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 0.001459/0.001459, allocations: 115 kB / 16.37 MB, free: 5.539 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001503/0.001503, allocations: 189.4 kB / 17.3 MB, free: 5.18 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.417/1.417, allocations: 222.9 MB / 241 MB, free: 15.14 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06179/0.06179, allocations: 12.27 MB / 303.4 MB, free: 3.238 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001352/0.001352, allocations: 63.91 kB / 367.2 MB, free: 3.371 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2197/0.2211, allocations: 52.08 MB / 419.3 MB, free: 21.66 MB / 302.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.008959/0.2301, allocations: 8.483 MB / 427.8 MB, free: 13.16 MB / 302.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001362/0.2315, allocations: 0.819 MB / 428.6 MB, free: 12.35 MB / 302.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002883/0.2318, allocations: 46.62 kB / 428.6 MB, free: 12.31 MB / 302.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002378/0.232, allocations: 138.8 kB / 428.8 MB, free: 12.17 MB / 302.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0003721/0.2325, allocations: 197.3 kB / 429 MB, free: 11.98 MB / 302.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003171/0.2328, allocations: 195.8 kB / 429.2 MB, free: 11.79 MB / 302.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0005275/0.2333, allocations: 0.8454 MB / 430 MB, free: 10.94 MB / 302.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005829/0.2339, allocations: 0.5289 MB / 430.5 MB, free: 10.39 MB / 302.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002434/0.2342, allocations: 372.8 kB / 430.9 MB, free: 10.03 MB / 302.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003226/0.2345, allocations: 438 kB / 431.3 MB, free: 9.602 MB / 302.1 MB
Notification: Performance of NFPackage.collectConstants: time 9.54e-05/0.2346, allocations: 116 kB / 431.4 MB, free: 9.488 MB / 302.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 9.993e-05/0.2347, allocations: 116 kB / 431.5 MB, free: 9.375 MB / 302.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.000111/0.2348, allocations: 223.2 kB / 431.8 MB, free: 9.156 MB / 302.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002565/0.2351, allocations: 482.7 kB / 432.2 MB, free: 8.684 MB / 302.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0006555/0.2358, allocations: 1.17 MB / 433.4 MB, free: 7.516 MB / 302.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.242e-06/0.2358, allocations: 0 / 433.4 MB, free: 7.516 MB / 302.1 MB
Notification: Performance of FrontEnd: time 2.815e-06/0.2358, allocations: 0.8125 kB / 433.4 MB, free: 7.516 MB / 302.1 MB
Notification: Performance of Transformations before backend: time 1.256e-05/0.2358, allocations: 0 / 433.4 MB, free: 7.516 MB / 302.1 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 0.001333/0.2371, allocations: 1.12 MB / 434.5 MB, free: 6.348 MB / 302.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.625e-05/0.2372, allocations: 8.562 kB / 434.5 MB, free: 6.34 MB / 302.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001118/0.2373, allocations: 99.72 kB / 434.6 MB, free: 6.242 MB / 302.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002154/0.2375, allocations: 307.5 kB / 434.9 MB, free: 5.906 MB / 302.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.932e-05/0.2376, allocations: 76.06 kB / 435 MB, free: 5.836 MB / 302.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001057/0.2377, allocations: 100.3 kB / 435.1 MB, free: 5.738 MB / 302.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0011/0.2388, allocations: 0.8763 MB / 436 MB, free: 4.848 MB / 302.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.645e-05/0.2388, allocations: 5.094 kB / 436 MB, free: 4.844 MB / 302.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 5.769e-05/0.2389, allocations: 39.94 kB / 436 MB, free: 4.805 MB / 302.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.414e-05/0.2389, allocations: 25.06 kB / 436 MB, free: 4.781 MB / 302.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008587/0.2398, allocations: 0.6248 MB / 436.7 MB, free: 4.156 MB / 302.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003424/0.2432, allocations: 2.837 MB / 439.5 MB, free: 1.246 MB / 302.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008329/0.2441, allocations: 0.5221 MB / 440 MB, free: 0.707 MB / 302.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003397/0.2444, allocations: 315 kB / 440.3 MB, free: 404 kB / 302.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.168e-05/0.2445, allocations: 4.438 kB / 440.3 MB, free: 400 kB / 302.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.101e-05/0.2445, allocations: 43.09 kB / 440.4 MB, free: 352 kB / 302.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.783e-06/0.2445, allocations: 0 / 440.4 MB, free: 352 kB / 302.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004957/0.2495, allocations: 2.163 MB / 442.6 MB, free: 14.14 MB / 318.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.651e-05/0.2495, allocations: 93.69 kB / 442.6 MB, free: 14.03 MB / 318.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003579/0.2499, allocations: 357.5 kB / 443 MB, free: 13.68 MB / 318.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.568e-05/0.2499, allocations: 37.64 kB / 443 MB, free: 13.63 MB / 318.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002808/0.2502, allocations: 454.1 kB / 443.5 MB, free: 13.18 MB / 318.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.000158/0.2504, allocations: 220.8 kB / 443.7 MB, free: 12.96 MB / 318.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001896/0.2506, allocations: 138.6 kB / 443.8 MB, free: 12.82 MB / 318.