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 0.001085/0.001085, allocations: 110.7 kB / 16.42 MB, free: 6.465 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001108/0.001108, allocations: 190.7 kB / 17.35 MB, free: 5.715 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.302/1.302, allocations: 222.9 MB / 241 MB, free: 15.1 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.0635/0.0635, allocations: 12.27 MB / 303.5 MB, free: 3.211 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001243/0.001243, allocations: 63.16 kB / 420.7 MB, free: 17 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.07518/0.07643, allocations: 52.07 MB / 472.8 MB, free: 12.93 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01136/0.08782, allocations: 8.486 MB / 481.3 MB, free: 4.414 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001485/0.08933, allocations: 0.8068 MB / 482.1 MB, free: 3.605 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0004767/0.08982, allocations: 44 kB / 482.1 MB, free: 3.562 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.000377/0.09021, allocations: 146.8 kB / 482.3 MB, free: 3.418 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0005572/0.09079, allocations: 206 kB / 482.5 MB, free: 3.215 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.000392/0.09119, allocations: 191.8 kB / 482.7 MB, free: 3.027 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.000736/0.09194, allocations: 0.8415 MB / 483.5 MB, free: 2.184 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006892/0.09263, allocations: 0.5453 MB / 484.1 MB, free: 1.613 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002891/0.09293, allocations: 362.7 kB / 484.4 MB, free: 1.258 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003956/0.09334, allocations: 434 kB / 484.8 MB, free: 0.832 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001224/0.09347, allocations: 116 kB / 484.9 MB, free: 0.7188 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001358/0.09361, allocations: 116 kB / 485.1 MB, free: 0.6055 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001539/0.09377, allocations: 223.3 kB / 485.3 MB, free: 396 kB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003734/0.09415, allocations: 485.8 kB / 485.8 MB, free: 15.91 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0009404/0.0951, allocations: 1.168 MB / 486.9 MB, free: 14.74 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.099e-06/0.09511, allocations: 4 kB / 486.9 MB, free: 14.73 MB / 366.1 MB
Notification: Performance of FrontEnd: time 1.222e-06/0.09512, allocations: 4 kB / 486.9 MB, free: 14.73 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 9.858e-06/0.09513, allocations: 0 / 486.9 MB, free: 14.73 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 0.001543/0.09668, allocations: 1.127 MB / 488.1 MB, free: 13.55 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.383e-05/0.09672, allocations: 8.031 kB / 488.1 MB, free: 13.54 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001307/0.09686, allocations: 95.81 kB / 488.2 MB, free: 13.45 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002613/0.09713, allocations: 306.8 kB / 488.5 MB, free: 13.11 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.157e-05/0.09719, allocations: 74.38 kB / 488.5 MB, free: 13.04 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001292/0.09732, allocations: 100.4 kB / 488.6 MB, free: 12.94 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001286/0.09862, allocations: 0.8725 MB / 489.5 MB, free: 12.05 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.06e-05/0.09866, allocations: 8.094 kB / 489.5 MB, free: 12.05 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.213e-05/0.09873, allocations: 43.94 kB / 489.5 MB, free: 12 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.802e-05/0.09876, allocations: 24 kB / 489.6 MB, free: 11.98 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001052/0.09982, allocations: 0.6247 MB / 490.2 MB, free: 11.35 MB / 366.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004051/0.1039, allocations: 2.827 MB / 493 MB, free: 8.441 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0009811/0.1049, allocations: 0.521 MB / 493.5 MB, free: 7.906 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004073/0.1053, allocations: 319 kB / 493.9 MB, free: 7.59 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.391e-05/0.1053, allocations: 4.438 kB / 493.9 MB, free: 7.586 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.342e-05/0.1054, allocations: 43 kB / 493.9 MB, free: 7.531 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.763e-06/0.1054, allocations: 0 / 493.9 MB, free: 7.531 MB / 366.