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) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001425/0.001425, allocations: 113.9 kB / 17.61 MB, free: 4.684 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001407/0.001407, allocations: 185.9 kB / 20.78 MB, free: 1.52 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.445/1.445, allocations: 225.6 MB / 249.4 MB, free: 3.16 MB / 190.1 MB
"
[Timeout remaining time 178]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06858/0.06858, allocations: 12.42 MB / 316.9 MB, free: 15.88 MB / 254.1 MB
"
[Timeout remaining time 180]
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: translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container")
translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container") [Timeout 660]
"Warning: Ignoring unknown experiment annotation option: Algorithm = \"dassl\"
Notification: Performance of FrontEnd - loaded program: time 0.002034/0.002034, allocations: 71.81 kB / 442.9 MB, free: 3.883 MB / 366.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3132/0.3152, allocations: 54.91 MB / 497.8 MB, free: 23.7 MB / 366.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01077/0.326, allocations: 8.554 MB / 0.4945 GB, free: 17.93 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001891/0.3279, allocations: 0.8127 MB / 0.4953 GB, free: 17.22 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003665/0.3283, allocations: 45.53 kB / 0.4953 GB, free: 17.21 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002973/0.3286, allocations: 147.8 kB / 0.4955 GB, free: 17.08 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004706/0.329, allocations: 210 kB / 0.4957 GB, free: 16.9 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003674/0.3294, allocations: 189.1 kB / 0.4959 GB, free: 16.73 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0007212/0.3301, allocations: 0.8436 MB / 0.4967 GB, free: 16.2 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005724/0.3307, allocations: 380.3 kB / 0.497 GB, free: 15.92 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003079/0.331, allocations: 369.9 kB / 0.4974 GB, free: 15.68 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003724/0.3314, allocations: 430.2 kB / 0.4978 GB, free: 15.35 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.000156/0.3315, allocations: 114.9 kB / 0.4979 GB, free: 15.35 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001695/0.3317, allocations: 116.9 kB / 0.498 GB, free: 15.35 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001338/0.3318, allocations: 230.6 kB / 0.4982 GB, free: 15.15 MB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003325/0.3322, allocations: 478.7 kB / 0.4987 GB, free: 14.8 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0009781/0.3332, allocations: 1.178 MB / 0.4999 GB, free: 13.87 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.591e-06/0.3332, allocations: 1.219 kB / 0.4999 GB, free: 13.87 MB / 366.1 MB
Notification: Performance of FrontEnd: time 1.853e-06/0.3332, allocations: 0 / 0.4999 GB, free: 13.87 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 1.841e-05/0.3332, allocations: 0 / 0.4999 GB, free: 13.87 MB / 366.1 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 0.001544/0.3347, allocations: 1.144 MB / 0.501 GB, free: 12.97 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.02e-05/0.3348, allocations: 9.75 kB / 0.501 GB, free: 12.97 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001456/0.3349, allocations: 100.5 kB / 0.5011 GB, free: 12.92 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002547/0.3352, allocations: 309.4 kB / 0.5014 GB, free: 12.61 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.748e-05/0.3352, allocations: 74.53 kB / 0.5014 GB, free: 12.58 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001257/0.3354, allocations: 105.3 kB / 0.5015 GB, free: 12.54 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001184/0.3365, allocations: 0.8693 MB / 0.5024 GB, free: 12.04 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.103e-05/0.3366, allocations: 1.344 kB / 0.5024 GB, free: 12.04 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.252e-05/0.3366, allocations: 44.91 kB / 0.5024 GB, free: 12 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.342e-05/0.3367, allocations: 27.59 kB / 0.5025 GB, free: 12 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009788/0.3376, allocations: 0.6265 MB / 0.5031 GB, free: 11.7 MB / 366.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.00386/0.3415, allocations: 2.84 MB / 0.5058 GB, free: 9.578 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0009669/0.3425, allocations: 0.4997 MB / 0.5063 GB, free: 9.301 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.000366/0.3428, allocations: 275.4 kB / 0.5066 GB, free: 9.172 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.125e-05/0.3429, allocations: 5.062 kB / 0.5066 GB, free: 9.172 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.904e-05/0.3429, allocations: 41.88 kB / 0.5066 GB, free: 9.121 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=50): time 2.084e-06/0.3429, allocations: 0 / 0.5066 GB, free: 9.121 MB / 366.