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001525/0.2507, allocations: 354.8 kB / 444.2 MB, free: 12.46 MB / 318.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003972/0.2512, allocations: 252.7 kB / 444.4 MB, free: 12.21 MB / 318.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005315/0.2517, allocations: 484.9 kB / 444.9 MB, free: 11.62 MB / 318.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005456/0.2572, allocations: 1.696 MB / 446.6 MB, free: 9.797 MB / 318.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.259e-06/0.2572, allocations: 4 kB / 446.6 MB, free: 9.793 MB / 318.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001188/0.2584, allocations: 0.7995 MB / 447.4 MB, free: 8.984 MB / 318.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.53e-05/0.2584, allocations: 12 kB / 447.4 MB, free: 8.973 MB / 318.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.346e-05/0.2584, allocations: 12.03 kB / 447.4 MB, free: 8.961 MB / 318.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.578e-05/0.2585, allocations: 16 kB / 447.4 MB, free: 8.945 MB / 318.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006523/0.2591, allocations: 183.7 kB / 447.6 MB, free: 8.766 MB / 318.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.998e-05/0.2591, allocations: 15.94 kB / 447.6 MB, free: 8.75 MB / 318.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003164/0.2595, allocations: 28 kB / 447.6 MB, free: 8.723 MB / 318.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.072e-05/0.2595, allocations: 36 kB / 447.7 MB, free: 8.688 MB / 318.1 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 0.0005118/0.26, allocations: 298.6 kB / 448 MB, free: 8.398 MB / 318.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001038/0.2602, allocations: 47.44 kB / 448 MB, free: 8.352 MB / 318.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000128/0.2603, allocations: 68.91 kB / 448.1 MB, free: 8.285 MB / 318.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 8.967e-06/0.2603, allocations: 8 kB / 448.1 MB, free: 8.277 MB / 318.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.783e-06/0.2603, allocations: 0 / 448.1 MB, free: 8.277 MB / 318.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.595e-06/0.2603, allocations: 3.984 kB / 448.1 MB, free: 8.273 MB / 318.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001134/0.2615, allocations: 0.7554 MB / 448.9 MB, free: 7.469 MB / 318.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.565e-06/0.2615, allocations: 0 / 448.9 MB, free: 7.469 MB / 318.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005374/0.262, allocations: 111.8 kB / 449 MB, free: 7.359 MB / 318.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 8.716e-06/0.2621, allocations: 4 kB / 449 MB, free: 7.355 MB / 318.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.999e-05/0.2621, allocations: 23.92 kB / 449 MB, free: 7.332 MB / 318.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.388e-06/0.2621, allocations: 4 kB / 449 MB, free: 7.328 MB / 318.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.655e-06/0.2621, allocations: 0 / 449 MB, free: 7.328 MB / 318.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00117/0.2633, allocations: 0.9321 MB / 449.9 MB, free: 6.383 MB / 318.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 9.335e-05/0.2634, allocations: 112.5 kB / 450 MB, free: 6.254 MB / 318.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.826e-05/0.2635, allocations: 24 kB / 450.1 MB, free: 6.23 MB / 318.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002573/0.2637, allocations: 8 kB / 450.1 MB, free: 6.223 MB / 318.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.703e-05/0.2638, allocations: 36.5 kB / 450.1 MB, free: 6.188 MB / 318.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.164e-05/0.2638, allocations: 19.98 kB / 450.1 MB, free: 6.168 MB / 318.1 MB
Notification: Performance of sorting global known variables: time 0.0002268/0.2641, allocations: 235.1 kB / 450.4 MB, free: 5.938 MB / 318.1 MB
Notification: Performance of sort global known variables: time 1.71e-07/0.2641, allocations: 0 / 450.4 MB, free: 5.938 MB / 318.1 MB
Notification: Performance of remove unused functions: time 0.0005855/0.2647, allocations: 160 kB / 450.5 MB, free: 5.781 MB / 318.1 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 0.0001296/0.2648, allocations: 123.4 kB / 450.6 MB, free: 5.652 MB / 318.1 MB
Notification: Performance of simCode: created initialization part: time 0.0008417/0.2657, allocations: 0.5828 MB / 451.2 MB, free: 5.074 MB / 318.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.504e-06/0.2657, allocations: 4.688 kB / 451.2 MB, free: 5.07 MB / 318.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003313/0.266, allocations: 267.1 kB / 451.5 MB, free: 4.809 MB / 318.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004786/0.2665, allocations: 67.02 kB / 451.5 MB, free: 4.746 MB / 318.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002723/0.2692, allocations: 1.779 MB / 453.3 MB, free: 2.93 MB / 318.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004904/0.2697, allocations: 0.9465 MB / 454.3 MB, free: 1.957 MB / 318.1 MB
Notification: Performance of simCode: alias equations: time 0.000231/0.27, allocations: 60.59 kB / 454.3 MB, free: 1.898 MB / 318.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001412/0.2701, allocations: 43.42 kB / 454.4 MB, free: 1.855 MB / 318.1 MB
Notification: Performance of SimCode: time 2.71e-07/0.2701, allocations: 4 kB / 454.4 MB, free: 1.852 MB / 318.1 MB
Notification: Performance of Templates: time 0.009775/0.2799, allocations: 5.351 MB / 459.7 MB, free: 12.54 MB / 334.1 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 -s cvode -lv LOG_STATS > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1)