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 0.007828/0.007828, allocations: 103.6 kB / 15.74 MB, free: 6.039 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.002369/0.002369, allocations: 198.5 kB / 16.68 MB, free: 5.953 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.488/1.488, allocations: 222.9 MB / 240.4 MB, free: 15.13 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06411/0.06411, allocations: 12.28 MB / 302.8 MB, free: 3.195 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.00132/0.00132, allocations: 59.83 kB / 420 MB, free: 16.98 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1515/0.1528, allocations: 52.07 MB / 472.1 MB, free: 12.92 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01286/0.1657, allocations: 8.482 MB / 480.6 MB, free: 4.406 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.002005/0.1678, allocations: 0.8107 MB / 481.4 MB, free: 3.594 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003476/0.1682, allocations: 44 kB / 481.5 MB, free: 3.551 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0003152/0.1686, allocations: 138.8 kB / 481.6 MB, free: 3.414 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004908/0.1691, allocations: 206 kB / 481.8 MB, free: 3.211 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0004302/0.1695, allocations: 199.8 kB / 482 MB, free: 3.016 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0008541/0.1704, allocations: 0.8415 MB / 482.8 MB, free: 2.172 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0008159/0.1712, allocations: 0.5336 MB / 483.4 MB, free: 1.613 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003991/0.1716, allocations: 370.7 kB / 483.7 MB, free: 1.25 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0005102/0.1721, allocations: 430 kB / 484.1 MB, free: 0.8281 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001488/0.1723, allocations: 116 kB / 484.3 MB, free: 0.7148 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001418/0.1724, allocations: 116 kB / 484.4 MB, free: 0.6016 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001697/0.1726, allocations: 231.3 kB / 484.6 MB, free: 384 kB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0004092/0.173, allocations: 481.7 kB / 485.1 MB, free: 15.9 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.001109/0.1741, allocations: 1.168 MB / 486.2 MB, free: 14.73 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.112e-06/0.1741, allocations: 0 / 486.2 MB, free: 14.73 MB / 366.1 MB
Notification: Performance of FrontEnd: time 2.354e-06/0.1742, allocations: 4 kB / 486.2 MB, free: 14.73 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 1.227e-05/0.1742, allocations: 4 kB / 486.2 MB, free: 14.72 MB / 366.1 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 0.001837/0.176, allocations: 1.123 MB / 487.4 MB, free: 13.55 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.833e-05/0.1761, allocations: 12.03 kB / 487.4 MB, free: 13.54 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001514/0.1762, allocations: 95.75 kB / 487.5 MB, free: 13.44 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003698/0.1766, allocations: 314.7 kB / 487.8 MB, free: 13.09 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 6.77e-05/0.1767, allocations: 74.38 kB / 487.8 MB, free: 13.02 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001398/0.1768, allocations: 96.38 kB / 487.9 MB, free: 12.93 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001636/0.1785, allocations: 0.8764 MB / 488.8 MB, free: 12.04 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.215e-05/0.1785, allocations: 8.031 kB / 488.8 MB, free: 12.03 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 8.404e-05/0.1786, allocations: 47.92 kB / 488.9 MB, free: 11.98 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.608e-05/0.1786, allocations: 24 kB / 488.9 MB, free: 11.96 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001087/0.1797, allocations: 0.6208 MB / 489.5 MB, free: 11.34 MB / 366.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004534/0.1843, allocations: 2.823 MB / 492.3 MB, free: 8.43 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.001045/0.1853, allocations: 0.5182 MB / 492.9 MB, free: 7.895 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004674/0.1858, allocations: 315 kB / 493.2 MB, free: 7.582 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.214e-05/0.1859, allocations: 8.438 kB / 493.2 MB, free: 7.574 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.359e-05/0.1859, allocations: 39 kB / 493.2 MB, free: 7.523 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=50): time 2.274e-06/0.1859, allocations: 4 kB / 493.2 MB, free: 7.52 MB / 366.1 MB
