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 4.0.0+maint.om/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/BioChem 1.1.2-master/package.mo", uses=false)
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/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 ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/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/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0009342/0.0009343, allocations: 99.58 kB / 16.02 MB, free: 76 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.000994/0.000994, allocations: 181 kB / 16.92 MB, free: 6.918 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.323/1.323, allocations: 223.3 MB / 241 MB, free: 5.332 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1607/0.1607, allocations: 12.26 MB / 304.3 MB, free: 2.129 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0002744/0.0002744, allocations: 8 kB / 368.2 MB, free: 9.469 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.07812/0.07841, allocations: 53.09 MB / 421.3 MB, free: 4.266 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.1588/0.2373, allocations: 8.02 MB / 429.3 MB, free: 35.02 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.00128/0.2386, allocations: 0.8153 MB / 430.1 MB, free: 34.84 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0004032/0.239, allocations: 43.19 kB / 430.2 MB, free: 34.84 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.000261/0.2393, allocations: 106.8 kB / 430.3 MB, free: 34.8 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.000506/0.2398, allocations: 167.8 kB / 430.4 MB, free: 34.73 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003387/0.2401, allocations: 164.8 kB / 430.6 MB, free: 34.73 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0006182/0.2408, allocations: 0.7842 MB / 431.4 MB, free: 34.54 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005435/0.2413, allocations: 472.7 kB / 431.8 MB, free: 34.48 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001907/0.2415, allocations: 265 kB / 432.1 MB, free: 34.41 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002462/0.2418, allocations: 326.5 kB / 432.4 MB, free: 34.3 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 6.366e-05/0.2418, allocations: 40.72 kB / 432.5 MB, free: 34.3 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 7.457e-05/0.2419, allocations: 42.41 kB / 432.5 MB, free: 34.3 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 7.25e-05/0.242, allocations: 134.8 kB / 432.6 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.000227/0.2422, allocations: 412.8 kB / 433 MB, free: 34.1 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0005415/0.2428, allocations: 0.8759 MB / 433.9 MB, free: 34.04 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 3.767e-06/0.2428, allocations: 0 / 433.9 MB, free: 34.04 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.924e-06/0.2428, allocations: 11.47 kB / 433.9 MB, free: 34.04 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.05e-05/0.2428, allocations: 0 / 433.9 MB, free: 34.04 MB / 350.1 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 0.001172/0.244, allocations: 0.9345 MB / 434.9 MB, free: 33.45 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.13e-05/0.244, allocations: 10.38 kB / 434.9 MB, free: 33.45 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001208/0.2442, allocations: 95.94 kB / 435 MB, free: 33.4 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001748/0.2443, allocations: 307.8 kB / 435.3 MB, free: 33.12 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.026e-05/0.2444, allocations: 73.56 kB / 435.3 MB, free: 33.11 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001142/0.2445, allocations: 99.75 kB / 435.4 MB, free: 33.11 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001196/0.2457, allocations: 0.8777 MB / 436.3 MB, free: 33.04 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.809e-05/0.2457, allocations: 3.516 kB / 436.3 MB, free: 33.04 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.818e-05/0.2458, allocations: 44.41 kB / 436.4 MB, free: 33.03 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.641e-05/0.2458, allocations: 23.47 kB / 436.4 MB, free: 33.03 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009286/0.2468, allocations: 0.6216 MB / 437 MB, free: 33.02 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003562/0.2503, allocations: 2.851 MB / 439.9 MB, free: 32.08 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.000858/0.2512, allocations: 0.5084 MB / 440.4 MB, free: 31.84 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003468/0.2516, allocations: 322.5 kB / 440.7 MB, free: 31.71 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.26e-05/0.2516, allocations: 3.781 kB / 440.7 MB, free: 31.71 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.458e-05/0.2516, allocations: 40.81 kB / 440.7 MB, free: 31.66 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 2.185e-06/0.2516, allocations: 0 / 440.7 MB, free: 31.66 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004578/0.2562, allocations: 2.179 MB / 442.9 MB, free: 30.67 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.461e-05/0.2563, allocations: 88.05 kB / 443 MB, free: 30.57 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002742/0.2565, allocations: 362.5 kB / 443.3 MB, free: 30.38 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.106e-05/0.2566, allocations: 36.89 kB / 443.4 MB, free: 30.34 