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: translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container")
translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001245/0.001245, allocations: 105.5 kB / 16.41 MB, free: 6.461 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001247/0.001247, allocations: 187 kB / 17.34 MB, free: 5.719 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.431/1.431, allocations: 222.9 MB / 241 MB, free: 15.09 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06268/0.06268, allocations: 12.27 MB / 303.5 MB, free: 3.223 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.00121/0.00121, allocations: 60.25 kB / 420.7 MB, free: 17.01 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09537/0.09659, allocations: 52.08 MB / 472.8 MB, free: 12.94 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01075/0.1074, allocations: 8.482 MB / 481.3 MB, free: 4.422 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001602/0.109, allocations: 0.8107 MB / 482.1 MB, free: 3.609 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003431/0.1094, allocations: 40 kB / 482.1 MB, free: 3.57 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002969/0.1097, allocations: 146.8 kB / 482.3 MB, free: 3.426 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.000442/0.1102, allocations: 210 kB / 482.5 MB, free: 3.219 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003733/0.1105, allocations: 191.8 kB / 482.7 MB, free: 3.031 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0007126/0.1113, allocations: 0.8415 MB / 483.5 MB, free: 2.188 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006948/0.112, allocations: 0.5336 MB / 484 MB, free: 1.629 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003155/0.1123, allocations: 366.7 kB / 484.4 MB, free: 1.27 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003849/0.1127, allocations: 434 kB / 484.8 MB, free: 0.8438 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001244/0.1128, allocations: 116 kB / 484.9 MB, free: 0.7305 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.000121/0.1129, allocations: 116 kB / 485.1 MB, free: 0.6172 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001486/0.1131, allocations: 227.3 kB / 485.3 MB, free: 404 kB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003596/0.1135, allocations: 481.7 kB / 485.7 MB, free: 15.92 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0009459/0.1144, allocations: 1.172 MB / 486.9 MB, free: 14.75 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 3.978e-06/0.1144, allocations: 0 / 486.9 MB, free: 14.75 MB / 366.1 MB
Notification: Performance of FrontEnd: time 1.523e-06/0.1144, allocations: 4 kB / 486.9 MB, free: 14.74 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 1.314e-05/0.1145, allocations: 0 / 486.9 MB, free: 14.74 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 0.001545/0.116, allocations: 1.131 MB / 488 MB, free: 13.56 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.728e-05/0.1161, allocations: 8.031 kB / 488.1 MB, free: 13.55 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001334/0.1162, allocations: 95.81 kB / 488.2 MB, free: 13.46 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002611/0.1165, allocations: 306.8 kB / 488.5 MB, free: 13.12 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.223e-05/0.1165, allocations: 74.38 kB / 488.5 MB, free: 13.04 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001174/0.1167, allocations: 100.4 kB / 488.6 MB, free: 12.95 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001235/0.1179, allocations: 0.8725 MB / 489.5 MB, free: 12.06 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.923e-05/0.1179, allocations: 12.09 kB / 489.5 MB, free: 12.05 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.066e-05/0.118, allocations: 43.92 kB / 489.5 MB, free: 12.01 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.396e-05/0.118, allocations: 24 kB / 489.6 MB, free: 11.98 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009685/0.119, allocations: 0.6286 MB / 490.2 MB, free: 11.35 MB / 366.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.00413/0.1232, allocations: 2.819 MB / 493 MB, free: 8.449 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0009374/0.1241, allocations: 0.5221 MB / 493.5 MB, free: 7.91 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.000472/0.1246, allocations: 315 kB / 493.8 MB, free: 7.598 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.088e-05/0.1246, allocations: 4.438 kB / 493.9 MB, free: 7.594 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.139e-05/0.1247, allocations: 43 kB / 493.9 MB, free: 7.539 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.974e-06/0.1247, allocations: 0 / 493.9 MB, free: 7.539 MB / 366.1 MB
