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 0.00111/0.00111, allocations: 110.8 kB / 16.42 MB, free: 6.449 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001122/0.001122, allocations: 187.9 kB / 17.35 MB, free: 5.699 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 / 241.1 MB, free: 15.05 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06349/0.06349, allocations: 12.27 MB / 303.5 MB, free: 3.195 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001334/0.001334, allocations: 68.75 kB / 420.7 MB, free: 16.99 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.08211/0.08345, allocations: 52.07 MB / 472.8 MB, free: 12.93 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01192/0.09541, allocations: 8.49 MB / 481.3 MB, free: 4.406 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001582/0.09703, allocations: 0.8146 MB / 482.1 MB, free: 3.59 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0005332/0.09761, allocations: 40 kB / 482.1 MB, free: 3.551 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0004543/0.09808, allocations: 146.8 kB / 482.3 MB, free: 3.406 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0007649/0.09885, allocations: 210 kB / 482.5 MB, free: 3.199 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0004639/0.09933, allocations: 191.8 kB / 482.7 MB, free: 3.012 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0008872/0.1002, allocations: 0.8415 MB / 483.5 MB, free: 2.168 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0007405/0.101, allocations: 0.5336 MB / 484.1 MB, free: 1.609 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003561/0.1013, allocations: 370.7 kB / 484.4 MB, free: 1.246 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0004155/0.1018, allocations: 434 kB / 484.8 MB, free: 0.8203 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001342/0.1019, allocations: 116 kB / 485 MB, free: 0.707 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001393/0.1021, allocations: 116 kB / 485.1 MB, free: 0.5938 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001553/0.1022, allocations: 219.3 kB / 485.3 MB, free: 388 kB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.000398/0.1026, allocations: 485.7 kB / 485.8 MB, free: 15.9 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.001062/0.1037, allocations: 1.175 MB / 486.9 MB, free: 14.72 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.268e-06/0.1037, allocations: 0 / 486.9 MB, free: 14.72 MB / 366.1 MB
Notification: Performance of FrontEnd: time 1.443e-06/0.1037, allocations: 0 / 486.9 MB, free: 14.72 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 1.302e-05/0.1037, allocations: 0 / 486.9 MB, free: 14.72 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 0.00159/0.1053, allocations: 1.153 MB / 488.1 MB, free: 13.52 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.499e-05/0.1054, allocations: 8.031 kB / 488.1 MB, free: 13.51 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001347/0.1055, allocations: 104.3 kB / 488.2 MB, free: 13.41 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002579/0.1058, allocations: 303 kB / 488.5 MB, free: 13.07 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.672e-05/0.1058, allocations: 74.38 kB / 488.6 MB, free: 13 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001258/0.106, allocations: 100.3 kB / 488.7 MB, free: 12.9 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001348/0.1073, allocations: 0.8842 MB / 489.5 MB, free: 12 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.048e-05/0.1074, allocations: 4.188 kB / 489.6 MB, free: 12 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.829e-05/0.1075, allocations: 43.94 kB / 489.6 MB, free: 11.96 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.275e-05/0.1075, allocations: 24 kB / 489.6 MB, free: 11.93 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001052/0.1085, allocations: 0.6208 MB / 490.2 MB, free: 11.31 MB / 366.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004166/0.1127, allocations: 2.836 MB / 493.1 MB, free: 8.391 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0009811/0.1137, allocations: 0.5207 MB / 493.6 MB, free: 7.855 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004139/0.1141, allocations: 319 kB / 493.9 MB, free: 7.539 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.304e-05/0.1142, allocations: 8.438 kB / 493.9 MB, free: 7.531 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.449e-05/0.1142, allocations: 39 kB / 494 MB, free: 7.48 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=50): time 2.235e-06/0.1142, allocations: 0 / 494 MB, free: 7.48 MB / 366.1 MB
