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 0.001577/0.001577, allocations: 105.7 kB / 16.27 MB, free: 6.414 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001692/0.001692, allocations: 189.8 kB / 17.2 MB, free: 5.953 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.327/1.327, allocations: 222.9 MB / 240.9 MB, free: 15.27 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: 12.29 MB / 303.3 MB, free: 3.312 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001433/0.001433, allocations: 59.91 kB / 366.4 MB, free: 4.121 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2013/0.2027, allocations: 52.08 MB / 418.5 MB, free: 21.82 MB / 302.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.008696/0.2114, allocations: 8.48 MB / 427 MB, free: 13.31 MB / 302.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001331/0.2128, allocations: 0.8128 MB / 427.8 MB, free: 12.51 MB / 302.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003156/0.2132, allocations: 40.62 kB / 427.8 MB, free: 12.47 MB / 302.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002343/0.2134, allocations: 146.8 kB / 428 MB, free: 12.32 MB / 302.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0003824/0.2138, allocations: 202.3 kB / 428.2 MB, free: 12.13 MB / 302.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003357/0.2142, allocations: 196.6 kB / 428.4 MB, free: 11.94 MB / 302.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0004581/0.2146, allocations: 0.8376 MB / 429.2 MB, free: 11.1 MB / 302.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005446/0.2152, allocations: 0.5336 MB / 429.7 MB, free: 10.55 MB / 302.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002152/0.2154, allocations: 366.7 kB / 430.1 MB, free: 10.19 MB / 302.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002843/0.2157, allocations: 435.1 kB / 430.5 MB, free: 9.762 MB / 302.1 MB
Notification: Performance of NFPackage.collectConstants: time 9.594e-05/0.2158, allocations: 116 kB / 430.6 MB, free: 9.648 MB / 302.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001053/0.2159, allocations: 116 kB / 430.8 MB, free: 9.535 MB / 302.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001071/0.2161, allocations: 234.8 kB / 431 MB, free: 9.309 MB / 302.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002594/0.2163, allocations: 485.6 kB / 431.5 MB, free: 8.832 MB / 302.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0006095/0.2169, allocations: 1.139 MB / 432.6 MB, free: 7.691 MB / 302.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.27e-06/0.2169, allocations: 0 / 432.6 MB, free: 7.691 MB / 302.1 MB
Notification: Performance of FrontEnd: time 1.593e-06/0.217, allocations: 0 / 432.6 MB, free: 7.691 MB / 302.1 MB
Notification: Performance of Transformations before backend: time 1.156e-05/0.217, allocations: 0 / 432.6 MB, free: 7.691 MB / 302.1 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 0.001293/0.2183, allocations: 1.12 MB / 433.7 MB, free: 6.523 MB / 302.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.616e-05/0.2183, allocations: 8.031 kB / 433.7 MB, free: 6.516 MB / 302.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.00012/0.2184, allocations: 102.2 kB / 433.8 MB, free: 6.418 MB / 302.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001888/0.2186, allocations: 314.8 kB / 434.1 MB, free: 6.074 MB / 302.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.099e-05/0.2187, allocations: 74.38 kB / 434.2 MB, free: 6.004 MB / 302.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 9.469e-05/0.2188, allocations: 100.3 kB / 434.3 MB, free: 5.906 MB / 302.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001053/0.2198, allocations: 0.8777 MB / 435.2 MB, free: 5.016 MB / 302.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.693e-05/0.2199, allocations: 192 / 435.2 MB, free: 5.016 MB / 302.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.167e-05/0.2199, allocations: 43.94 kB / 435.2 MB, free: 4.973 MB / 302.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.421e-05/0.22, allocations: 24 kB / 435.2 MB, free: 4.949 MB / 302.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.00085/0.2208, allocations: 0.6216 MB / 435.9 MB, free: 4.328 MB / 302.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003348/0.2242, allocations: 2.892 MB / 438.8 MB, free: 1.367 MB / 302.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008092/0.225, allocations: 0.5183 MB / 439.3 MB, free: 0.832 MB / 302.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003238/0.2253, allocations: 319 kB / 439.6 MB, free: 0.5156 MB / 302.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.012e-05/0.2254, allocations: 4.438 kB / 439.6 MB, free: 0.5117 MB / 302.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.303e-05/0.2254, allocations: 43 kB / 439.6 MB, free: 472 kB / 302.1 MB
Notification: Performance of pre-optimization done (n=50): time 2.204e-06/0.2254, allocations: 0 / 439.6 MB, free: 472 kB / 302.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004729/0.2302, allocations: 2.165 MB / 441.8 MB, free: 14.25 MB / 318.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.479e-05/0.2302, allocations: 89.7 kB / 441.9 MB, free: 14.14 MB / 318.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003473/0.2306, allocations: 357.5 kB / 442.2 MB, free: 13.79 MB / 318.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.619e-05/0.2306, allocations: 37.7 kB / 442.3 MB, free: 13.75 MB / 318.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002378/0.2309, allocations: 446.1 kB / 442.7 MB, free: 13.3 MB / 318.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001557/0.231, allocations: 224.8 kB / 442.9 MB, free: 13.08 MB / 318.