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004966/0.1103, allocations: 2.169 MB / 496.1 MB, free: 5.316 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.201e-05/0.1104, allocations: 85.67 kB / 496.2 MB, free: 5.215 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003368/0.1107, allocations: 357.5 kB / 496.5 MB, free: 4.859 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.448e-05/0.1108, allocations: 33.7 kB / 496.5 MB, free: 4.82 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002434/0.111, allocations: 458.1 kB / 497 MB, free: 4.363 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001475/0.1112, allocations: 220.8 kB / 497.2 MB, free: 4.145 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001815/0.1114, allocations: 138.6 kB / 497.3 MB, free: 4 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001256/0.1115, allocations: 358.8 kB / 497.7 MB, free: 3.641 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003666/0.1119, allocations: 244.8 kB / 497.9 MB, free: 3.402 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004713/0.1124, allocations: 484.9 kB / 498.4 MB, free: 2.809 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005889/0.1183, allocations: 1.707 MB / 0.4884 GB, free: 0.9805 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.181e-06/0.1183, allocations: 4 kB / 0.4884 GB, free: 0.9766 MB / 366.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001179/0.1195, allocations: 0.803 MB / 0.4892 GB, free: 168 kB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.815e-05/0.1195, allocations: 8 kB / 0.4892 GB, free: 160 kB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.119e-05/0.1195, allocations: 8 kB / 0.4892 GB, free: 152 kB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.46e-05/0.1195, allocations: 12 kB / 0.4892 GB, free: 140 kB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007062/0.1203, allocations: 183.7 kB / 0.4894 GB, free: 15.96 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.316e-05/0.1203, allocations: 24.45 kB / 0.4894 GB, free: 15.93 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000316/0.1206, allocations: 24 kB / 0.4894 GB, free: 15.91 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.443e-05/0.1207, allocations: 40 kB / 0.4895 GB, free: 15.87 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 0.0004294/0.1211, allocations: 282.3 kB / 0.4897 GB, free: 15.59 MB / 382.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.957e-05/0.1212, allocations: 51.36 kB / 0.4898 GB, free: 15.54 MB / 382.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001321/0.1214, allocations: 72.91 kB / 0.4898 GB, free: 15.46 MB / 382.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.514e-06/0.1214, allocations: 3.984 kB / 0.4899 GB, free: 15.46 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.803e-06/0.1214, allocations: 0 / 0.4899 GB, free: 15.46 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 8.136e-05/0.1215, allocations: 120.5 kB / 0.49 GB, free: 15.32 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.138e-05/0.1215, allocations: 12 kB / 0.49 GB, free: 15.31 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002892/0.1218, allocations: 12 kB / 0.49 GB, free: 15.3 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.45e-05/0.1219, allocations: 40.44 kB / 0.49 GB, free: 15.26 MB / 382.1 MB
Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.001233/0.1231, allocations: 0.7088 MB / 0.4907 GB, free: 14.55 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.00121/0.1244, allocations: 0.9901 MB / 0.4917 GB, free: 13.54 MB / 382.1 MB
Notification: Performance of postOpt setEvaluationStage (simulation): time 0.0003218/0.1247, allocations: 232.4 kB / 0.4919 GB, free: 13.31 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0002237/0.1249, allocations: 243.1 kB / 0.4921 GB, free: 13.07 MB / 382.1 MB
Notification: Performance of Backend: time 5.51e-07/0.1249, allocations: 4.031 kB / 0.4921 GB, free: 13.07 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.0009696/0.1259, allocations: 0.4936 MB / 0.4926 GB, free: 12.57 MB / 382.1 MB
Notification: Performance of SimCode: time 0.002275/0.1282, allocations: 2.01 MB / 0.4946 GB, free: 10.5 MB / 382.1 MB
Notification: Performance of Templates: time 0.01058/0.1388, allocations: 6.06 MB / 0.5005 GB, free: 4.449 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)