Notification: Performance of matching and sorting (n=59): time 0.005085/0.1193, allocations: 2.186 MB / 496.1 MB, free: 5.254 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.247e-05/0.1194, allocations: 85.66 kB / 496.2 MB, free: 5.152 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003765/0.1198, allocations: 365.6 kB / 496.6 MB, free: 4.789 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.573e-05/0.1198, allocations: 37.7 kB / 496.6 MB, free: 4.746 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002586/0.1201, allocations: 467.6 kB / 497.1 MB, free: 4.281 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001546/0.1202, allocations: 222.1 kB / 497.3 MB, free: 4.062 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001912/0.1204, allocations: 142.6 kB / 497.4 MB, free: 3.914 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001317/0.1206, allocations: 358.8 kB / 497.8 MB, free: 3.555 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003774/0.1209, allocations: 252.7 kB / 498 MB, free: 3.309 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005118/0.1215, allocations: 484.9 kB / 498.5 MB, free: 2.715 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.00589/0.1274, allocations: 1.7 MB / 0.4885 GB, free: 0.8945 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.819e-06/0.1274, allocations: 8 kB / 0.4885 GB, free: 0.8867 MB / 366.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001196/0.1286, allocations: 0.8029 MB / 0.4893 GB, free: 76 kB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.788e-05/0.1286, allocations: 11.12 kB / 0.4893 GB, free: 68 kB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.339e-05/0.1286, allocations: 8 kB / 0.4893 GB, free: 60 kB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.321e-05/0.1287, allocations: 12.81 kB / 0.4893 GB, free: 48 kB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006921/0.1294, allocations: 191.7 kB / 0.4895 GB, free: 15.86 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.624e-05/0.1294, allocations: 23.92 kB / 0.4895 GB, free: 15.84 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003081/0.1297, allocations: 24 kB / 0.4895 GB, free: 15.81 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.977e-05/0.1298, allocations: 40 kB / 0.4896 GB, free: 15.77 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 0.0004716/0.1303, allocations: 291.7 kB / 0.4898 GB, free: 15.48 MB / 382.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.694e-05/0.1304, allocations: 51.61 kB / 0.4899 GB, free: 15.43 MB / 382.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001541/0.1305, allocations: 68.91 kB / 0.49 GB, free: 15.36 MB / 382.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.244e-06/0.1305, allocations: 3.984 kB / 0.49 GB, free: 15.36 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.063e-06/0.1305, allocations: 0 / 0.49 GB, free: 15.36 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 7.755e-05/0.1306, allocations: 116.8 kB / 0.4901 GB, free: 15.22 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.38e-05/0.1307, allocations: 16 kB / 0.4901 GB, free: 15.21 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002818/0.131, allocations: 12 kB / 0.4901 GB, free: 15.2 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.574e-05/0.1311, allocations: 36.45 kB / 0.4901 GB, free: 15.16 MB / 382.1 MB
Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.001258/0.1323, allocations: 0.7088 MB / 0.4908 GB, free: 14.45 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.001238/0.1336, allocations: 0.9943 MB / 0.4918 GB, free: 13.43 MB / 382.1 MB
Notification: Performance of postOpt setEvaluationStage (simulation): time 0.0003312/0.1339, allocations: 228.4 kB / 0.492 GB, free: 13.21 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0002383/0.1342, allocations: 247.1 kB / 0.4923 GB, free: 12.97 MB / 382.1 MB
Notification: Performance of Backend: time 6.51e-07/0.1342, allocations: 0 / 0.4923 GB, free: 12.97 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.0009926/0.1352, allocations: 0.4954 MB / 0.4927 GB, free: 12.47 MB / 382.1 MB
Notification: Performance of SimCode: time 0.002323/0.1375, allocations: 2.043 MB / 0.4947 GB, free: 10.36 MB / 382.1 MB
Notification: Performance of Templates: time 0.01103/0.1486, allocations: 6.052 MB / 0.5006 GB, free: 4.316 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)