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001825/0.2312, allocations: 138.6 kB / 443.1 MB, free: 12.94 MB / 318.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001398/0.2314, allocations: 354.8 kB / 443.4 MB, free: 12.58 MB / 318.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003535/0.2317, allocations: 255.7 kB / 443.7 MB, free: 12.33 MB / 318.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004848/0.2322, allocations: 480.9 kB / 444.1 MB, free: 11.74 MB / 318.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005557/0.2378, allocations: 1.713 MB / 445.8 MB, free: 9.902 MB / 318.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.032e-06/0.2378, allocations: 7.938 kB / 445.9 MB, free: 9.895 MB / 318.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001167/0.239, allocations: 0.7957 MB / 446.6 MB, free: 9.094 MB / 318.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.139e-05/0.239, allocations: 16 kB / 446.7 MB, free: 9.078 MB / 318.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.244e-05/0.239, allocations: 8 kB / 446.7 MB, free: 9.07 MB / 318.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.874e-05/0.2391, allocations: 12 kB / 446.7 MB, free: 9.059 MB / 318.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006805/0.2398, allocations: 191.6 kB / 446.9 MB, free: 8.871 MB / 318.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.83e-05/0.2398, allocations: 15.94 kB / 446.9 MB, free: 8.855 MB / 318.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003171/0.2401, allocations: 24 kB / 446.9 MB, free: 8.832 MB / 318.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.96e-05/0.2402, allocations: 43.98 kB / 447 MB, free: 8.789 MB / 318.1 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 0.0004493/0.2406, allocations: 272.2 kB / 447.2 MB, free: 8.516 MB / 318.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.549e-05/0.2407, allocations: 47.44 kB / 447.3 MB, free: 8.469 MB / 318.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001401/0.2409, allocations: 68.89 kB / 447.3 MB, free: 8.402 MB / 318.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 9.508e-06/0.2409, allocations: 8 kB / 447.3 MB, free: 8.395 MB / 318.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.305e-06/0.2409, allocations: 7.938 kB / 447.3 MB, free: 8.387 MB / 318.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.31e-06/0.2409, allocations: 0 / 447.3 MB, free: 8.387 MB / 318.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001043/0.242, allocations: 0.7671 MB / 448.1 MB, free: 7.57 MB / 318.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.056e-06/0.242, allocations: 0 / 448.1 MB, free: 7.57 MB / 318.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005422/0.2425, allocations: 107.9 kB / 448.2 MB, free: 7.465 MB / 318.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 8.526e-06/0.2425, allocations: 4 kB / 448.2 MB, free: 7.461 MB / 318.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.595e-05/0.2426, allocations: 19.94 kB / 448.2 MB, free: 7.441 MB / 318.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.167e-06/0.2426, allocations: 4 kB / 448.2 MB, free: 7.438 MB / 318.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.603e-06/0.2426, allocations: 0 / 448.2 MB, free: 7.438 MB / 318.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001131/0.2437, allocations: 0.936 MB / 449.2 MB, free: 6.484 MB / 318.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 7.627e-05/0.2438, allocations: 116.5 kB / 449.3 MB, free: 6.352 MB / 318.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.117e-05/0.2439, allocations: 16 kB / 449.3 MB, free: 6.336 MB / 318.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002577/0.2441, allocations: 8 kB / 449.3 MB, free: 6.328 MB / 318.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.861e-05/0.2442, allocations: 32.52 kB / 449.4 MB, free: 6.297 MB / 318.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.235e-05/0.2442, allocations: 19.98 kB / 449.4 MB, free: 6.277 MB / 318.1 MB
Notification: Performance of sorting global known variables: time 0.0002144/0.2445, allocations: 239.2 kB / 449.6 MB, free: 6.043 MB / 318.1 MB
Notification: Performance of sort global known variables: time 1.21e-07/0.2445, allocations: 0 / 449.6 MB, free: 6.043 MB / 318.1 MB
Notification: Performance of remove unused functions: time 0.0005742/0.2451, allocations: 156 kB / 449.8 MB, free: 5.891 MB / 318.1 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 0.0001296/0.2452, allocations: 123.3 kB / 449.9 MB, free: 5.762 MB / 318.1 MB
Notification: Performance of simCode: created initialization part: time 0.00109/0.2463, allocations: 0.6185 MB / 450.5 MB, free: 5.148 MB / 318.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.424e-06/0.2463, allocations: 4.062 kB / 450.5 MB, free: 5.145 MB / 318.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003404/0.2466, allocations: 263.1 kB / 450.8 MB, free: 4.891 MB / 318.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005146/0.2472, allocations: 67.22 kB / 450.8 MB, free: 4.828 MB / 318.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002958/0.2501, allocations: 1.828 MB / 452.7 MB, free: 2.957 MB / 318.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004725/0.2506, allocations: 0.9465 MB / 453.6 MB, free: 1.984 MB / 318.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001792/0.2508, allocations: 55.42 kB / 453.7 MB, free: 1.93 MB / 318.1 MB
Notification: Performance of SimCode: time 5.61e-07/0.2508, allocations: 0 / 453.7 MB, free: 1.93 MB / 318.1 MB
Notification: Performance of Templates: time 0.01003/0.2609, allocations: 7.41 MB / 461.1 MB, free: 10.53 MB / 334.1 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)