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: "" <> buildModelFMU(BioChem.Examples.CircadianOscillator.Container,fileNamePrefix="BioChem_BioChem_Examples_CircadianOscillator_Container",fmuType="me",version="2.0",platforms={"static"})
"" <> buildModelFMU(BioChem.Examples.CircadianOscillator.Container,fileNamePrefix="BioChem_BioChem_Examples_CircadianOscillator_Container",fmuType="me",version="2.0",platforms={"static"})
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001126/0.001125, allocations: 108 kB / 15.61 MB, free: 152 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001144/0.001144, allocations: 194.2 kB / 16.53 MB, free: 6.664 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.337/1.337, allocations: 222.9 MB / 240.2 MB, free: 4.391 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1975/0.1975, allocations: 12.27 MB / 302.7 MB, free: 1.309 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001467/0.001467, allocations: 68.11 kB / 365.9 MB, free: 9.723 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1134/0.1149, allocations: 52.07 MB / 417.9 MB, free: 5.551 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.1911/0.306, allocations: 8.474 MB / 426.4 MB, free: 36.41 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.000982/0.307, allocations: 0.8155 MB / 427.2 MB, free: 36.3 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002478/0.3073, allocations: 43.16 kB / 427.3 MB, free: 36.3 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002115/0.3075, allocations: 143.7 kB / 427.4 MB, free: 36.3 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0003675/0.3079, allocations: 203 kB / 427.6 MB, free: 36.27 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.000296/0.3082, allocations: 193.4 kB / 427.8 MB, free: 36.26 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0004806/0.3087, allocations: 0.8338 MB / 428.6 MB, free: 36.07 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005657/0.3093, allocations: 0.5349 MB / 429.2 MB, free: 36 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002078/0.3095, allocations: 375.8 kB / 429.5 MB, free: 35.91 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002727/0.3098, allocations: 429.8 kB / 430 MB, free: 35.81 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 9.707e-05/0.3099, allocations: 118.6 kB / 430.1 MB, free: 35.81 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001062/0.31, allocations: 116.1 kB / 430.2 MB, free: 35.81 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001/0.3101, allocations: 228.8 kB / 430.4 MB, free: 35.77 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.000246/0.3103, allocations: 487.3 kB / 430.9 MB, free: 35.47 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0005922/0.3109, allocations: 1.139 MB / 432 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.218e-06/0.311, allocations: 0.5938 kB / 432 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.804e-06/0.311, allocations: 0 / 432 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.212e-05/0.311, allocations: 5.25 kB / 432 MB, free: 34.99 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 0.001311/0.3123, allocations: 1.119 MB / 433.1 MB, free: 34.23 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.733e-05/0.3123, allocations: 9.344 kB / 433.2 MB, free: 34.23 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.0001167/0.3125, allocations: 152.3 kB / 433.3 MB, free: 34.12 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001111/0.3126, allocations: 95 kB / 433.4 MB, free: 34.08 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001855/0.3128, allocations: 305.8 kB / 433.7 MB, free: 33.79 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.301e-05/0.3128, allocations: 77.5 kB / 433.8 MB, free: 33.76 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 9.906e-05/0.3129, allocations: 97.81 kB / 433.9 MB, free: 33.72 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001031/0.314, allocations: 0.8807 MB / 434.7 MB, free: 33.34 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.642e-05/0.314, allocations: 11.19 kB / 434.8 MB, free: 33.34 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 5.827e-05/0.3141, allocations: 38.62 kB / 434.8 MB, free: 33.3 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.479e-05/0.3141, allocations: 27.34 kB / 434.8 MB, free: 33.3 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000834/0.3149, allocations: 0.6198 MB / 435.4 MB, free: 33.08 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.00332/0.3183, allocations: 2.872 MB / 438.3 MB, free: 31.54 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0007954/0.3191, allocations: 0.5199 MB / 438.8 MB, free: 31.3 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003226/0.3194, allocations: 314.7 kB / 439.1 MB, free: 31.16 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.476e-05/0.3194, allocations: 10.97 kB / 439.2 MB, free: 31.16 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.491e-05/0.3195, allocations: 39.38 kB / 439.2 MB, free: 31.12 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.773e-06/0.3195, allocations: 1.188 kB / 439.2 MB, free: 31.12 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004176/0.3236, allocations: 2.172 MB / 441.4 MB, free: 30.12 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.072e-05/0.3237, allocations: 87.98 kB / 441.4 MB, free: 30.02 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002699/0.324, allocations: 357.6 kB / 441.8 MB, free: 29.84 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.771e-05/0.324, allocations: 36.98 kB / 441.8 MB, free: 29.8 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001552/0.3242, allocations: 452.4 kB / 442.3 MB, free: 29.45 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001016/0.3243, allocations: 221.9 kB / 442.5 MB, free: 29.27 