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 0.001389/0.001389, allocations: 69.98 kB / 20.65 MB, free: 3.848 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 0.001838/0.001838, allocations: 173 kB / 24.06 MB, free: 452 kB / 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 0.9302/0.9302, allocations: 177.1 MB / 204.5 MB, free: 5.512 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 0.06641/0.06641, allocations: 9.55 MB / 270.6 MB, free: 3.805 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 1.163e-06/1.163e-06, allocations: 0 / 344.1 MB, free: 7.52 MB / 314.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.85e-05/1.966e-05, allocations: 6.141 kB / 344.1 MB, free: 7.516 MB / 314.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.005988/0.006008, allocations: 6.492 MB / 350.6 MB, free: 0.9961 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.001392/0.0074, allocations: 0.8379 MB / 351.4 MB, free: 160 kB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003531/0.007753, allocations: 40 kB / 351.5 MB, free: 120 kB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002383/0.007991, allocations: 138.9 kB / 351.6 MB, free: 15.98 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.000474/0.008465, allocations: 221.7 kB / 351.8 MB, free: 15.76 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.000322/0.008787, allocations: 203.7 kB / 352 MB, free: 15.56 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0006874/0.009475, allocations: 0.8606 MB / 352.9 MB, free: 14.7 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0004132/0.009888, allocations: 355 kB / 353.2 MB, free: 14.34 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000465/0.01035, allocations: 0.5692 MB / 353.8 MB, free: 13.77 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002931/0.01065, allocations: 315 kB / 354.1 MB, free: 13.46 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 9.609e-05/0.01074, allocations: 116 kB / 354.2 MB, free: 13.34 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 9.172e-05/0.01083, allocations: 120 kB / 354.4 MB, free: 13.23 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001174/0.01095, allocations: 235.2 kB / 354.6 MB, free: 13 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002158/0.01117, allocations: 323.2 kB / 354.9 MB, free: 12.68 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0005082/0.01168, allocations: 0.6655 MB / 355.6 MB, free: 12.01 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 2.695e-06/0.01168, allocations: 4 kB / 355.6 MB, free: 12.01 MB / 330.7 MB
Notification: Performance of FrontEnd: time 9.22e-07/0.01168, allocations: 0 / 355.6 MB, free: 12.01 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 8.245e-06/0.01169, allocations: 0 / 355.6 MB, free: 12.01 MB / 330.7 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 0.00101/0.0127, allocations: 1.174 MB / 356.7 MB, free: 10.79 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.47e-05/0.01273, allocations: 12.03 kB / 356.8 MB, free: 10.78 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001473/0.01288, allocations: 180.3 kB / 356.9 MB, free: 10.6 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001599/0.01304, allocations: 246.8 kB / 357.2 MB, free: 10.33 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.105e-05/0.01308, allocations: 78.38 kB / 357.2 MB, free: 10.26 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 8.574e-05/0.01317, allocations: 96.38 kB / 357.3 MB, free: 10.16 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005551/0.01372, allocations: 0.62 MB / 358 MB, free: 9.527 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.289e-05/0.01374, allocations: 4.141 kB / 358 MB, free: 9.523 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.028e-05/0.01378, allocations: 36.38 kB / 358 MB, free: 9.488 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.518e-05/0.0138, allocations: 24.38 kB / 358 MB, free: 9.465 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003382/0.01414, allocations: 281.7 kB / 358.3 MB, free: 9.191 MB / 330.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002331/0.01647, allocations: 2.364 MB / 360.7 MB, free: 6.762 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004734/0.01694, allocations: 419.9 kB / 361.1 MB, free: 6.328 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001759/0.01712, allocations: 184.8 kB / 361.3 MB, free: 6.141 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.89e-05/0.01714, allocations: 8.5 kB / 361.3 MB, free: 6.129 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.536e-05/0.01716, allocations: 41.89 kB / 361.3 MB, free: 6.078 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=50): time 1.783e-06/0.01716, allocations: 0 / 361.3 MB, free: 6.078 MB / 330.7 MB
Notification: Performance of matching and sorting (n=59): time 0.001854/0.01902, allocations: 1.304 MB / 362.6 MB, free: 4.75 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.716e-05/0.01906, allocations: 85.61 kB / 362.7 MB, free: 4.648 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002212/0.01929, allocations: 402.2 kB / 363.1 MB, free: 4.234 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 2.498e-05/0.01931, allocations: 37.7 kB / 363.1 MB, free: 4.191 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002098/0.01952, allocations: 0.4984 MB / 363.6 MB, free: 3.684 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.000112/0.01963, allocations: 230 kB / 363.8 MB, free: 3.457 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001174/0.01975, allocations: 140.2 kB / 364 MB, free: 3.312 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.000131/0.01988, allocations: 