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 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.001286/0.001286, allocations: 80.81 kB / 19.94 MB, free: 4.543 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.001498/0.001498, allocations: 177 kB / 23.36 MB, free: 1.125 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 0.963/0.963, allocations: 177.1 MB / 203.8 MB, free: 5.445 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo): time 0.03861/0.03861, allocations: 9.558 MB / 269.8 MB, free: 3.789 MB / 250.7 MB
"
[Timeout remaining time 180]
Using package BioChem with version 1.1.3 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo)
Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo)
Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo)
Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo)
Running command: translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container")
translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.423e-06/1.423e-06, allocations: 0 / 290.1 MB, free: 17.3 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.044e-05/1.186e-05, allocations: 2.312 kB / 290.1 MB, free: 17.3 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.005823/0.005835, allocations: 6.51 MB / 296.6 MB, free: 14.74 MB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.001402/0.007237, allocations: 0.8657 MB / 297.5 MB, free: 14.33 MB / 266.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002592/0.007496, allocations: 42.53 kB / 297.5 MB, free: 14.33 MB / 266.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002153/0.007712, allocations: 143.5 kB / 297.6 MB, free: 14.21 MB / 266.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004245/0.008136, allocations: 219.6 kB / 297.9 MB, free: 14.05 MB / 266.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003942/0.00853, allocations: 197.9 kB / 298.1 MB, free: 13.93 MB / 266.7 MB
Notification: Performance of NFFlatten.flatten: time 0.000736/0.009266, allocations: 0.8775 MB / 298.9 MB, free: 13.44 MB / 266.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.000459/0.009725, allocations: 369.1 kB / 299.3 MB, free: 13.21 MB / 266.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0005337/0.01026, allocations: 0.5692 MB / 299.9 MB, free: 12.93 MB / 266.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000362/0.01062, allocations: 324.5 kB / 300.2 MB, free: 12.8 MB / 266.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001282/0.01075, allocations: 116.8 kB / 300.3 MB, free: 12.8 MB / 266.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001277/0.01088, allocations: 117.2 kB / 300.4 MB, free: 12.8 MB / 266.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001104/0.01099, allocations: 229.1 kB / 300.6 MB, free: 12.64 MB / 266.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002618/0.01125, allocations: 332.8 kB / 301 MB, free: 12.46 MB / 266.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0005669/0.01182, allocations: 0.6505 MB / 301.6 MB, free: 12.09 MB / 266.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.587e-06/0.01182, allocations: 0 / 301.6 MB, free: 12.09 MB / 266.7 MB
Notification: Performance of FrontEnd: time 2.054e-06/0.01182, allocations: 1.453 kB / 301.6 MB, free: 12.09 MB / 266.7 MB
Notification: Performance of Transformations before backend: time 1.511e-05/0.01184, allocations: 1 kB / 301.6 MB, free: 12.09 MB / 266.7 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 0.001294/0.01313, allocations: 1.053 MB / 302.7 MB, free: 11.42 MB / 266.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.786e-05/0.01317, allocations: 12.91 kB / 302.7 MB, free: 11.41 MB / 266.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.000168/0.01334, allocations: 144.6 kB / 302.8 MB, free: 11.39 MB / 266.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001667/0.0135, allocations: 241 kB / 303 MB, free: 11.17 MB / 266.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.989e-05/0.01355, allocations: 70.25 kB / 303.1 MB, free: 11.14 MB / 266.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 9.518e-05/0.01365, allocations: 105.9 kB / 303.2 MB, free: 11.1 MB / 266.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005681/0.01422, allocations: 0.6334 MB / 303.9 MB, free: 10.83 MB / 266.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.244e-05/0.01424, allocations: 2.219 kB / 303.9 MB, free: 10.83 MB / 266.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.486e-05/0.01427, allocations: 39.03 kB / 303.9 MB, free: 10.8 MB / 266.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.071e-05/0.01429, allocations: 25.31 kB / 303.9 MB, free: 10.8 MB / 266.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000291/0.01459, allocations: 238.8 kB / 304.2 MB, free: 10.75 MB / 266.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002247/0.01683, allocations: 1.928 MB / 306.1 MB, free: 9.531 MB / 266.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004349/0.01727, allocations: 395 kB / 306.5 MB, free: 9.363 MB / 266.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001679/0.01744, allocations: 165.1 kB / 306.6 MB, free: 9.312 MB / 266.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.171e-05/0.01746, allocations: 10.62 kB / 306.6 MB, free: 9.312 MB / 266.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.076e-05/0.01748, allocations: 38 kB / 306.7 MB, free: 9.27 MB / 266.7 MB
Notification: Performance of pre-optimization done (n=50): time 1.733e-06/0.01748, allocations: 0 / 306.7 MB, free: 9.27 MB / 266.7 MB
Notification: Performance of matching and sorting (n=59): time 0.001576/0.01906, allocations: 1.247 MB / 307.9 MB, free: 8.598 MB / 266.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.494e-05/0.01908, allocations: 89.55 kB / 308 MB, free: 8.492 MB / 266.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001335/0.01921, allocations: 343.1 kB / 308.3 MB, free: 8.141 MB / 266.7 MB
Notification: Performance of collectPreVariables (initialization): time 1.67e-05/0.01923, allocations: 33.7 kB / 308.4 MB, free: 8.102 MB / 266.7 MB
Notification: Performance of collectInitialEqns (initialization): time 8.818e-05/0.01932, allocations: 445 kB / 308.8 MB, free: 7.66 MB / 266.7 MB
