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 0.007764/0.007763, allocations: 101.3 kB / 15.73 MB, free: 6.016 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001575/0.001576, allocations: 194.1 kB / 16.68 MB, free: 5.934 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.457/1.457, allocations: 222.9 MB / 240.4 MB, free: 4.156 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: 12.26 MB / 302.8 MB, free: 1.16 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001481/0.001481, allocations: 63.89 kB / 419.5 MB, free: 3.891 MB / 350.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2933/0.2948, allocations: 52.08 MB / 471.6 MB, free: 16.34 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01042/0.3053, allocations: 8.48 MB / 480.1 MB, free: 10.38 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001109/0.3064, allocations: 0.8217 MB / 480.9 MB, free: 9.66 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002459/0.3067, allocations: 39.88 kB / 481 MB, free: 9.66 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.000206/0.3069, allocations: 144.8 kB / 481.1 MB, free: 9.531 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0003757/0.3073, allocations: 214.1 kB / 481.3 MB, free: 9.344 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002808/0.3076, allocations: 196.9 kB / 481.5 MB, free: 9.164 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0005605/0.3082, allocations: 0.8358 MB / 482.3 MB, free: 8.641 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006165/0.3088, allocations: 0.5371 MB / 482.9 MB, free: 8.312 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002577/0.3091, allocations: 370.3 kB / 483.2 MB, free: 8.074 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003236/0.3094, allocations: 433.4 kB / 483.7 MB, free: 7.742 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001325/0.3095, allocations: 116.6 kB / 483.8 MB, free: 7.742 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001413/0.3097, allocations: 120.3 kB / 483.9 MB, free: 7.738 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.000111/0.3098, allocations: 222.7 kB / 484.1 MB, free: 7.543 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002939/0.3101, allocations: 487 kB / 484.6 MB, free: 7.184 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.000798/0.3109, allocations: 1.167 MB / 485.8 MB, free: 6.27 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.669e-06/0.3109, allocations: 0 / 485.8 MB, free: 6.27 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.114e-06/0.3109, allocations: 0 / 485.8 MB, free: 6.27 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.238e-05/0.3109, allocations: 5.062 kB / 485.8 MB, free: 6.266 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 0.00134/0.3123, allocations: 1.148 MB / 486.9 MB, free: 5.359 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.578e-05/0.3123, allocations: 8.844 kB / 486.9 MB, free: 5.359 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.0001218/0.3125, allocations: 152.2 kB / 487.1 MB, free: 5.234 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001179/0.3126, allocations: 100.5 kB / 487.2 MB, free: 5.184 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002148/0.3128, allocations: 305.9 kB / 487.5 MB, free: 4.883 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.224e-05/0.3129, allocations: 78.45 kB / 487.5 MB, free: 4.844 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000107/0.313, allocations: 101.4 kB / 487.6 MB, free: 4.809 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001148/0.3141, allocations: 0.8738 MB / 488.5 MB, free: 4.301 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.021e-05/0.3142, allocations: 5.062 kB / 488.5 MB, free: 4.297 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 5.834e-05/0.3142, allocations: 40.31 kB / 488.6 MB, free: 4.266 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.102e-05/0.3143, allocations: 27.44 kB / 488.6 MB, free: 4.262 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001011/0.3153, allocations: 0.6267 MB / 489.2 MB, free: 3.965 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003769/0.3191, allocations: 2.832 MB / 492 MB, free: 1.852 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008706/0.32, allocations: 0.5226 MB / 492.6 MB, free: 1.562 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003489/0.3203, allocations: 314.5 kB / 492.9 MB, free: 1.41 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.202e-05/0.3204, allocations: 7.062 kB / 492.9 MB, free: 1.41 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.712e-05/0.3204, allocations: 38.78 kB / 492.9 MB, free: 1.363 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.933e-06/0.3204, allocations: 0 / 492.9 MB, free: 1.363 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004457/0.3248, allocations: 2.187 MB / 495.1 MB, free: 108 kB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.014e-05/0.3249, allocations: 84.45 kB / 495.2 MB, free: 12 kB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003582/0.3253, allocations: 366.1 kB / 495.5 MB, free: 15.77 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.642e-05/0.3253, allocations: 40.44 kB / 495.6 MB, free: 15.73 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002427/0.3255, allocations: 457.2 kB / 496 MB, free: 15.28 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001572/0.3257, allocations: 234 kB / 496.3 MB, free: 15.05 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001811/0.3259, allocations: 142.6 kB / 496.4 MB, free: 14.9 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001264/0.326, allocations: 354.8 kB / 496.7 MB, free: 14.54 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003561/0.3264, allocations: 252.8 kB / 497 MB, free: 14.3 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004754/0.3269, allocations: 484.8 kB / 497.5 MB, free: 13.7 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005368/0.3323, allocations: 1.704 MB / 499.2 MB, free: 11.88 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.703e-06/0.3323, allocations: 7.938 kB / 499.2 MB, free: 11.87 MB / 366.