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: "" <> buildModelFMU(BioChem.Examples.CircadianOscillator.Container,fileNamePrefix="BioChem_BioChem_Examples_CircadianOscillator_Container",fmuType="me",version="2.0",platforms={"static"})
"" <> buildModelFMU(BioChem.Examples.CircadianOscillator.Container,fileNamePrefix="BioChem_BioChem_Examples_CircadianOscillator_Container",fmuType="me",version="2.0",platforms={"static"})
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.00503/0.00503, allocations: 99.81 kB / 15.73 MB, free: 6.055 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001151/0.001151, allocations: 195.1 kB / 16.67 MB, free: 5.969 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.361/1.361, allocations: 222.9 MB / 240.4 MB, free: 15.14 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06043/0.06043, allocations: 12.27 MB / 302.8 MB, free: 3.219 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001202/0.001202, allocations: 64.94 kB / 419.5 MB, free: 17.51 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1065/0.1077, allocations: 52.08 MB / 471.6 MB, free: 13.45 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01317/0.121, allocations: 8.482 MB / 480.1 MB, free: 4.93 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.00213/0.1231, allocations: 0.8146 MB / 480.9 MB, free: 4.113 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0007673/0.1239, allocations: 40 kB / 481 MB, free: 4.074 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0004034/0.1244, allocations: 138.8 kB / 481.1 MB, free: 3.938 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0005449/0.125, allocations: 214 kB / 481.3 MB, free: 3.727 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0004155/0.1254, allocations: 199.7 kB / 481.5 MB, free: 3.531 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0007468/0.1261, allocations: 0.8376 MB / 482.3 MB, free: 2.691 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0007306/0.1269, allocations: 0.5375 MB / 482.9 MB, free: 2.129 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000332/0.1272, allocations: 374.7 kB / 483.2 MB, free: 1.762 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0004392/0.1277, allocations: 434 kB / 483.7 MB, free: 1.336 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001304/0.1278, allocations: 116 kB / 483.8 MB, free: 1.223 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001244/0.1279, allocations: 116 kB / 483.9 MB, free: 1.109 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001666/0.1281, allocations: 223.3 kB / 484.1 MB, free: 0.8906 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0004243/0.1285, allocations: 485.6 kB / 484.6 MB, free: 424 kB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.001145/0.1297, allocations: 1.168 MB / 485.8 MB, free: 15.24 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 3.456e-06/0.1297, allocations: 0 / 485.8 MB, free: 15.24 MB / 366.1 MB
Notification: Performance of FrontEnd: time 1.292e-06/0.1297, allocations: 0 / 485.8 MB, free: 15.24 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 1.521e-05/0.1297, allocations: 0 / 485.8 MB, free: 15.24 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 0.001812/0.1315, allocations: 1.145 MB / 486.9 MB, free: 14.04 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.007e-05/0.1316, allocations: 16.02 kB / 486.9 MB, free: 14.03 MB / 366.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.0001631/0.1318, allocations: 148.4 kB / 487.1 MB, free: 13.88 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.000157/0.1319, allocations: 108.3 kB / 487.2 MB, free: 13.77 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003194/0.1323, allocations: 299 kB / 487.5 MB, free: 13.44 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 7.372e-05/0.1323, allocations: 78.38 kB / 487.5 MB, free: 13.36 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000129/0.1325, allocations: 100.3 kB / 487.6 MB, free: 13.26 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001411/0.1339, allocations: 0.8802 MB / 488.5 MB, free: 12.37 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.025e-05/0.1339, allocations: 3.938 kB / 488.5 MB, free: 12.37 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.487e-05/0.134, allocations: 44 kB / 488.6 MB, free: 12.32 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.235e-05/0.1341, allocations: 28 kB / 488.6 MB, free: 12.3 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001095/0.1352, allocations: 0.6169 MB / 489.2 MB, free: 11.68 MB / 366.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004718/0.1399, allocations: 2.836 MB / 492 MB, free: 8.758 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.001129/0.141, allocations: 0.5245 MB / 492.6 MB, free: 8.219 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004196/0.1415, allocations: 311 kB / 492.9 MB, free: 7.91 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.69e-05/0.1415, allocations: 8.375 kB / 492.9 MB, free: 7.902 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.437e-05/0.1415, allocations: 50.92 kB / 492.9 MB, free: 7.84 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=50): time 2.204e-06/0.1416, allocations: 0 / 492.9 MB, free: 7.84 MB / 366.1 MB
