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 0.01137/0.01137, allocations: 103.9 kB / 15.73 MB, free: 6.035 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001926/0.001926, allocations: 194.4 kB / 16.67 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 1.877/1.877, allocations: 222.9 MB / 240.4 MB, free: 4.32 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.2958/0.2958, allocations: 12.26 MB / 302.8 MB, free: 1.266 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001634/0.001634, allocations: 67.89 kB / 419.5 MB, free: 3.973 MB / 350.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3681/0.3697, allocations: 52.07 MB / 471.6 MB, free: 16.38 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.0136/0.3834, allocations: 8.479 MB / 480.1 MB, free: 10.41 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.002537/0.386, allocations: 0.8214 MB / 480.9 MB, free: 9.691 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001138/0.3872, allocations: 40.28 kB / 481 MB, free: 9.691 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0007584/0.388, allocations: 143.9 kB / 481.1 MB, free: 9.562 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.001365/0.3894, allocations: 203.9 kB / 481.3 MB, free: 9.383 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.001014/0.3904, allocations: 201.2 kB / 481.5 MB, free: 9.199 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.001706/0.3922, allocations: 0.8402 MB / 482.3 MB, free: 8.672 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001056/0.3932, allocations: 0.5254 MB / 482.9 MB, free: 8.355 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000712/0.394, allocations: 370 kB / 483.2 MB, free: 8.117 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0008176/0.3948, allocations: 441.3 kB / 483.7 MB, free: 7.777 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0003521/0.3952, allocations: 116.8 kB / 483.8 MB, free: 7.777 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0004314/0.3956, allocations: 116.2 kB / 483.9 MB, free: 7.777 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002571/0.3959, allocations: 222.4 kB / 484.1 MB, free: 7.582 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.000888/0.3968, allocations: 487.7 kB / 484.6 MB, free: 7.223 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.001599/0.3984, allocations: 1.16 MB / 485.7 MB, free: 6.312 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 8.436e-06/0.3984, allocations: 0 / 485.7 MB, free: 6.312 MB / 350.1 MB
Notification: Performance of FrontEnd: time 5.29e-06/0.3984, allocations: 1.156 kB / 485.7 MB, free: 6.312 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 7.518e-05/0.3985, allocations: 3.938 kB / 485.7 MB, free: 6.309 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 0.002694/0.4012, allocations: 1.125 MB / 486.9 MB, free: 5.426 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.991e-05/0.4013, allocations: 9.719 kB / 486.9 MB, free: 5.426 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.0002992/0.4016, allocations: 152.1 kB / 487 MB, free: 5.301 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0003496/0.402, allocations: 95.81 kB / 487.1 MB, free: 5.254 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.00048/0.4024, allocations: 310.6 kB / 487.4 MB, free: 4.949 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 9.506e-05/0.4026, allocations: 74.03 kB / 487.5 MB, free: 4.914 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002031/0.4028, allocations: 96.22 kB / 487.6 MB, free: 4.883 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001945/0.4047, allocations: 0.8741 MB / 488.5 MB, free: 4.375 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 4.73e-05/0.4048, allocations: 13.22 kB / 488.5 MB, free: 4.363 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.525e-05/0.4049, allocations: 40.86 kB / 488.5 MB, free: 4.332 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.601e-05/0.4049, allocations: 23.66 kB / 488.5 MB, free: 4.332 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.00131/0.4062, allocations: 0.6304 MB / 489.2 MB, free: 4.031 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004578/0.4108, allocations: 2.823 MB / 492 MB, free: 1.926 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.001021/0.4119, allocations: 0.5216 MB / 492.5 MB, free: 1.637 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004396/0.4123, allocations: 314.9 kB / 492.8 MB, free: 1.484 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.89e-05/0.4124, allocations: 10 kB / 492.8 MB, free: 1.48 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.671e-05/0.4124, allocations: 38.25 kB / 492.9 MB, free: 1.434 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 3.276e-06/0.4124, allocations: 4 kB / 492.9 MB, free: 1.43 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.005221/0.4176, allocations: 2.17 MB / 495 MB, free: 196 kB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.315e-05/0.4177, allocations: 84.55 kB / 495.1 MB, free: 100 kB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004403/0.4181, allocations: 357.1 kB / 495.5 MB, free: 15.87 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.801e-05/0.4182, allocations: 32.42 kB / 495.5 MB, free: 15.83 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003126/0.4185, allocations: 457.2 kB / 496 MB, free: 15.39 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001808/0.4187, allocations: 220.8 kB / 496.2 MB, free: 15.17 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001926/0.4189, allocations: 130.6 kB / 496.3 MB, free: 15.04 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001473/0.4191, allocations: 366.8 kB / 496.7 MB, free: 14.67 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003477/0.4194, allocations: 252.7 kB / 496.9 MB, free: 14.42 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005097/0.4199, allocations: 484.9 kB / 497.4 MB, free: 13.83 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005696/0.4256, allocations: 1.696 MB / 499.1 MB, free: 12.01 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.322e-05/0.4257, allocations: 7.938 kB / 499.1 MB, free: 12 MB / 366.