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001145/0.3334, allocations: 0.7957 MB / 500 MB, free: 11.07 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.05e-05/0.3335, allocations: 16.22 kB / 500 MB, free: 11.05 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.186e-05/0.3335, allocations: 8 kB / 500 MB, free: 11.04 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.335e-05/0.3335, allocations: 12 kB / 0.4883 GB, free: 11.03 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006462/0.3342, allocations: 183.7 kB / 0.4885 GB, free: 10.85 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.172e-05/0.3342, allocations: 23.92 kB / 0.4885 GB, free: 10.83 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003132/0.3345, allocations: 20 kB / 0.4885 GB, free: 10.81 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.689e-05/0.3346, allocations: 40 kB / 0.4885 GB, free: 10.77 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 0.000438/0.335, allocations: 293.8 kB / 0.4888 GB, free: 10.48 MB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.9e-05/0.3351, allocations: 51.67 kB / 0.4889 GB, free: 10.43 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001588/0.3353, allocations: 64.91 kB / 0.4889 GB, free: 10.36 MB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.843e-06/0.3353, allocations: 8 kB / 0.4889 GB, free: 10.35 MB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.212e-05/0.3353, allocations: 0 / 0.4889 GB, free: 10.35 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.123e-06/0.3353, allocations: 3.984 kB / 0.4889 GB, free: 10.35 MB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001081/0.3364, allocations: 0.7593 MB / 0.4897 GB, free: 9.539 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.006e-06/0.3364, allocations: 7.938 kB / 0.4897 GB, free: 9.531 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005572/0.337, allocations: 103.9 kB / 0.4898 GB, free: 9.43 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 6.342e-06/0.337, allocations: 4 kB / 0.4898 GB, free: 9.426 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.938e-05/0.337, allocations: 15.98 kB / 0.4898 GB, free: 9.41 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 6.311e-06/0.3371, allocations: 4 kB / 0.4898 GB, free: 9.406 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.605e-06/0.3371, allocations: 0 / 0.4898 GB, free: 9.406 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001144/0.3382, allocations: 0.9363 MB / 0.4907 GB, free: 8.449 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 9e-05/0.3383, allocations: 128.8 kB / 0.4909 GB, free: 8.305 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.896e-05/0.3384, allocations: 12 kB / 0.4909 GB, free: 8.293 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002572/0.3386, allocations: 8 kB / 0.4909 GB, free: 8.285 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.346e-05/0.3387, allocations: 36.5 kB / 0.4909 GB, free: 8.25 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.842e-05/0.3388, allocations: 16 kB / 0.4909 GB, free: 8.234 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 0.0002189/0.339, allocations: 239.2 kB / 0.4912 GB, free: 8.004 MB / 366.1 MB
Notification: Performance of sort global known variables: time 1.2e-07/0.339, allocations: 0 / 0.4912 GB, free: 8.004 MB / 366.1 MB
Notification: Performance of remove unused functions: time 0.0006147/0.3396, allocations: 156 kB / 0.4913 GB, free: 7.852 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 0.001373/0.341, allocations: 1.492 MB / 0.4928 GB, free: 6.336 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.0008914/0.3419, allocations: 0.5978 MB / 0.4933 GB, free: 5.742 MB / 366.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.094e-06/0.3419, allocations: 0 / 0.4933 GB, free: 5.742 MB / 366.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003401/0.3422, allocations: 267.1 kB / 0.4936 GB, free: 5.48 MB / 366.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005024/0.3428, allocations: 71.34 kB / 0.4937 GB, free: 5.41 MB / 366.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.007752/0.3505, allocations: 5.861 MB / 0.4994 GB, free: 15.21 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005335/0.3511, allocations: 0.9389 MB / 0.5003 GB, free: 14.25 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.0002716/0.3514, allocations: 60.81 kB / 0.5004 GB, free: 14.2 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003583/0.3517, allocations: 283.3 kB / 0.5006 GB, free: 13.92 MB / 382.1 MB
Notification: Performance of SimCode: time 9.32e-07/0.3517, allocations: 3.938 kB / 0.5006 GB, free: 13.91 MB / 382.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.03587/0.3876, allocations: 10.98 MB / 0.5114 GB, free: 3.043 MB / 382.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 8.666/9.054, allocations: 7.188 kB / 0.5114 GB, free: 3.039 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)