Notification: Performance of collectInitialBindings (initialization): time 7.069e-05/0.01939, allocations: 234 kB / 309 MB, free: 7.43 MB / 266.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.869e-05/0.01948, allocations: 134.6 kB / 309.2 MB, free: 7.293 MB / 266.7 MB
Notification: Performance of setup shared object (initialization): time 4.481e-05/0.01952, allocations: 367.6 kB / 309.5 MB, free: 6.926 MB / 266.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.697e-05/0.01961, allocations: 128.7 kB / 309.7 MB, free: 6.801 MB / 266.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001298/0.01974, allocations: 361.7 kB / 310 MB, free: 6.332 MB / 266.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003583/0.0201, allocations: 0.629 MB / 310.6 MB, free: 5.59 MB / 266.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.266e-06/0.0201, allocations: 4 kB / 310.6 MB, free: 5.586 MB / 266.7 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0003352/0.02044, allocations: 493.9 kB / 311.1 MB, free: 5.105 MB / 266.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.296e-05/0.02045, allocations: 8 kB / 311.1 MB, free: 5.098 MB / 266.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.806e-06/0.02046, allocations: 11.09 kB / 311.1 MB, free: 5.09 MB / 266.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.765e-05/0.02048, allocations: 16 kB / 311.2 MB, free: 5.074 MB / 266.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003038/0.02078, allocations: 187.6 kB / 311.3 MB, free: 4.891 MB / 266.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.947e-06/0.02079, allocations: 15.94 kB / 311.4 MB, free: 4.875 MB / 266.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001325/0.02092, allocations: 28 kB / 311.4 MB, free: 4.848 MB / 266.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.931e-05/0.02094, allocations: 31.98 kB / 311.4 MB, free: 4.816 MB / 266.7 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 0.0001685/0.02111, allocations: 213.2 kB / 311.6 MB, free: 4.605 MB / 266.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 5.34e-05/0.02116, allocations: 47.95 kB / 311.7 MB, free: 4.559 MB / 266.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.126e-05/0.02121, allocations: 64.91 kB / 311.7 MB, free: 4.492 MB / 266.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.196e-06/0.02122, allocations: 8 kB / 311.7 MB, free: 4.484 MB / 266.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.358e-06/0.02122, allocations: 3.938 kB / 311.7 MB, free: 4.48 MB / 266.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.739e-06/0.02123, allocations: 3.984 kB / 311.7 MB, free: 4.477 MB / 266.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003902/0.02162, allocations: 386 kB / 312.1 MB, free: 4.082 MB / 266.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.974e-06/0.02162, allocations: 0 / 312.1 MB, free: 4.082 MB / 266.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002382/0.02186, allocations: 111.8 kB / 312.2 MB, free: 3.973 MB / 266.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.284e-06/0.02186, allocations: 4 kB / 312.2 MB, free: 3.969 MB / 266.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.07e-05/0.02188, allocations: 22.42 kB / 312.3 MB, free: 3.949 MB / 266.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.705e-06/0.02188, allocations: 4 kB / 312.3 MB, free: 3.945 MB / 266.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.192e-06/0.02188, allocations: 0 / 312.3 MB, free: 3.945 MB / 266.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003373/0.02222, allocations: 0.584 MB / 312.8 MB, free: 3.344 MB / 266.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.65e-05/0.02225, allocations: 35.72 kB / 312.9 MB, free: 3.309 MB / 266.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.117e-05/0.02228, allocations: 16 kB / 312.9 MB, free: 3.293 MB / 266.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001089/0.02239, allocations: 8 kB / 312.9 MB, free: 3.285 MB / 266.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.049e-05/0.02242, allocations: 40.42 kB / 312.9 MB, free: 3.242 MB / 266.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.252e-05/0.02243, allocations: 15.94 kB / 313 MB, free: 3.227 MB / 266.7 MB
Notification: Performance of sorting global known variables: time 6.023e-05/0.02249, allocations: 128.7 kB / 313.1 MB, free: 3.098 MB / 266.7 MB
Notification: Performance of sort global known variables: time 5e-08/0.02249, allocations: 0 / 313.1 MB, free: 3.098 MB / 266.7 MB
Notification: Performance of remove unused functions: time 0.0003323/0.02282, allocations: 156 kB / 313.2 MB, free: 2.945 MB / 266.7 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 9.304e-05/0.02292, allocations: 92.36 kB / 313.3 MB, free: 2.848 MB / 266.7 MB
Notification: Performance of simCode: created initialization part: time 0.0003714/0.02329, allocations: 370.4 kB / 313.7 MB, free: 2.488 MB / 266.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.333e-05/0.0233, allocations: 11.19 kB / 313.7 MB, free: 2.48 MB / 266.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001453/0.02345, allocations: 156.6 kB / 313.9 MB, free: 2.32 MB / 266.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003265/0.02377, allocations: 77.55 kB / 313.9 MB, free: 2.25 MB / 266.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001172/0.02494, allocations: 1.383 MB / 315.3 MB, free: 0.832 MB / 266.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 6.742e-05/0.02501, allocations: 155.9 kB / 315.5 MB, free: 0.6602 MB / 266.7 MB
Notification: Performance of simCode: alias equations: time 0.0001396/0.02515, allocations: 68.56 kB / 315.5 MB, free: 0.5938 MB / 266.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001551/0.02531, allocations: 151.2 kB / 315.7 MB, free: 456 kB / 266.7 MB
Notification: Performance of SimCode: time 6.01e-07/0.02531, allocations: 0 / 315.7 MB, free: 456 kB / 266.7 MB
Notification: Performance of Templates: time 0.008014/0.03332, allocations: 5.787 MB / 321.5 MB, free: 10.78 MB / 282.7 MB
"
[Timeout remaining time 660]
make -j1 -f BioChem_BioChem.Examples.CircadianOscillator.Container.makefile [Timeout 660]
(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=240  -lv LOG_STATS > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 2.8145816703327]