Notification: Performance of matching and sorting (n=59): time 0.005304/0.1469, allocations: 2.183 MB / 495.1 MB, free: 5.613 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.374e-05/0.1469, allocations: 81.67 kB / 495.2 MB, free: 5.516 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003863/0.1473, allocations: 361.5 kB / 495.5 MB, free: 5.156 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.581e-05/0.1474, allocations: 33.7 kB / 495.6 MB, free: 5.117 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003048/0.1477, allocations: 471.6 kB / 496 MB, free: 4.648 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001966/0.1479, allocations: 226.1 kB / 496.3 MB, free: 4.426 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000189/0.1481, allocations: 146.6 kB / 496.4 MB, free: 4.273 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001822/0.1483, allocations: 354.8 kB / 496.7 MB, free: 3.918 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003769/0.1487, allocations: 260.6 kB / 497 MB, free: 3.664 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0007378/0.1494, allocations: 484.9 kB / 497.5 MB, free: 3.07 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005599/0.155, allocations: 1.696 MB / 499.2 MB, free: 1.254 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.093e-06/0.155, allocations: 7.938 kB / 499.2 MB, free: 1.246 MB / 366.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.00121/0.1563, allocations: 0.8035 MB / 500 MB, free: 444 kB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.624e-05/0.1563, allocations: 8 kB / 500 MB, free: 436 kB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.464e-05/0.1563, allocations: 8 kB / 500 MB, free: 428 kB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.997e-05/0.1564, allocations: 12 kB / 0.4883 GB, free: 416 kB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000662/0.157, allocations: 183.7 kB / 0.4885 GB, free: 232 kB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.174e-05/0.1571, allocations: 23.92 kB / 0.4885 GB, free: 208 kB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003352/0.1574, allocations: 32 kB / 0.4885 GB, free: 176 kB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.425e-05/0.1575, allocations: 32 kB / 0.4885 GB, free: 144 kB / 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 0.0005844/0.1581, allocations: 278.5 kB / 0.4888 GB, free: 15.86 MB / 382.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000101/0.1582, allocations: 51.67 kB / 0.4889 GB, free: 15.81 MB / 382.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001331/0.1583, allocations: 76.78 kB / 0.4889 GB, free: 15.73 MB / 382.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.121e-06/0.1583, allocations: 8 kB / 0.4889 GB, free: 15.73 MB / 382.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.748e-05/0.1583, allocations: 4 kB / 0.4889 GB, free: 15.72 MB / 382.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.234e-06/0.1584, allocations: 0 / 0.4889 GB, free: 15.72 MB / 382.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001161/0.1595, allocations: 0.7592 MB / 0.4897 GB, free: 14.91 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.336e-06/0.1595, allocations: 0 / 0.4897 GB, free: 14.91 MB / 382.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005629/0.1601, allocations: 119.8 kB / 0.4898 GB, free: 14.8 MB / 382.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 6.923e-06/0.1601, allocations: 4 kB / 0.4898 GB, free: 14.79 MB / 382.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.698e-05/0.1602, allocations: 12 kB / 0.4898 GB, free: 14.78 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.719e-06/0.1602, allocations: 4 kB / 0.4898 GB, free: 14.78 MB / 382.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.873e-06/0.1602, allocations: 0 / 0.4898 GB, free: 14.78 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001233/0.1614, allocations: 0.9364 MB / 0.4907 GB, free: 13.82 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001032/0.1615, allocations: 124.7 kB / 0.4909 GB, free: 13.68 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.669e-05/0.1616, allocations: 20 kB / 0.4909 GB, free: 13.66 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002683/0.1619, allocations: 12 kB / 0.4909 GB, free: 13.65 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.746e-05/0.1619, allocations: 32.52 kB / 0.4909 GB, free: 13.62 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.951e-05/0.162, allocations: 15.98 kB / 0.4909 GB, free: 13.6 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0002331/0.1622, allocations: 235.2 kB / 0.4912 GB, free: 13.38 MB / 382.1 MB
Notification: Performance of sort global known variables: time 1.61e-07/0.1622, allocations: 4 kB / 0.4912 GB, free: 13.37 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.0006186/0.1629, allocations: 164 kB / 0.4913 GB, free: 13.21 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 0.00161/0.1645, allocations: 1.486 MB / 0.4928 GB, free: 11.7 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.0009159/0.1654, allocations: 0.591 MB / 0.4933 GB, free: 11.11 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.625e-06/0.1654, allocations: 0 / 0.4933 GB, free: 11.11 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003713/0.1658, allocations: 267.1 kB / 0.4936 GB, free: 10.85 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005187/0.1663, allocations: 61.97 kB / 0.4937 GB, free: 10.79 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.007461/0.1738, allocations: 5.873 MB / 0.4994 GB, free: 4.582 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005641/0.1744, allocations: 0.935 MB / 0.5003 GB, free: 3.625 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.00027/0.1747, allocations: 64.59 kB / 0.5004 GB, free: 3.562 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0005001/0.1752, allocations: 279.3 kB / 0.5006 GB, free: 3.289 MB / 382.1 MB
Notification: Performance of SimCode: time 9.32e-07/0.1752, allocations: 0 / 0.5006 GB, free: 3.289 MB / 382.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.2513/0.4265, allocations: 10.98 MB / 0.5114 GB, free: 41.27 MB / 382.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 8.595/9.021, allocations: 5.406 kB / 0.5114 GB, free: 41.27 MB / 382.1 MB
(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 & python3 -m fmpy simulate  --output-file BioChem_BioChem.Examples.CircadianOscillator.Container_res.csv --start-time 0 --stop-time 150 --timeout 50 --relative-tolerance 1e-06 --interface-type ModelExchange --solver CVode --output-interval 150 BioChem_BioChem_Examples_CircadianOscillator_Container.fmu > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1)