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 0.001556/0.001556, allocations: 80.94 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 0.001205/0.001205, allocations: 181 kB / 23.36 MB, free: 1.129 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 1.031/1.031, allocations: 177.1 MB / 203.8 MB, free: 5.492 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 0.05552/0.05552, allocations: 9.557 MB / 269.8 MB, free: 3.836 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 1.382e-06/1.382e-06, allocations: 0 / 290.1 MB, free: 17.22 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.176e-05/1.314e-05, allocations: 2.312 kB / 290.1 MB, free: 17.21 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.007009/0.007022, allocations: 6.553 MB / 296.7 MB, free: 14.64 MB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.001595/0.008616, allocations: 0.8683 MB / 297.6 MB, free: 14.23 MB / 266.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003702/0.008987, allocations: 40.44 kB / 297.6 MB, free: 14.23 MB / 266.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002756/0.009262, allocations: 148.8 kB / 297.7 MB, free: 14.11 MB / 266.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004458/0.009708, allocations: 217.2 kB / 297.9 MB, free: 13.95 MB / 266.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003497/0.01006, allocations: 196.1 kB / 298.1 MB, free: 13.83 MB / 266.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0006669/0.01072, allocations: 0.8688 MB / 299 MB, free: 13.35 MB / 266.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0004303/0.01115, allocations: 372.1 kB / 299.4 MB, free: 13.12 MB / 266.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000555/0.01171, allocations: 0.5745 MB / 299.9 MB, free: 12.83 MB / 266.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003848/0.01209, allocations: 317.8 kB / 300.3 MB, free: 12.71 MB / 266.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001502/0.01224, allocations: 117.1 kB / 300.4 MB, free: 12.71 MB / 266.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001302/0.01238, allocations: 116.6 kB / 300.5 MB, free: 12.71 MB / 266.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001033/0.01248, allocations: 237.9 kB / 300.7 MB, free: 12.54 MB / 266.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003067/0.01279, allocations: 328.9 kB / 301 MB, free: 12.37 MB / 266.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0006107/0.0134, allocations: 0.6541 MB / 301.7 MB, free: 12 MB / 266.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.267e-06/0.0134, allocations: 1.25 kB / 301.7 MB, free: 12 MB / 266.7 MB
Notification: Performance of FrontEnd: time 1.272e-06/0.0134, allocations: 0 / 301.7 MB, free: 12 MB / 266.7 MB
Notification: Performance of Transformations before backend: time 2.385e-05/0.01342, allocations: 0 / 301.7 MB, free: 12 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 0.001087/0.01451, allocations: 1.055 MB / 302.7 MB, free: 11.32 MB / 266.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.262e-05/0.01454, allocations: 8.75 kB / 302.8 MB, free: 11.32 MB / 266.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001503/0.01469, allocations: 145.6 kB / 302.9 MB, free: 11.29 MB / 266.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001643/0.01486, allocations: 240.6 kB / 303.1 MB, free: 11.07 MB / 266.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.762e-05/0.01491, allocations: 79.11 kB / 303.2 MB, free: 11.04 MB / 266.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 9.157e-05/0.015, allocations: 102 kB / 303.3 MB, free: 11 MB / 266.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0006078/0.01561, allocations: 0.6287 MB / 303.9 MB, free: 10.73 MB / 266.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.459e-05/0.01563, allocations: 192 / 303.9 MB, free: 10.73 MB / 266.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.686e-05/0.01567, allocations: 41.94 kB / 304 MB, free: 10.7 MB / 266.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.911e-05/0.01569, allocations: 25.28 kB / 304 MB, free: 10.7 MB / 266.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003353/0.01602, allocations: 235.3 kB / 304.2 MB, free: 10.65 MB / 266.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002434/0.01846, allocations: 1.936 MB / 306.2 MB, free: 9.422 MB / 266.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004608/0.01892, allocations: 386.4 kB / 306.5 MB, free: 9.266 MB / 266.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001697/0.01909, allocations: 175.8 kB / 306.7 MB, free: 9.203 MB / 266.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.33e-05/0.01911, allocations: 13.38 kB / 306.7 MB, free: 9.199 MB / 266.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.193e-05/0.01913, allocations: 40.23 kB / 306.8 MB, free: 9.156 MB / 266.7 MB
Notification: Performance of pre-optimization done (n=50): time 2.344e-06/0.01913, allocations: 0 / 306.8 MB, free: 9.156 MB / 266.7 MB
Notification: Performance of matching and sorting (n=59): time 0.001703/0.02084, allocations: 1.238 MB / 308 MB, free: 8.504 MB / 266.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.203e-05/0.02086, allocations: 89.55 kB / 308.1 MB, free: 8.398 MB / 266.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000145/0.021, allocations: 348.3 kB / 308.4 MB, free: 8.043 MB / 266.7 MB
Notification: Performance of collectPreVariables (initialization): time 1.844e-05/0.02102, allocations: 37.7 kB / 308.5 MB, free: 8 MB / 266.7 MB
Notification: Performance of collectInitialEqns (initialization): time 9.256e-05/0.02111, allocations: 436.2 kB / 308.9 MB, free: 7.566 MB / 266.7 MB
Notification: Performance of collectInitialBindings (initialization): time 7.795e-05/0.02119, allocations: 230 kB / 309.1 MB, free: 7.34 MB / 266.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.553e-05/0.02129, allocations: 143.2 kB / 309.3 MB, free: 7.195 MB / 266.7 MB