0.5351 MB / 364.5 MB, free: 2.766 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001319/0.02001, allocations: 143.5 kB / 364.7 MB, free: 2.625 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002618/0.02027, allocations: 483 kB / 365.1 MB, free: 1.992 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005297/0.0208, allocations: 0.7596 MB / 365.9 MB, free: 1.066 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.865e-06/0.02081, allocations: 4 kB / 365.9 MB, free: 1.062 MB / 330.7 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.000526/0.02133, allocations: 0.6019 MB / 366.5 MB, free: 464 kB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.724e-05/0.02135, allocations: 8.781 kB / 366.5 MB, free: 456 kB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.158e-06/0.02136, allocations: 8.906 kB / 366.5 MB, free: 448 kB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.588e-05/0.02138, allocations: 19.94 kB / 366.5 MB, free: 428 kB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000339/0.02171, allocations: 187.7 kB / 366.7 MB, free: 240 kB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.337e-06/0.02172, allocations: 15.94 kB / 366.7 MB, free: 224 kB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001467/0.02187, allocations: 27.98 kB / 366.8 MB, free: 196 kB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.639e-05/0.0219, allocations: 32 kB / 366.8 MB, free: 164 kB / 330.7 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 0.0002496/0.02215, allocations: 260.8 kB / 367 MB, free: 15.9 MB / 346.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 7.669e-05/0.02222, allocations: 59.72 kB / 367.1 MB, free: 15.84 MB / 346.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.522e-05/0.0223, allocations: 76.84 kB / 367.2 MB, free: 15.77 MB / 346.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.449e-06/0.0223, allocations: 7.938 kB / 367.2 MB, free: 15.76 MB / 346.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.09e-06/0.02231, allocations: 4 kB / 367.2 MB, free: 15.76 MB / 346.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.958e-06/0.02231, allocations: 0 / 367.2 MB, free: 15.76 MB / 346.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005019/0.02281, allocations: 429.2 kB / 367.6 MB, free: 15.31 MB / 346.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.985e-06/0.02282, allocations: 4 kB / 367.6 MB, free: 15.31 MB / 346.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002755/0.02309, allocations: 107.9 kB / 367.7 MB, free: 15.2 MB / 346.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.147e-06/0.0231, allocations: 4 kB / 367.7 MB, free: 15.2 MB / 346.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.464e-05/0.02312, allocations: 19.92 kB / 367.7 MB, free: 15.18 MB / 346.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.745e-06/0.02312, allocations: 8 kB / 367.7 MB, free: 15.17 MB / 346.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.303e-06/0.02313, allocations: 0 / 367.7 MB, free: 15.17 MB / 346.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005477/0.02367, allocations: 0.7628 MB / 368.5 MB, free: 14.39 MB / 346.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.556e-05/0.02371, allocations: 47.67 kB / 368.6 MB, free: 14.34 MB / 346.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.782e-05/0.02375, allocations: 15.98 kB / 368.6 MB, free: 14.33 MB / 346.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001229/0.02387, allocations: 8 kB / 368.6 MB, free: 14.32 MB / 346.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.961e-05/0.02391, allocations: 40.38 kB / 368.6 MB, free: 14.28 MB / 346.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.649e-05/0.02393, allocations: 11.98 kB / 368.6 MB, free: 14.27 MB / 346.7 MB
Notification: Performance of sorting global known variables: time 0.0001178/0.02404, allocations: 239 kB / 368.9 MB, free: 14.04 MB / 346.7 MB
Notification: Performance of sort global known variables: time 5e-08/0.02404, allocations: 4 kB / 368.9 MB, free: 14.03 MB / 346.7 MB
Notification: Performance of remove unused functions: time 0.0003399/0.02438, allocations: 156 kB / 369 MB, free: 13.88 MB / 346.7 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 9.622e-05/0.02448, allocations: 111.1 kB / 369.1 MB, free: 13.76 MB / 346.7 MB
Notification: Performance of simCode: created initialization part: time 0.0003567/0.02484, allocations: 406.4 kB / 369.5 MB, free: 13.36 MB / 346.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.675e-06/0.02484, allocations: 4 kB / 369.5 MB, free: 13.35 MB / 346.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001469/0.02499, allocations: 179.3 kB / 369.7 MB, free: 13.17 MB / 346.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003143/0.0253, allocations: 70.16 kB / 369.8 MB, free: 13.11 MB / 346.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001551/0.02685, allocations: 1.565 MB / 371.3 MB, free: 11.49 MB / 346.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 9.599e-05/0.02695, allocations: 152 kB / 371.5 MB, free: 11.32 MB / 346.7 MB
Notification: Performance of simCode: alias equations: time 0.0001515/0.0271, allocations: 64.58 kB / 371.5 MB, free: 11.26 MB / 346.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001843/0.02728, allocations: 162.2 kB / 371.7 MB, free: 11.1 MB / 346.7 MB
Notification: Performance of SimCode: time 4.91e-07/0.02728, allocations: 0 / 371.7 MB, free: 11.1 MB / 346.7 MB
Notification: Performance of Templates: time 0.007848/0.03513, allocations: 5.954 MB / 377.7 MB, free: 5.246 MB / 346.7 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: 2.988963124807924]