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 0.001546/0.001546, allocations: 102.4 kB / 16.35 MB, free: 5.875 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001898/0.001898, allocations: 191 kB / 17.29 MB, free: 5.516 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.339/1.339, allocations: 222.9 MB / 241 MB, free: 15 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06018/0.06018, allocations: 12.28 MB / 303.4 MB, free: 3.223 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001217/0.001217, allocations: 68.12 kB / 367.2 MB, free: 3.363 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1895/0.1907, allocations: 52.08 MB / 419.3 MB, free: 21.69 MB / 302.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01034/0.2011, allocations: 8.478 MB / 427.8 MB, free: 13.19 MB / 302.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001371/0.2025, allocations: 0.8169 MB / 428.6 MB, free: 12.38 MB / 302.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0005055/0.203, allocations: 44 kB / 428.6 MB, free: 12.34 MB / 302.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0004537/0.2035, allocations: 139.4 kB / 428.7 MB, free: 12.2 MB / 302.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0005799/0.2041, allocations: 206.3 kB / 429 MB, free: 12 MB / 302.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003375/0.2045, allocations: 195.7 kB / 429.1 MB, free: 11.81 MB / 302.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0005018/0.205, allocations: 0.854 MB / 430 MB, free: 10.96 MB / 302.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005563/0.2055, allocations: 0.5329 MB / 430.5 MB, free: 10.41 MB / 302.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002182/0.2058, allocations: 366.7 kB / 430.9 MB, free: 10.05 MB / 302.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000301/0.2061, allocations: 431 kB / 431.3 MB, free: 9.625 MB / 302.1 MB
Notification: Performance of NFPackage.collectConstants: time 9.452e-05/0.2062, allocations: 116 kB / 431.4 MB, free: 9.512 MB / 302.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 9.388e-05/0.2063, allocations: 116.9 kB / 431.5 MB, free: 9.398 MB / 302.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001089/0.2064, allocations: 235.2 kB / 431.8 MB, free: 9.168 MB / 302.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002559/0.2067, allocations: 477.7 kB / 432.2 MB, free: 8.699 MB / 302.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0006333/0.2073, allocations: 1.165 MB / 433.4 MB, free: 7.539 MB / 302.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.999e-06/0.2073, allocations: 0 / 433.4 MB, free: 7.539 MB / 302.1 MB
Notification: Performance of FrontEnd: time 1.623e-06/0.2073, allocations: 0 / 433.4 MB, free: 7.539 MB / 302.1 MB
Notification: Performance of Transformations before backend: time 1.132e-05/0.2073, allocations: 0 / 433.4 MB, free: 7.539 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 0.001294/0.2086, allocations: 1.119 MB / 434.5 MB, free: 6.371 MB / 302.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.472e-05/0.2087, allocations: 12.94 kB / 434.5 MB, free: 6.359 MB / 302.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001143/0.2088, allocations: 99.72 kB / 434.6 MB, free: 6.262 MB / 302.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001943/0.209, allocations: 308.5 kB / 434.9 MB, free: 5.926 MB / 302.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.771e-05/0.209, allocations: 74.38 kB / 435 MB, free: 5.855 MB / 302.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001016/0.2092, allocations: 104.3 kB / 435.1 MB, free: 5.754 MB / 302.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001036/0.2102, allocations: 0.8743 MB / 436 MB, free: 4.867 MB / 302.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.414e-05/0.2102, allocations: 192 / 436 MB, free: 4.867 MB / 302.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 5.722e-05/0.2103, allocations: 43.94 kB / 436 MB, free: 4.824 MB / 302.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.284e-05/0.2103, allocations: 24 kB / 436 MB, free: 4.801 MB / 302.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008487/0.2112, allocations: 0.6208 MB / 436.7 MB, free: 4.18 MB / 302.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003277/0.2145, allocations: 2.841 MB / 439.5 MB, free: 1.266 MB / 302.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008028/0.2153, allocations: 0.5143 MB / 440 MB, free: 0.7344 MB / 302.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003362/0.2156, allocations: 323 kB / 440.3 MB, free: 424 kB / 302.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.775e-05/0.2157, allocations: 4.438 kB / 440.3 MB, free: 420 kB / 302.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.882e-05/0.2157, allocations: 46.53 kB / 440.4 MB, free: 368 kB / 302.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.803e-06/0.2157, allocations: 0 / 440.4 MB, free: 368 kB / 302.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004779/0.2205, allocations: 2.159 MB / 442.5 MB, free: 14.16 MB / 318.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.274e-05/0.2205, allocations: 89.7 kB / 442.6 MB, free: 14.05 MB / 318.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003362/0.2209, allocations: 353.5 kB / 443 MB, free: 13.7 MB / 318.1 MB
