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 0.0009168/0.0009168, allocations: 88.2 kB / 20.19 MB, free: 4.363 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 0.0009096/0.0009096, allocations: 173 kB / 23.5 MB, free: 1.051 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 1.024/1.024, allocations: 177.1 MB / 203.8 MB, free: 5.641 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 0.04017/0.04017, allocations: 9.543 MB / 269.8 MB, free: 4.012 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 1.633e-06/1.633e-06, allocations: 0 / 342.9 MB, free: 7.07 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.066e-05/2.229e-05, allocations: 4.562 kB / 342.9 MB, free: 7.066 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.005199/0.005221, allocations: 6.575 MB / 349.5 MB, free: 476 kB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.001239/0.006461, allocations: 0.8264 MB / 350.3 MB, free: 15.63 MB / 282.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003226/0.006783, allocations: 40 kB / 350.3 MB, free: 15.59 MB / 282.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002285/0.007012, allocations: 146.8 kB / 350.5 MB, free: 15.45 MB / 282.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0003797/0.007391, allocations: 225.8 kB / 350.7 MB, free: 15.23 MB / 282.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003231/0.007714, allocations: 199.7 kB / 350.9 MB, free: 15.03 MB / 282.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0006533/0.008368, allocations: 0.8607 MB / 351.8 MB, free: 14.16 MB / 282.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0004319/0.0088, allocations: 355.1 kB / 352.1 MB, free: 13.79 MB / 282.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0004623/0.009262, allocations: 0.5692 MB / 352.7 MB, free: 13.22 MB / 282.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002802/0.009542, allocations: 315 kB / 353 MB, free: 12.91 MB / 282.7 MB
Notification: Performance of NFPackage.collectConstants: time 9.367e-05/0.009636, allocations: 116 kB / 353.1 MB, free: 12.8 MB / 282.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 8.83e-05/0.009724, allocations: 116 kB / 353.2 MB, free: 12.69 MB / 282.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001089/0.009833, allocations: 235.2 kB / 353.4 MB, free: 12.46 MB / 282.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002019/0.01003, allocations: 323.2 kB / 353.8 MB, free: 12.14 MB / 282.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0005222/0.01056, allocations: 0.6694 MB / 354.4 MB, free: 11.47 MB / 282.7 MB
Notification: Performance of FrontEnd - DAE generated: time 2.485e-06/0.01056, allocations: 3.938 kB / 354.4 MB, free: 11.46 MB / 282.7 MB
Notification: Performance of FrontEnd: time 1.172e-06/0.01056, allocations: 4 kB / 354.4 MB, free: 11.46 MB / 282.7 MB
Notification: Performance of Transformations before backend: time 7.223e-06/0.01057, allocations: 0 / 354.4 MB, free: 11.46 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 0.001087/0.01165, allocations: 1.166 MB / 355.6 MB, free: 10.25 MB / 282.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.937e-05/0.01169, allocations: 12.03 kB / 355.6 MB, free: 10.24 MB / 282.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001597/0.01185, allocations: 180.3 kB / 355.8 MB, free: 10.07 MB / 282.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001911/0.01204, allocations: 250.8 kB / 356 MB, free: 9.793 MB / 282.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.614e-05/0.01209, allocations: 70.38 kB / 356.1 MB, free: 9.723 MB / 282.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 8.915e-05/0.01218, allocations: 104.4 kB / 356.2 MB, free: 9.621 MB / 282.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0007881/0.01297, allocations: 0.6748 MB / 356.9 MB, free: 8.934 MB / 282.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.54e-05/0.01299, allocations: 8.188 kB / 356.9 MB, free: 8.926 MB / 282.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.824e-05/0.01304, allocations: 40.38 kB / 356.9 MB, free: 8.887 MB / 282.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.865e-05/0.01306, allocations: 24.38 kB / 357 MB, free: 8.863 MB / 282.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0005526/0.01361, allocations: 355.7 kB / 357.3 MB, free: 8.512 MB / 282.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002675/0.01629, allocations: 2.438 MB / 359.7 MB, free: 6.004 MB / 282.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0005777/0.01687, allocations: 444.5 kB / 360.2 MB, free: 5.547 MB / 282.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002499/0.01712, allocations: 216.8 kB / 360.4 MB, free: 5.328 MB / 282.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.643e-05/0.01713, allocations: 8.5 kB / 360.4 MB, free: 5.32 MB / 282.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.523e-05/0.01716, allocations: 41.89 kB / 360.4 MB, free: 5.27 MB / 282.7 MB
Notification: Performance of pre-optimization done (n=50): time 2.404e-06/0.01716, allocations: 0 / 360.4 MB, free: 5.27 MB / 282.7 MB
Notification: Performance of matching and sorting (n=59): time 0.002229/0.01939, allocations: 1.585 MB / 362 MB, free: 3.656 MB / 282.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.985e-05/0.01943, allocations: 85.61 kB / 362.1 MB, free: 3.555 MB / 282.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002798/0.01971, allocations: 418.4 kB / 362.5 MB, free: 3.125 MB / 282.7 MB
