.7734 MB / 314.7 MB
Notification: Performance of simCode: created event and clocks part: time 3.928e-06/0.1772, allocations: 0 / 454.9 MB, free: 0.7734 MB / 314.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.000665/0.1779, allocations: 259.1 kB / 455.1 MB, free: 0.5195 MB / 314.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005783/0.1785, allocations: 53.48 kB / 455.2 MB, free: 480 kB / 314.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.005658/0.1842, allocations: 2.235 MB / 457.4 MB, free: 14.19 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0007189/0.185, allocations: 0.9547 MB / 458.4 MB, free: 13.2 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 0.0005536/0.1855, allocations: 68.58 kB / 458.5 MB, free: 13.14 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002706/0.1858, allocations: 43.42 kB / 458.5 MB, free: 13.09 MB / 330.7 MB
Notification: Performance of SimCode: time 1.162e-06/0.1858, allocations: 4 kB / 458.5 MB, free: 13.09 MB / 330.7 MB
Notification: Performance of Templates: time 0.01709/0.2029, allocations: 4.875 MB / 463.4 MB, free: 8.246 MB / 330.7 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)