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001369/0.427, allocations: 0.7956 MB / 499.9 MB, free: 11.2 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 3.248e-05/0.4271, allocations: 8 kB / 499.9 MB, free: 11.19 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 3.627e-05/0.4271, allocations: 15.98 kB / 499.9 MB, free: 11.18 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 4.803e-05/0.4272, allocations: 12 kB / 499.9 MB, free: 11.16 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007405/0.428, allocations: 179.7 kB / 0.4884 GB, free: 10.99 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.811e-05/0.428, allocations: 15.94 kB / 0.4884 GB, free: 10.97 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0004851/0.4285, allocations: 28 kB / 0.4884 GB, free: 10.95 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.335e-05/0.4286, allocations: 32 kB / 0.4884 GB, free: 10.91 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 0.0007278/0.4293, allocations: 298.9 kB / 0.4887 GB, free: 10.62 MB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000165/0.4295, allocations: 51.38 kB / 0.4888 GB, free: 10.57 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001842/0.4297, allocations: 72.84 kB / 0.4888 GB, free: 10.49 MB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.156e-05/0.4297, allocations: 8 kB / 0.4888 GB, free: 10.48 MB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.21e-05/0.4297, allocations: 4 kB / 0.4888 GB, free: 10.48 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.045e-05/0.4297, allocations: 7.984 kB / 0.4889 GB, free: 10.47 MB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001428/0.4312, allocations: 0.7593 MB / 0.4896 GB, free: 9.664 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 7.945e-06/0.4312, allocations: 0 / 0.4896 GB, free: 9.664 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005651/0.4317, allocations: 103.9 kB / 0.4897 GB, free: 9.562 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 1.091e-05/0.4318, allocations: 4 kB / 0.4897 GB, free: 9.559 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.492e-05/0.4318, allocations: 19.98 kB / 0.4897 GB, free: 9.539 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.256e-06/0.4318, allocations: 0 / 0.4897 GB, free: 9.539 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.576e-06/0.4318, allocations: 4 kB / 0.4897 GB, free: 9.535 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001217/0.4331, allocations: 0.9399 MB / 0.4906 GB, free: 8.574 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001309/0.4332, allocations: 112.7 kB / 0.4907 GB, free: 8.445 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 7.478e-05/0.4333, allocations: 23.92 kB / 0.4908 GB, free: 8.422 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003057/0.4336, allocations: 12 kB / 0.4908 GB, free: 8.41 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.362e-05/0.4337, allocations: 32.52 kB / 0.4908 GB, free: 8.379 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.987e-05/0.4337, allocations: 15.98 kB / 0.4908 GB, free: 8.363 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 0.0002678/0.434, allocations: 239.2 kB / 0.4911 GB, free: 8.133 MB / 366.1 MB
Notification: Performance of sort global known variables: time 1.31e-07/0.434, allocations: 0 / 0.4911 GB, free: 8.133 MB / 366.1 MB
Notification: Performance of remove unused functions: time 0.000787/0.4348, allocations: 164 kB / 0.4912 GB, free: 7.973 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 0.001549/0.4363, allocations: 1.481 MB / 0.4927 GB, free: 6.465 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.0009452/0.4373, allocations: 0.599 MB / 0.4932 GB, free: 5.871 MB / 366.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.386e-06/0.4373, allocations: 0 / 0.4932 GB, free: 5.871 MB / 366.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003638/0.4377, allocations: 259.1 kB / 0.4935 GB, free: 5.617 MB / 366.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006154/0.4383, allocations: 69.72 kB / 0.4936 GB, free: 5.547 MB / 366.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.007956/0.4463, allocations: 5.816 MB / 0.4992 GB, free: 15.4 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005627/0.4469, allocations: 0.9389 MB / 0.5002 GB, free: 14.44 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.0002841/0.4472, allocations: 68.56 kB / 0.5002 GB, free: 14.37 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003789/0.4476, allocations: 287.3 kB / 0.5005 GB, free: 14.09 MB / 382.1 MB
Notification: Performance of SimCode: time 1.854e-06/0.4476, allocations: 0 / 0.5005 GB, free: 14.09 MB / 382.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.03851/0.4861, allocations: 11.07 MB / 0.5113 GB, free: 3.133 MB / 382.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 9.837/10.32, allocations: 8.75 kB / 0.5113 GB, free: 3.129 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 & /home/hudson/saved_omc/OMSimulator/install/bin/OMSimulator  --tempDir=temp_BioChem_BioChem_Examples_CircadianOscillator_Container_fmu --startTime=0 --stopTime=150 --timeout=50 --tolerance=1e-06 BioChem_BioChem_Examples_CircadianOscillator_Container.fmu > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1)