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 0.005255/0.005255, allocations: 97.62 kB / 15.73 MB, free: 6.047 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.00129/0.00129, allocations: 202.6 kB / 16.68 MB, free: 5.969 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.508/1.508, allocations: 222.9 MB / 240.4 MB, free: 4.336 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1811/0.1811, allocations: 12.27 MB / 302.8 MB, free: 1.234 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001934/0.001934, allocations: 59.91 kB / 419.5 MB, free: 4 MB / 350.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2783/0.2802, allocations: 52.08 MB / 471.6 MB, free: 16.41 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.009428/0.2897, allocations: 8.482 MB / 480.1 MB, free: 10.41 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001567/0.2913, allocations: 0.8099 MB / 480.9 MB, free: 9.699 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003971/0.2917, allocations: 45.31 kB / 481 MB, free: 9.695 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002852/0.2921, allocations: 139.6 kB / 481.1 MB, free: 9.57 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004582/0.2926, allocations: 208 kB / 481.3 MB, free: 9.387 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003675/0.2929, allocations: 201 kB / 481.5 MB, free: 9.203 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.000768/0.2937, allocations: 0.8389 MB / 482.3 MB, free: 8.676 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0007987/0.2945, allocations: 0.538 MB / 482.9 MB, free: 8.348 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003907/0.2949, allocations: 369.7 kB / 483.2 MB, free: 8.109 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000423/0.2953, allocations: 429 kB / 483.7 MB, free: 7.781 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001658/0.2955, allocations: 115.7 kB / 483.8 MB, free: 7.781 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001722/0.2957, allocations: 116.1 kB / 483.9 MB, free: 7.781 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001407/0.2958, allocations: 231.8 kB / 484.1 MB, free: 7.578 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003614/0.2962, allocations: 483.1 kB / 484.6 MB, free: 7.223 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0008961/0.2971, allocations: 1.171 MB / 485.7 MB, free: 6.305 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.751e-06/0.2971, allocations: 0 / 485.7 MB, free: 6.305 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.285e-06/0.2971, allocations: 0 / 485.7 MB, free: 6.305 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.359e-05/0.2971, allocations: 0 / 485.7 MB, free: 6.305 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 0.001459/0.2986, allocations: 1.148 MB / 486.9 MB, free: 5.398 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.217e-05/0.2987, allocations: 10.16 kB / 486.9 MB, free: 5.398 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.0001268/0.2988, allocations: 151.5 kB / 487.1 MB, free: 5.273 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001323/0.2989, allocations: 100.1 kB / 487.1 MB, free: 5.223 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002483/0.2992, allocations: 310.8 kB / 487.5 MB, free: 4.918 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.727e-05/0.2993, allocations: 73.44 kB / 487.5 MB, free: 4.883 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001404/0.2994, allocations: 100.5 kB / 487.6 MB, free: 4.848 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001334/0.3007, allocations: 0.8749 MB / 488.5 MB, free: 4.34 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.345e-05/0.3008, allocations: 9.078 kB / 488.5 MB, free: 4.332 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.632e-05/0.3009, allocations: 44.44 kB / 488.6 MB, free: 4.297 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.104e-05/0.3009, allocations: 23.84 kB / 488.6 MB, free: 4.297 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001022/0.3019, allocations: 0.6183 MB / 489.2 MB, free: 4.008 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003618/0.3056, allocations: 2.843 MB / 492 MB, free: 1.883 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0009078/0.3065, allocations: 0.517 MB / 492.6 MB, free: 1.602 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003659/0.3068, allocations: 319.2 kB / 492.9 MB, free: 1.445 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.042e-05/0.3069, allocations: 6.688 kB / 492.9 MB, free: 1.445 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.762e-05/0.3069, allocations: 46.56 kB / 492.9 MB, free: 1.391 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.873e-06/0.3069, allocations: 0 / 492.9 MB, free: 1.391 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004773/0.3117, allocations: 2.182 MB / 495.1 MB, free: 144 kB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.155e-05/0.3117, allocations: 84.55 kB / 495.2 MB, free: 48 kB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000432/0.3122, allocations: 365.4 kB / 495.5 MB, free: 15.8 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.834e-05/0.3122, allocations: 36.45 kB / 495.6 MB, free: 15.77 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004265/0.3127, allocations: 460.7 kB / 496 MB, free: 15.34 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002011/0.3129, allocations: 234.1 kB / 496.3 MB, free: 15.11 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002169/0.3131, allocations: 142.6 kB / 496.4 MB, free: 14.96 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0002268/0.3133, allocations: 358.8 kB / 496.7 MB, free: 14.6 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0004158/0.3138, allocations: 248.7 kB / 497 MB, free: 14.36 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0006799/0.3144, allocations: 488.9 kB / 497.5 MB, free: 13.76 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.006069/0.3205, allocations: 1.692 MB / 499.2 MB, free: 11.95 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 9.198e-06/0.3205, allocations: 7.938 kB / 499.2 MB, free: 11.94 MB / 366.