Notification: Performance of matching and sorting (n=59): time 0.00507/0.1298, allocations: 2.172 MB / 496.1 MB, free: 5.324 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.613e-05/0.1298, allocations: 81.67 kB / 496.1 MB, free: 5.227 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.00046/0.1303, allocations: 357.5 kB / 496.5 MB, free: 4.871 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.664e-05/0.1304, allocations: 33.7 kB / 496.5 MB, free: 4.832 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002697/0.1306, allocations: 454.1 kB / 497 MB, free: 4.379 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001618/0.1308, allocations: 228.8 kB / 497.2 MB, free: 4.152 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001775/0.131, allocations: 134.6 kB / 497.3 MB, free: 4.012 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.000209/0.1312, allocations: 358.8 kB / 497.7 MB, free: 3.652 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003882/0.1316, allocations: 248.8 kB / 497.9 MB, free: 3.41 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005345/0.1321, allocations: 484.9 kB / 498.4 MB, free: 2.816 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005748/0.1379, allocations: 1.704 MB / 0.4884 GB, free: 0.9922 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.045e-06/0.1379, allocations: 4 kB / 0.4884 GB, free: 0.9883 MB / 366.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001159/0.1391, allocations: 0.8069 MB / 0.4892 GB, free: 176 kB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.566e-05/0.1391, allocations: 11.12 kB / 0.4892 GB, free: 168 kB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.316e-05/0.1392, allocations: 8 kB / 0.4892 GB, free: 160 kB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.686e-05/0.1392, allocations: 12 kB / 0.4892 GB, free: 148 kB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000728/0.1399, allocations: 183.7 kB / 0.4894 GB, free: 15.96 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.555e-05/0.14, allocations: 23.92 kB / 0.4894 GB, free: 15.94 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003161/0.1403, allocations: 24.47 kB / 0.4894 GB, free: 15.92 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.249e-05/0.1403, allocations: 40 kB / 0.4895 GB, free: 15.88 MB / 382.1 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 0.0005163/0.1409, allocations: 287.4 kB / 0.4897 GB, free: 15.59 MB / 382.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001012/0.141, allocations: 51.42 kB / 0.4898 GB, free: 15.54 MB / 382.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001483/0.1411, allocations: 72.91 kB / 0.4899 GB, free: 15.47 MB / 382.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.144e-06/0.1411, allocations: 8 kB / 0.4899 GB, free: 15.46 MB / 382.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.196e-06/0.1411, allocations: 0 / 0.4899 GB, free: 15.46 MB / 382.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.765e-06/0.1412, allocations: 3.984 kB / 0.4899 GB, free: 15.46 MB / 382.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001044/0.1422, allocations: 0.7593 MB / 0.4906 GB, free: 14.65 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.729e-06/0.1422, allocations: 0 / 0.4906 GB, free: 14.65 MB / 382.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005443/0.1428, allocations: 111.8 kB / 0.4907 GB, free: 14.54 MB / 382.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 6.062e-06/0.1428, allocations: 4 kB / 0.4907 GB, free: 14.54 MB / 382.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 9.718e-05/0.1429, allocations: 19.98 kB / 0.4907 GB, free: 14.52 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.481e-06/0.1429, allocations: 4 kB / 0.4907 GB, free: 14.51 MB / 382.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.382e-06/0.1429, allocations: 0 / 0.4907 GB, free: 14.51 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001211/0.1441, allocations: 0.9322 MB / 0.4916 GB, free: 13.56 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 9.054e-05/0.1442, allocations: 116.5 kB / 0.4918 GB, free: 13.43 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.781e-05/0.1443, allocations: 16 kB / 0.4918 GB, free: 13.41 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002653/0.1446, allocations: 8 kB / 0.4918 GB, free: 13.4 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.213e-05/0.1446, allocations: 40.5 kB / 0.4918 GB, free: 13.36 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.154e-05/0.1447, allocations: 12 kB / 0.4918 GB, free: 13.35 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0002432/0.1449, allocations: 239.2 kB / 0.4921 GB, free: 13.12 MB / 382.1 MB
Notification: Performance of sort global known variables: time 1.5e-07/0.1449, allocations: 3.938 kB / 0.4921 GB, free: 13.12 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.0005967/0.1455, allocations: 160 kB / 0.4922 GB, free: 12.96 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 0.0001351/0.1457, allocations: 111.7 kB / 0.4923 GB, free: 12.84 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.0008791/0.1466, allocations: 0.5939 MB / 0.4929 GB, free: 12.25 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.897e-06/0.1466, allocations: 4 kB / 0.4929 GB, free: 12.25 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003311/0.1469, allocations: 263 kB / 0.4932 GB, free: 11.99 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005122/0.1474, allocations: 74.91 kB / 0.4932 GB, free: 11.92 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002988/0.1504, allocations: 1.808 MB / 0.495 GB, free: 10.07 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005332/0.151, allocations: 0.9389 MB / 0.4959 GB, free: 9.105 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001686/0.1512, allocations: 51.42 kB / 0.496 GB, free: 9.055 MB / 382.1 MB
Notification: Performance of SimCode: time 2e-07/0.1512, allocations: 0 / 0.496 GB, free: 9.055 MB / 382.1 MB
Notification: Performance of Templates: time 0.009889/0.1611, allocations: 7.501 MB / 0.5033 GB, free: 1.551 MB / 382.1 MB
make -j1 -f BioChem_BioChem.Examples.CircadianOscillator.Container.makefile
(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)