Notification: Performance of setup shared object (initialization): time 5.099e-05/0.02134, allocations: 362.7 kB / 309.6 MB, free: 6.832 MB / 266.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 9.255e-05/0.02143, allocations: 125.2 kB / 309.7 MB, free: 6.711 MB / 266.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001463/0.02158, allocations: 365.4 kB / 310.1 MB, free: 6.238 MB / 266.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003921/0.02197, allocations: 0.6295 MB / 310.7 MB, free: 5.496 MB / 266.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.727e-06/0.02197, allocations: 4 kB / 310.7 MB, free: 5.492 MB / 266.7 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0003777/0.02235, allocations: 487.9 kB / 311.2 MB, free: 5.016 MB / 266.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.59e-05/0.02237, allocations: 12 kB / 311.2 MB, free: 5.004 MB / 266.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.558e-06/0.02238, allocations: 8 kB / 311.2 MB, free: 4.996 MB / 266.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.99e-05/0.0224, allocations: 13.31 kB / 311.2 MB, free: 4.984 MB / 266.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003585/0.02276, allocations: 199.6 kB / 311.4 MB, free: 4.789 MB / 266.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.498e-06/0.02276, allocations: 23.98 kB / 311.5 MB, free: 4.766 MB / 266.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001487/0.02291, allocations: 31.94 kB / 311.5 MB, free: 4.734 MB / 266.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.165e-05/0.02294, allocations: 27.94 kB / 311.5 MB, free: 4.707 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 0.0002029/0.02314, allocations: 206.1 kB / 311.7 MB, free: 4.504 MB / 266.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 5.889e-05/0.0232, allocations: 55.91 kB / 311.8 MB, free: 4.449 MB / 266.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.916e-05/0.02326, allocations: 72.89 kB / 311.8 MB, free: 4.375 MB / 266.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.378e-06/0.02326, allocations: 8 kB / 311.9 MB, free: 4.367 MB / 266.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.218e-06/0.02326, allocations: 3.938 kB / 311.9 MB, free: 4.363 MB / 266.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.4e-06/0.02327, allocations: 0 / 311.9 MB, free: 4.363 MB / 266.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004301/0.0237, allocations: 382 kB / 312.2 MB, free: 3.973 MB / 266.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.946e-06/0.0237, allocations: 4 kB / 312.2 MB, free: 3.969 MB / 266.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002825/0.02399, allocations: 119.8 kB / 312.4 MB, free: 3.852 MB / 266.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.236e-06/0.02399, allocations: 0 / 312.4 MB, free: 3.852 MB / 266.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.213e-05/0.02401, allocations: 23.98 kB / 312.4 MB, free: 3.828 MB / 266.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.855e-06/0.02401, allocations: 4 kB / 312.4 MB, free: 3.824 MB / 266.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.613e-06/0.02402, allocations: 0 / 312.4 MB, free: 3.824 MB / 266.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003778/0.02439, allocations: 0.5801 MB / 313 MB, free: 3.227 MB / 266.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.303e-05/0.02443, allocations: 39.72 kB / 313 MB, free: 3.188 MB / 266.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.494e-05/0.02446, allocations: 16 kB / 313 MB, free: 3.172 MB / 266.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001194/0.02458, allocations: 4 kB / 313 MB, free: 3.168 MB / 266.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.132e-05/0.02462, allocations: 40.36 kB / 313.1 MB, free: 3.125 MB / 266.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.66e-05/0.02464, allocations: 23.92 kB / 313.1 MB, free: 3.102 MB / 266.7 MB
Notification: Performance of sorting global known variables: time 7.257e-05/0.02471, allocations: 128.7 kB / 313.2 MB, free: 2.973 MB / 266.7 MB
Notification: Performance of sort global known variables: time 5e-08/0.02471, allocations: 4 kB / 313.2 MB, free: 2.969 MB / 266.7 MB
Notification: Performance of remove unused functions: time 0.000342/0.02505, allocations: 156 kB / 313.4 MB, free: 2.816 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 8.767e-05/0.02514, allocations: 88.36 kB / 313.4 MB, free: 2.723 MB / 266.7 MB
Notification: Performance of simCode: created initialization part: time 0.0003087/0.02545, allocations: 375.5 kB / 313.8 MB, free: 2.359 MB / 266.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.51e-05/0.02546, allocations: 5.25 kB / 313.8 MB, free: 2.355 MB / 266.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001151/0.02558, allocations: 160.6 kB / 314 MB, free: 2.191 MB / 266.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002872/0.02587, allocations: 78.84 kB / 314.1 MB, free: 2.121 MB / 266.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001382/0.02725, allocations: 1.376 MB / 315.4 MB, free: 0.7148 MB / 266.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 7.965e-05/0.02733, allocations: 160 kB / 315.6 MB, free: 0.5391 MB / 266.7 MB
Notification: Performance of simCode: alias equations: time 0.0001625/0.02749, allocations: 69.66 kB / 315.7 MB, free: 484 kB / 266.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001736/0.02766, allocations: 143.3 kB / 315.8 MB, free: 340 kB / 266.7 MB
Notification: Performance of SimCode: time 1.392e-06/0.02767, allocations: 0 / 315.8 MB, free: 340 kB / 266.7 MB
Notification: Performance of Templates: time 0.009933/0.0376, allocations: 5.799 MB / 321.6 MB, free: 10.67 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 -s gbode -gbm=radauIIA3 -lv LOG_STATS > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 2.8649987829849124]