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001313/0.3219, allocations: 0.8034 MB / 500 MB, free: 11.13 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 3.829e-05/0.3219, allocations: 9.719 kB / 500 MB, free: 11.12 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.954e-05/0.3219, allocations: 11.98 kB / 500 MB, free: 11.11 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.791e-05/0.322, allocations: 12 kB / 500 MB, free: 11.1 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006768/0.3226, allocations: 191.6 kB / 0.4885 GB, free: 10.91 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.362e-05/0.3227, allocations: 23.92 kB / 0.4885 GB, free: 10.89 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003299/0.323, allocations: 24 kB / 0.4885 GB, free: 10.86 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.302e-05/0.3231, allocations: 36.41 kB / 0.4885 GB, free: 10.83 MB / 366.1 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 0.0005779/0.3237, allocations: 290.7 kB / 0.4888 GB, free: 10.54 MB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001158/0.3238, allocations: 47.67 kB / 0.4889 GB, free: 10.49 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000175/0.324, allocations: 68.91 kB / 0.4889 GB, free: 10.42 MB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.035e-05/0.324, allocations: 12 kB / 0.4889 GB, free: 10.41 MB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.836e-05/0.324, allocations: 0 / 0.4889 GB, free: 10.41 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.495e-05/0.324, allocations: 7.984 kB / 0.4889 GB, free: 10.4 MB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001362/0.3254, allocations: 0.7554 MB / 0.4897 GB, free: 9.598 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.206e-06/0.3254, allocations: 0 / 0.4897 GB, free: 9.598 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000562/0.326, allocations: 107.8 kB / 0.4898 GB, free: 9.492 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 8.937e-06/0.326, allocations: 4 kB / 0.4898 GB, free: 9.488 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.34e-05/0.326, allocations: 19.98 kB / 0.4898 GB, free: 9.469 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.661e-06/0.3261, allocations: 4 kB / 0.4898 GB, free: 9.465 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.485e-06/0.3261, allocations: 0 / 0.4898 GB, free: 9.465 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001322/0.3274, allocations: 0.9441 MB / 0.4907 GB, free: 8.5 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001146/0.3275, allocations: 120.7 kB / 0.4909 GB, free: 8.363 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.056e-05/0.3276, allocations: 12 kB / 0.4909 GB, free: 8.352 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000268/0.3279, allocations: 12 kB / 0.4909 GB, free: 8.34 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.765e-05/0.3279, allocations: 36.5 kB / 0.4909 GB, free: 8.305 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.854e-05/0.328, allocations: 12 kB / 0.4909 GB, free: 8.293 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 0.0002587/0.3282, allocations: 243.2 kB / 0.4912 GB, free: 8.059 MB / 366.1 MB
Notification: Performance of sort global known variables: time 1.3e-07/0.3282, allocations: 4 kB / 0.4912 GB, free: 8.055 MB / 366.1 MB
Notification: Performance of remove unused functions: time 0.0007212/0.329, allocations: 156 kB / 0.4913 GB, free: 7.902 MB / 366.1 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 0.001792/0.3308, allocations: 1.493 MB / 0.4928 GB, free: 6.383 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.001108/0.3319, allocations: 0.5908 MB / 0.4933 GB, free: 5.797 MB / 366.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.266e-06/0.3319, allocations: 0 / 0.4933 GB, free: 5.797 MB / 366.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0004034/0.3323, allocations: 263.7 kB / 0.4936 GB, free: 5.539 MB / 366.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006164/0.3329, allocations: 69.55 kB / 0.4937 GB, free: 5.469 MB / 366.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.008721/0.3417, allocations: 5.861 MB / 0.4994 GB, free: 15.27 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0006544/0.3424, allocations: 0.935 MB / 0.5003 GB, free: 14.32 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.0002875/0.3427, allocations: 68.58 kB / 0.5004 GB, free: 14.25 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000391/0.3431, allocations: 275.3 kB / 0.5006 GB, free: 13.98 MB / 382.1 MB
Notification: Performance of SimCode: time 7.51e-07/0.3431, allocations: 4 kB / 0.5006 GB, free: 13.98 MB / 382.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.03814/0.3812, allocations: 10.98 MB / 0.5114 GB, free: 3.109 MB / 382.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 8.95/9.331, allocations: 6.562 kB / 0.5114 GB, free: 3.105 MB / 382.1 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)