Notification: Performance of collectPreVariables (initialization): time 2.375e-05/0.01973, allocations: 33.73 kB / 362.5 MB, free: 3.086 MB / 282.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001951/0.01993, allocations: 0.4946 MB / 363 MB, free: 2.582 MB / 282.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001134/0.02004, allocations: 230 kB / 363.3 MB, free: 2.355 MB / 282.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001559/0.0202, allocations: 140.3 kB / 363.4 MB, free: 2.211 MB / 282.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001315/0.02033, allocations: 0.5313 MB / 363.9 MB, free: 1.668 MB / 282.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002102/0.02054, allocations: 167.6 kB / 364.1 MB, free: 1.504 MB / 282.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003429/0.02088, allocations: 0.4952 MB / 364.6 MB, free: 0.8477 MB / 282.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.000836/0.02172, allocations: 0.8417 MB / 365.4 MB, free: 15.84 MB / 298.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.917e-06/0.02172, allocations: 4 kB / 365.4 MB, free: 15.83 MB / 298.7 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0007026/0.02242, allocations: 0.6687 MB / 366.1 MB, free: 15.16 MB / 298.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.935e-05/0.02244, allocations: 12 kB / 366.1 MB, free: 15.14 MB / 298.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.258e-05/0.02246, allocations: 15.88 kB / 366.1 MB, free: 15.13 MB / 298.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.084e-05/0.02248, allocations: 12 kB / 366.1 MB, free: 15.12 MB / 298.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003664/0.02284, allocations: 187.7 kB / 366.3 MB, free: 14.93 MB / 298.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.416e-05/0.02286, allocations: 19.94 kB / 366.3 MB, free: 14.91 MB / 298.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001588/0.02302, allocations: 28.53 kB / 366.4 MB, free: 14.89 MB / 298.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.971e-05/0.02305, allocations: 36 kB / 366.4 MB, free: 14.85 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 0.0002562/0.0233, allocations: 254.3 kB / 366.7 MB, free: 14.6 MB / 298.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 7.75e-05/0.02338, allocations: 67.67 kB / 366.7 MB, free: 14.54 MB / 298.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 8.107e-05/0.02346, allocations: 72.84 kB / 366.8 MB, free: 14.46 MB / 298.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.408e-06/0.02346, allocations: 8 kB / 366.8 MB, free: 14.45 MB / 298.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.504e-06/0.02347, allocations: 4 kB / 366.8 MB, free: 14.45 MB / 298.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.64e-06/0.02348, allocations: 3.984 kB / 366.8 MB, free: 14.45 MB / 298.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005781/0.02406, allocations: 0.4968 MB / 367.3 MB, free: 13.91 MB / 298.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.934e-06/0.02406, allocations: 0 / 367.3 MB, free: 13.91 MB / 298.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002986/0.02436, allocations: 111.8 kB / 367.4 MB, free: 13.8 MB / 298.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.747e-06/0.02436, allocations: 4 kB / 367.4 MB, free: 13.8 MB / 298.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.936e-05/0.02439, allocations: 15.98 kB / 367.4 MB, free: 13.79 MB / 298.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.959e-06/0.02439, allocations: 7.922 kB / 367.4 MB, free: 13.78 MB / 298.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.312e-06/0.0244, allocations: 4 kB / 367.5 MB, free: 13.77 MB / 298.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0007382/0.02513, allocations: 0.8292 MB / 368.3 MB, free: 12.93 MB / 298.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.519e-05/0.02517, allocations: 35.72 kB / 368.3 MB, free: 12.89 MB / 298.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.94e-05/0.02521, allocations: 12 kB / 368.3 MB, free: 12.88 MB / 298.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001301/0.02534, allocations: 15.94 kB / 368.3 MB, free: 12.86 MB / 298.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.816e-05/0.02539, allocations: 36.42 kB / 368.4 MB, free: 12.83 MB / 298.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001559/0.02554, allocations: 19.98 kB / 368.4 MB, free: 12.81 MB / 298.7 MB
Notification: Performance of sorting global known variables: time 0.0001472/0.02569, allocations: 255.1 kB / 368.6 MB, free: 12.56 MB / 298.7 MB
Notification: Performance of sort global known variables: time 5e-08/0.02569, allocations: 3.938 kB / 368.7 MB, free: 12.55 MB / 298.7 MB
Notification: Performance of remove unused functions: time 0.0003656/0.02606, allocations: 160 kB / 368.8 MB, free: 12.4 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 0.0001027/0.02616, allocations: 117.6 kB / 368.9 MB, free: 12.28 MB / 298.7 MB
Notification: Performance of simCode: created initialization part: time 0.0005111/0.02667, allocations: 442.9 kB / 369.4 MB, free: 11.84 MB / 298.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.543e-06/0.02667, allocations: 4.25 kB / 369.4 MB, free: 11.84 MB / 298.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002074/0.02688, allocations: 207.3 kB / 369.6 MB, free: 11.63 MB / 298.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003437/0.02722, allocations: 69.41 kB / 369.6 MB, free: 11.56 MB / 298.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001719/0.02894, allocations: 1.577 MB / 371.2 MB, free: 9.941 MB / 298.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 9.532e-05/0.02904, allocations: 152 kB / 371.4 MB, free: 9.773 MB / 298.7 MB
Notification: Performance of simCode: alias equations: time 0.000161/0.0292, allocations: 68.58 kB / 371.4 MB, free: 9.707 MB / 298.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001041/0.0293, allocations: 48.48 kB / 371.5 MB, free: 9.66 MB / 298.7 MB
Notification: Performance of SimCode: time 9.62e-07/0.0293, allocations: 0 / 371.5 MB, free: 9.66 MB / 298.7 MB
Notification: Performance of Templates: time 0.007818/0.03712, allocations: 5.294 MB / 376.8 MB, free: 4.461 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: 3.0315334261395037]