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004701/0.3476, allocations: 2.185 MB / 0.5088 GB, free: 7.699 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.752e-05/0.3476, allocations: 85.67 kB / 0.5089 GB, free: 7.598 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002759/0.3479, allocations: 357.5 kB / 0.5092 GB, free: 7.242 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.582e-05/0.3479, allocations: 37.7 kB / 0.5092 GB, free: 7.199 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001492/0.3481, allocations: 467.6 kB / 0.5097 GB, free: 6.734 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 9.148e-05/0.3482, allocations: 234 kB / 0.5099 GB, free: 6.504 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001426/0.3483, allocations: 138.6 kB / 0.51 GB, free: 6.359 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 6.762e-05/0.3484, allocations: 362.8 kB / 0.5104 GB, free: 5.996 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002967/0.3487, allocations: 248.8 kB / 0.5106 GB, free: 5.754 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003549/0.349, allocations: 484.9 kB / 0.5111 GB, free: 5.16 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.00503/0.3541, allocations: 1.692 MB / 0.5127 GB, free: 3.352 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.38e-06/0.3541, allocations: 4 kB / 0.5127 GB, free: 3.348 MB / 366.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001001/0.3551, allocations: 0.8073 MB / 0.5135 GB, free: 2.531 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.539e-05/0.3551, allocations: 8 kB / 0.5135 GB, free: 2.523 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.587e-05/0.3551, allocations: 12 kB / 0.5135 GB, free: 2.512 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 3.371e-05/0.3551, allocations: 12 kB / 0.5136 GB, free: 2.5 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006132/0.3558, allocations: 179.7 kB / 0.5137 GB, free: 2.324 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.015e-05/0.3558, allocations: 23.86 kB / 0.5137 GB, free: 2.301 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003583/0.3561, allocations: 28 kB / 0.5138 GB, free: 2.273 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.195e-05/0.3562, allocations: 32 kB / 0.5138 GB, free: 2.242 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 0.0005837/0.3568, allocations: 294.3 kB / 0.5141 GB, free: 1.949 MB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.784e-05/0.3568, allocations: 55.66 kB / 0.5141 GB, free: 1.895 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001301/0.357, allocations: 68.91 kB / 0.5142 GB, free: 1.824 MB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.751e-06/0.357, allocations: 8 kB / 0.5142 GB, free: 1.816 MB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.657e-06/0.357, allocations: 4 kB / 0.5142 GB, free: 1.812 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.643e-06/0.357, allocations: 3.984 kB / 0.5142 GB, free: 1.809 MB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0009612/0.358, allocations: 0.7593 MB / 0.515 GB, free: 1 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.725e-06/0.358, allocations: 0 / 0.515 GB, free: 1 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005129/0.3585, allocations: 103.9 kB / 0.5151 GB, free: 0.8984 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 5.721e-06/0.3585, allocations: 4 kB / 0.5151 GB, free: 0.8945 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.043e-05/0.3585, allocations: 19.98 kB / 0.5151 GB, free: 0.875 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.227e-06/0.3585, allocations: 4 kB / 0.5151 GB, free: 0.8711 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.705e-06/0.3585, allocations: 3.938 kB / 0.5151 GB, free: 0.8672 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001037/0.3596, allocations: 0.9363 MB / 0.516 GB, free: 15.91 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001312/0.3597, allocations: 120.8 kB / 0.5161 GB, free: 15.77 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.746e-05/0.3598, allocations: 16 kB / 0.5161 GB, free: 15.75 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002645/0.36, allocations: 12 kB / 0.5161 GB, free: 15.74 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.648e-05/0.3601, allocations: 36.5 kB / 0.5162 GB, free: 15.71 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.461e-05/0.3601, allocations: 12 kB / 0.5162 GB, free: 15.7 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0003755/0.3605, allocations: 239.2 kB / 0.5164 GB, free: 15.46 MB / 382.1 MB
Notification: Performance of sort global known variables: time 1.1e-07/0.3605, allocations: 4 kB / 0.5164 GB, free: 15.46 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.0007185/0.3612, allocations: 160 kB / 0.5166 GB, free: 15.3 MB / 382.1 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 0.0001455/0.3614, allocations: 111.7 kB / 0.5167 GB, free: 15.18 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.001037/0.3624, allocations: 0.5515 MB / 0.5172 GB, free: 14.63 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.106e-06/0.3624, allocations: 0 / 0.5172 GB, free: 14.63 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003527/0.3628, allocations: 247.1 kB / 0.5175 GB, free: 14.39 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005096/0.3633, allocations: 70.3 kB / 0.5175 GB, free: 14.32 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003658/0.3669, allocations: 1.82 MB / 0.5193 GB, free: 12.46 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0006574/0.3676, allocations: 0.935 MB / 0.5202 GB, free: 11.51 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.0002852/0.3679, allocations: 68.58 kB / 0.5203 GB, free: 11.44 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001488/0.368, allocations: 47.36 kB / 0.5203 GB, free: 11.39 MB / 382.1 MB
Notification: Performance of SimCode: time 1.273e-06/0.368, allocations: 0 / 0.5203 GB, free: 11.39 MB / 382.1 MB
Notification: Performance of Templates: time 0.01259/0.3806, allocations: 5.809 MB / 0.526 GB, free: 5.625 MB / 382.1 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=480 -lv LOG_STATS > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 4.892732511274517]