Notification: Performance of matching and sorting (n=59): time 0.005402/0.1913, allocations: 2.165 MB / 495.4 MB, free: 5.309 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.638e-05/0.1914, allocations: 85.67 kB / 495.5 MB, free: 5.207 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004123/0.1918, allocations: 357.5 kB / 495.8 MB, free: 4.852 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 4.855e-05/0.1919, allocations: 37.7 kB / 495.9 MB, free: 4.809 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003272/0.1922, allocations: 450.1 kB / 496.3 MB, free: 4.359 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002087/0.1924, allocations: 224.8 kB / 496.5 MB, free: 4.137 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001921/0.1926, allocations: 134.6 kB / 496.6 MB, free: 3.996 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001762/0.1928, allocations: 362.8 kB / 497 MB, free: 3.633 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003733/0.1932, allocations: 248.8 kB / 497.2 MB, free: 3.391 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005609/0.1938, allocations: 480.9 kB / 497.7 MB, free: 2.801 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005536/0.1993, allocations: 1.707 MB / 499.4 MB, free: 0.9727 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.001e-06/0.1993, allocations: 4 kB / 499.4 MB, free: 0.9688 MB / 366.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001232/0.2006, allocations: 0.8029 MB / 0.4885 GB, free: 160 kB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.169e-05/0.2006, allocations: 8 kB / 0.4885 GB, free: 152 kB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.735e-05/0.2006, allocations: 15.98 kB / 0.4885 GB, free: 136 kB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 3.669e-05/0.2007, allocations: 16 kB / 0.4885 GB, free: 120 kB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006741/0.2013, allocations: 179.7 kB / 0.4887 GB, free: 15.94 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.856e-05/0.2014, allocations: 20.48 kB / 0.4887 GB, free: 15.92 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003255/0.2017, allocations: 28 kB / 0.4888 GB, free: 15.89 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001553/0.2019, allocations: 36 kB / 0.4888 GB, free: 15.86 MB / 382.1 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 0.0005708/0.2025, allocations: 291 kB / 0.4891 GB, free: 15.57 MB / 382.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001106/0.2026, allocations: 47.44 kB / 0.4891 GB, free: 15.52 MB / 382.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001736/0.2028, allocations: 72.91 kB / 0.4892 GB, free: 15.45 MB / 382.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 8.035e-06/0.2028, allocations: 8 kB / 0.4892 GB, free: 15.44 MB / 382.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 9.538e-06/0.2028, allocations: 0 / 0.4892 GB, free: 15.44 MB / 382.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.707e-06/0.2028, allocations: 3.984 kB / 0.4892 GB, free: 15.44 MB / 382.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001182/0.204, allocations: 0.7593 MB / 0.4899 GB, free: 14.63 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.881e-06/0.204, allocations: 0 / 0.4899 GB, free: 14.63 MB / 382.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005584/0.2046, allocations: 103.9 kB / 0.49 GB, free: 14.53 MB / 382.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 8.626e-06/0.2046, allocations: 11.88 kB / 0.49 GB, free: 14.52 MB / 382.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.699e-05/0.2047, allocations: 19.98 kB / 0.4901 GB, free: 14.5 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.819e-06/0.2047, allocations: 4 kB / 0.4901 GB, free: 14.49 MB / 382.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.864e-06/0.2048, allocations: 4 kB / 0.4901 GB, free: 14.49 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001319/0.2061, allocations: 0.9322 MB / 0.491 GB, free: 13.54 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 9.344e-05/0.2062, allocations: 116.5 kB / 0.4911 GB, free: 13.4 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.699e-05/0.2063, allocations: 16 kB / 0.4911 GB, free: 13.39 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002684/0.2065, allocations: 8 kB / 0.4911 GB, free: 13.38 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.739e-05/0.2066, allocations: 36.5 kB / 0.4912 GB, free: 13.34 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.361e-05/0.2067, allocations: 16 kB / 0.4912 GB, free: 13.33 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0002426/0.2069, allocations: 243.2 kB / 0.4914 GB, free: 13.09 MB / 382.1 MB
Notification: Performance of sort global known variables: time 1.4e-07/0.2069, allocations: 0 / 0.4914 GB, free: 13.09 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.0006195/0.2075, allocations: 156 kB / 0.4915 GB, free: 12.94 MB / 382.1 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 0.0001723/0.2077, allocations: 115.7 kB / 0.4917 GB, free: 12.82 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.0009521/0.2087, allocations: 0.5937 MB / 0.4922 GB, free: 12.23 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.436e-06/0.2087, allocations: 0 / 0.4922 GB, free: 12.23 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003803/0.2091, allocations: 268.7 kB / 0.4925 GB, free: 11.97 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000543/0.2096, allocations: 69.47 kB / 0.4926 GB, free: 11.9 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003298/0.2129, allocations: 1.775 MB / 0.4943 GB, free: 10.09 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0006307/0.2136, allocations: 0.9428 MB / 0.4952 GB, free: 9.121 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.0002752/0.2139, allocations: 60.58 kB / 0.4953 GB, free: 9.059 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001556/0.214, allocations: 47.42 kB / 0.4953 GB, free: 9.012 MB / 382.1 MB
Notification: Performance of SimCode: time 6.01e-07/0.214, allocations: 0 / 0.4953 GB, free: 9.012 MB / 382.1 MB
Notification: Performance of Templates: time 0.01304/0.2271, allocations: 5.521 MB / 0.5007 GB, free: 3.531 MB / 382.1 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)