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001443/0.3244, allocations: 139.3 kB / 442.6 MB, free: 29.2 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 6.703e-05/0.3245, allocations: 356.5 kB / 443 MB, free: 28.87 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002895/0.3248, allocations: 251.8 kB / 443.2 MB, free: 28.76 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003461/0.3251, allocations: 484.9 kB / 443.7 MB, free: 28.34 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.004891/0.33, allocations: 1.722 MB / 445.4 MB, free: 27.52 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.739e-06/0.3301, allocations: 3.938 kB / 445.4 MB, free: 27.51 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0009541/0.331, allocations: 0.7942 MB / 446.2 MB, free: 27.16 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.187e-05/0.3311, allocations: 10.12 kB / 446.2 MB, free: 27.16 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.257e-05/0.3311, allocations: 13.31 kB / 446.2 MB, free: 27.15 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.631e-05/0.3311, allocations: 12.34 kB / 446.3 MB, free: 27.15 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000577/0.3317, allocations: 189.6 kB / 446.4 MB, free: 27.13 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.726e-05/0.3317, allocations: 19.66 kB / 446.5 MB, free: 27.12 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002991/0.332, allocations: 24.34 kB / 446.5 MB, free: 27.11 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.786e-05/0.3321, allocations: 36.88 kB / 446.5 MB, free: 27.11 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 0.0004403/0.3325, allocations: 284.6 kB / 446.8 MB, free: 26.89 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.457e-05/0.3326, allocations: 50.06 kB / 446.8 MB, free: 26.86 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001275/0.3327, allocations: 66.27 kB / 446.9 MB, free: 26.81 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.171e-06/0.3327, allocations: 8.984 kB / 446.9 MB, free: 26.81 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.212e-05/0.3328, allocations: 0 / 446.9 MB, free: 26.81 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.063e-06/0.3328, allocations: 6.484 kB / 446.9 MB, free: 26.81 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000888/0.3337, allocations: 0.76 MB / 447.7 MB, free: 26.39 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.915e-06/0.3337, allocations: 3.094 kB / 447.7 MB, free: 26.39 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004873/0.3342, allocations: 113.4 kB / 447.8 MB, free: 26.37 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.847e-06/0.3342, allocations: 2.875 kB / 447.8 MB, free: 26.37 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.325e-05/0.3342, allocations: 15.09 kB / 447.8 MB, free: 26.36 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.925e-06/0.3342, allocations: 3.094 kB / 447.8 MB, free: 26.36 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.303e-06/0.3342, allocations: 0 / 447.8 MB, free: 26.36 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000973/0.3352, allocations: 0.9354 MB / 448.8 MB, free: 25.83 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.988e-05/0.3353, allocations: 116.6 kB / 448.9 MB, free: 25.71 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.999e-05/0.3354, allocations: 20.81 kB / 448.9 MB, free: 25.7 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002467/0.3356, allocations: 8 kB / 448.9 MB, free: 25.69 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.651e-05/0.3357, allocations: 39.61 kB / 448.9 MB, free: 25.69 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.374e-05/0.3357, allocations: 13.09 kB / 448.9 MB, free: 25.68 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001844/0.3359, allocations: 239.7 kB / 449.2 MB, free: 25.55 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.3e-07/0.3359, allocations: 0 / 449.2 MB, free: 25.55 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0005601/0.3365, allocations: 157.1 kB / 449.3 MB, free: 25.54 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 0.001248/0.3377, allocations: 1.488 MB / 450.8 MB, free: 24.46 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0009591/0.3387, allocations: 0.6236 MB / 451.4 MB, free: 24.22 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 4.028e-06/0.3387, allocations: 0 / 451.4 MB, free: 24.22 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.000279/0.339, allocations: 268.2 kB / 451.7 MB, free: 24.12 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004849/0.3395, allocations: 65.27 kB / 451.8 MB, free: 24.09 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.006016/0.3455, allocations: 5.938 MB / 457.7 MB, free: 20.07 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003579/0.3459, allocations: 0.9426 MB / 458.7 MB, free: 19.37 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0002695/0.3462, allocations: 63.12 kB / 458.7 MB, free: 19.35 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003113/0.3465, allocations: 284.8 kB / 459 MB, free: 19.13 MB / 350.1 MB
Notification: Performance of SimCode: time 6.61e-07/0.3465, allocations: 0 / 459 MB, free: 19.13 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.03808/0.3846, allocations: 10.63 MB / 469.6 MB, free: 18.22 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 7.312/7.696, allocations: 6.094 kB / 469.6 MB, free: 18.22 MB / 350.1 MB
(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 & python3 -m fmpy simulate  --output-file BioChem_BioChem.Examples.CircadianOscillator.Container_res.csv --start-time 0 --stop-time 150 --timeout 50 --relative-tolerance 1e-06 --interface-type ModelExchange --solver CVode --output-interval 150 BioChem_BioChem_Examples_CircadianOscillator_Container.fmu > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1)