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001401/0.2567, allocations: 451.6 kB / 443.8 MB, free: 29.99 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 9.628e-05/0.2568, allocations: 214.3 kB / 444 MB, free: 29.83 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.28e-05/0.2569, allocations: 77.72 kB / 444.1 MB, free: 29.79 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 5.745e-05/0.257, allocations: 356.6 kB / 444.5 MB, free: 29.46 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003151/0.2573, allocations: 251.1 kB / 444.7 MB, free: 29.35 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003595/0.2577, allocations: 486.2 kB / 445.2 MB, free: 28.92 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.006196/0.2639, allocations: 1.755 MB / 446.9 MB, free: 28.12 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.268e-06/0.2639, allocations: 3.094 kB / 446.9 MB, free: 28.12 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0009984/0.2649, allocations: 0.8005 MB / 447.7 MB, free: 27.76 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.621e-05/0.2649, allocations: 14.53 kB / 447.7 MB, free: 27.75 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.021e-05/0.2649, allocations: 6.688 kB / 447.7 MB, free: 27.75 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.956e-05/0.265, allocations: 14.03 kB / 447.8 MB, free: 27.75 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006325/0.2656, allocations: 184.6 kB / 447.9 MB, free: 27.73 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.528e-05/0.2656, allocations: 16.94 kB / 448 MB, free: 27.73 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003559/0.266, allocations: 45.84 kB / 448 MB, free: 27.71 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.276e-05/0.266, allocations: 45.28 kB / 448 MB, free: 27.7 MB / 350.1 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 0.0003636/0.2664, allocations: 279.3 kB / 448.3 MB, free: 27.48 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.418e-05/0.2665, allocations: 42.91 kB / 448.4 MB, free: 27.46 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001648/0.2667, allocations: 73.06 kB / 448.4 MB, free: 27.41 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.38e-06/0.2667, allocations: 11.17 kB / 448.4 MB, free: 27.4 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 9.197e-06/0.2667, allocations: 3.406 kB / 448.4 MB, free: 27.4 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.212e-06/0.2667, allocations: 3.141 kB / 448.5 MB, free: 27.4 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008972/0.2676, allocations: 0.7656 MB / 449.2 MB, free: 26.99 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.475e-06/0.2676, allocations: 0 / 449.2 MB, free: 26.99 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005603/0.2682, allocations: 114.6 kB / 449.3 MB, free: 26.98 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.416e-06/0.2682, allocations: 0.6562 kB / 449.3 MB, free: 26.98 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.493e-05/0.2682, allocations: 17.25 kB / 449.3 MB, free: 26.97 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.456e-06/0.2682, allocations: 3.062 kB / 449.4 MB, free: 26.97 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.162e-06/0.2682, allocations: 0 / 449.4 MB, free: 26.97 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009451/0.2692, allocations: 0.9346 MB / 450.3 MB, free: 26.43 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.492e-05/0.2693, allocations: 120.8 kB / 450.4 MB, free: 26.31 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.618e-05/0.2693, allocations: 11.12 kB / 450.4 MB, free: 26.3 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003235/0.2697, allocations: 32.61 kB / 450.4 MB, free: 26.29 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.803e-05/0.2697, allocations: 36.88 kB / 450.5 MB, free: 26.29 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.668e-05/0.2698, allocations: 13.59 kB / 450.5 MB, free: 26.28 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001712/0.2699, allocations: 243.6 kB / 450.7 MB, free: 26.15 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.4e-07/0.2699, allocations: 0 / 450.7 MB, free: 26.15 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0005446/0.2705, allocations: 157.3 kB / 450.9 MB, free: 26.13 MB / 350.1 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 9.048e-05/0.2706, allocations: 114 kB / 451 MB, free: 26.02 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0007138/0.2713, allocations: 0.5916 MB / 451.6 MB, free: 25.8 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.394e-06/0.2713, allocations: 0.6875 kB / 451.6 MB, free: 25.8 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002846/0.2716, allocations: 259.8 kB / 451.8 MB, free: 25.71 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005105/0.2721, allocations: 73.38 kB / 451.9 MB, free: 25.67 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002585/0.2747, allocations: 2.368 MB / 454.3 MB, free: 24.07 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002935/0.275, allocations: 0.9397 MB / 455.2 MB, free: 23.36 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001696/0.2752, allocations: 49.11 kB / 455.3 MB, free: 23.35 MB / 350.1 MB
Notification: Performance of SimCode: time 3.41e-07/0.2752, allocations: 4.281 kB / 455.3 MB, free: 23.35 MB / 350.1 MB
Notification: Performance of Templates: time 0.007649/0.2829, allocations: 7.316 MB / 462.6 MB, free: 22.6 MB / 350.1 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)