Notification: Performance of collectPreVariables (initialization): time 4.212e-05/0.2209, allocations: 37.7 kB / 443 MB, free: 13.66 MB / 318.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002464/0.2212, allocations: 454.1 kB / 443.5 MB, free: 13.2 MB / 318.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001469/0.2213, allocations: 224.8 kB / 443.7 MB, free: 12.98 MB / 318.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000175/0.2215, allocations: 130.6 kB / 443.8 MB, free: 12.85 MB / 318.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001346/0.2216, allocations: 358.8 kB / 444.2 MB, free: 12.49 MB / 318.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003727/0.222, allocations: 260.7 kB / 444.4 MB, free: 12.23 MB / 318.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004876/0.2225, allocations: 484.8 kB / 444.9 MB, free: 11.63 MB / 318.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005811/0.2283, allocations: 1.696 MB / 446.6 MB, free: 9.812 MB / 318.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.271e-05/0.2284, allocations: 4 kB / 446.6 MB, free: 9.809 MB / 318.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001233/0.2296, allocations: 0.7994 MB / 447.4 MB, free: 9 MB / 318.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.371e-05/0.2296, allocations: 12 kB / 447.4 MB, free: 8.988 MB / 318.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.394e-05/0.2297, allocations: 16.14 kB / 447.4 MB, free: 8.973 MB / 318.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.672e-05/0.2297, allocations: 12 kB / 447.4 MB, free: 8.961 MB / 318.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006627/0.2304, allocations: 183.7 kB / 447.6 MB, free: 8.781 MB / 318.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.48e-05/0.2304, allocations: 23.91 kB / 447.6 MB, free: 8.758 MB / 318.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003102/0.2307, allocations: 28 kB / 447.6 MB, free: 8.73 MB / 318.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.106e-05/0.2308, allocations: 36 kB / 447.7 MB, free: 8.695 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 0.0004917/0.2313, allocations: 279 kB / 448 MB, free: 8.418 MB / 318.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.737e-05/0.2314, allocations: 51.42 kB / 448 MB, free: 8.367 MB / 318.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001467/0.2315, allocations: 68.91 kB / 448.1 MB, free: 8.301 MB / 318.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 9.998e-06/0.2316, allocations: 8 kB / 448.1 MB, free: 8.293 MB / 318.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.207e-05/0.2316, allocations: 0 / 448.1 MB, free: 8.293 MB / 318.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.013e-05/0.2316, allocations: 3.984 kB / 448.1 MB, free: 8.289 MB / 318.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001115/0.2327, allocations: 0.7554 MB / 448.8 MB, free: 7.484 MB / 318.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.178e-06/0.2327, allocations: 3.984 kB / 448.8 MB, free: 7.48 MB / 318.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005527/0.2333, allocations: 111.8 kB / 449 MB, free: 7.371 MB / 318.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 5.45e-06/0.2333, allocations: 4 kB / 449 MB, free: 7.367 MB / 318.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.44e-05/0.2333, allocations: 16 kB / 449 MB, free: 7.352 MB / 318.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.761e-06/0.2334, allocations: 7.984 kB / 449 MB, free: 7.344 MB / 318.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.342e-06/0.2334, allocations: 0 / 449 MB, free: 7.344 MB / 318.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001233/0.2346, allocations: 0.9244 MB / 449.9 MB, free: 6.406 MB / 318.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001135/0.2347, allocations: 116.5 kB / 450 MB, free: 6.273 MB / 318.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.732e-05/0.2348, allocations: 27.94 kB / 450 MB, free: 6.246 MB / 318.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002734/0.2351, allocations: 7.938 kB / 450.1 MB, free: 6.238 MB / 318.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.914e-05/0.2352, allocations: 32.52 kB / 450.1 MB, free: 6.207 MB / 318.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.353e-05/0.2352, allocations: 19.98 kB / 450.1 MB, free: 6.188 MB / 318.1 MB
Notification: Performance of sorting global known variables: time 0.0002666/0.2355, allocations: 239.3 kB / 450.3 MB, free: 5.953 MB / 318.1 MB
Notification: Performance of sort global known variables: time 1.6e-07/0.2355, allocations: 3.938 kB / 450.3 MB, free: 5.949 MB / 318.1 MB
Notification: Performance of remove unused functions: time 0.0006446/0.2361, allocations: 156 kB / 450.5 MB, free: 5.797 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 0.0001466/0.2363, allocations: 123.7 kB / 450.6 MB, free: 5.664 MB / 318.1 MB
Notification: Performance of simCode: created initialization part: time 0.0009012/0.2372, allocations: 0.5912 MB / 451.2 MB, free: 5.078 MB / 318.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.345e-06/0.2372, allocations: 0 / 451.2 MB, free: 5.078 MB / 318.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003512/0.2376, allocations: 267.2 kB / 451.5 MB, free: 4.816 MB / 318.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004961/0.2381, allocations: 61.48 kB / 451.5 MB, free: 4.758 MB / 318.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002753/0.2408, allocations: 1.775 MB / 453.3 MB, free: 2.945 MB / 318.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000518/0.2414, allocations: 0.9465 MB / 454.3 MB, free: 1.973 MB / 318.1 MB
Notification: Performance of simCode: alias equations: time 0.0002367/0.2416, allocations: 64.58 kB / 454.3 MB, free: 1.91 MB / 318.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000136/0.2417, allocations: 47.42 kB / 454.4 MB, free: 1.863 MB / 318.1 MB
Notification: Performance of SimCode: time 1.9e-07/0.2417, allocations: 0 / 454.4 MB, free: 1.863 MB / 318.1 MB
Notification: Performance of Templates: time 0.009816/0.2516, allocations: 5.362 MB / 459.7 MB, free: 12.55 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 gbode -lv LOG_STATS > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1)