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) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001232/0.001232, allocations: 106.6 kB / 16.45 MB, free: 6.504 MB / 14.72 MB " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001329/0.001329, allocations: 191.7 kB / 19.41 MB, free: 3.68 MB / 14.72 MB " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.415/1.415, allocations: 225.6 MB / 247.8 MB, free: 13.95 MB / 206.1 MB " [Timeout remaining time 178] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.07353/0.07353, allocations: 12.41 MB / 315.1 MB, free: 14.12 MB / 254.1 MB " [Timeout remaining time 180] 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"}) [Timeout 660] "Warning: Ignoring unknown experiment annotation option: Algorithm = \"dassl\" Notification: Performance of FrontEnd - loaded program: time 0.001901/0.001901, allocations: 69.53 kB / 439.5 MB, free: 8.113 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1106/0.1125, allocations: 54.91 MB / 494.5 MB, free: 1.129 MB / 350.1 MB Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01287/0.1254, allocations: 8.524 MB / 0.4912 GB, free: 8.574 MB / 366.1 MB Notification: Performance of NFInst.instExpressions: time 0.00186/0.1272, allocations: 0.8068 MB / 0.492 GB, free: 7.766 MB / 366.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.0002861/0.1275, allocations: 44 kB / 0.492 GB, free: 7.723 MB / 366.1 MB Notification: Performance of NFTyping.typeComponents: time 0.0002918/0.1278, allocations: 150.8 kB / 0.4922 GB, free: 7.574 MB / 366.1 MB Notification: Performance of NFTyping.typeBindings: time 0.0004455/0.1282, allocations: 214 kB / 0.4924 GB, free: 7.363 MB / 366.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.0003845/0.1286, allocations: 187.8 kB / 0.4926 GB, free: 7.18 MB / 366.1 MB Notification: Performance of NFFlatten.flatten: time 0.0008338/0.1295, allocations: 0.8453 MB / 0.4934 GB, free: 6.332 MB / 366.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.0006199/0.1301, allocations: 374.6 kB / 0.4937 GB, free: 5.941 MB / 366.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.000479/0.1306, allocations: 366.7 kB / 0.4941 GB, free: 5.582 MB / 366.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.0006849/0.1312, allocations: 430 kB / 0.4945 GB, free: 5.16 MB / 366.1 MB Notification: Performance of NFPackage.collectConstants: time 0.0001359/0.1314, allocations: 116 kB / 0.4946 GB, free: 5.047 MB / 366.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.0001472/0.1315, allocations: 116 kB / 0.4947 GB, free: 4.934 MB / 366.1 MB Notification: Performance of NFScalarize.scalarize: time 0.0002443/0.1318, allocations: 231.2 kB / 0.4949 GB, free: 4.707 MB / 366.1 MB Notification: Performance of NFVerifyModel.verify: time 0.0004537/0.1322, allocations: 481.7 kB / 0.4954 GB, free: 4.234 MB / 366.1 MB Notification: Performance of NFConvertDAE.convert: time 0.001319/0.1335, allocations: 1.171 MB / 0.4965 GB, free: 3.059 MB / 366.1 MB Notification: Performance of FrontEnd - DAE generated: time 4.629e-06/0.1335, allocations: 0 / 0.4965 GB, free: 3.059 MB / 366.1 MB Notification: Performance of FrontEnd: time 2.224e-06/0.1335, allocations: 0 / 0.4965 GB, free: 3.059 MB / 366.1 MB Notification: Performance of Transformations before backend: time 1.313e-05/0.1336, allocations: 0 / 0.4965 GB, free: 3.059 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 0.001823/0.1354, allocations: 1.153 MB / 0.4977 GB, free: 1.852 MB / 366.1 MB Notification: Performance of prepare preOptimizeDAE: time 4.928e-05/0.1354, allocations: 8.031 kB / 0.4977 GB, free: 1.844 MB / 366.1 MB Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.0001817/0.1356, allocations: 152.4 kB / 0.4978 GB, free: 1.688 MB / 366.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001526/0.1358, allocations: 108.2 kB / 0.4979 GB, free: 1.582 MB / 366.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.000361/0.1361, allocations: 307 kB / 0.4982 GB, free: 1.242 MB / 366.1 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 6.854e-05/0.1362, allocations: 70.38 kB / 0.4983 GB, free: 1.172 MB / 366.1 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001439/0.1363, allocations: 112.3 kB / 0.4984 GB, free: 1.062 MB / 366.1 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.001626/0.138, allocations: 0.8725 MB / 0.4992 GB, free: 184 kB / 366.1 MB Notification: Performance of preOpt findStateOrder (simulation): time 2.991e-05/0.138, allocations: 3.938 kB / 0.4992 GB, free: 180 kB / 366.1 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 8.211e-05/0.1381, allocations: 44 kB / 0.4993 GB, free: 136 kB / 366.1 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.175e-05/0.1381, allocations: 24 kB / 0.4993 GB, free: 112 kB / 366.1 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001123/0.1392, allocations: 0.6248 MB / 0.4999 GB, free: 15.48 MB / 382.1 MB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004828/0.1441, allocations: 2.84 MB / 0.5027 GB, free: 12.56 MB / 382.1 MB Notification: Performance of preOpt comSubExp (simulation): time 0.001019/0.1451, allocations: 498.7 kB / 0.5032 GB, free: 12.05 MB / 382.1 MB Notification: Performance of preOpt resolveLoops (simulation): time 0.0004432/0.1455, allocations: 290.9 kB / 0.5034 GB, free: 11.77 MB / 382.1 MB Notification: Performance of preOpt evalFunc (simulation): time 2.73e-05/0.1455, allocations: 4.438 kB / 0.5035 GB, free: 11.76 MB / 382.1 MB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.872e-05/0.1456, allocations: 39 kB / 0.5035 GB, free: 11.71 MB / 382.1 MB Notification: Performance of pre-optimization done (n=50): time 2.024e-06/0.1456, allocations: 0 / 0.5035 GB, free: 11.71 MB / 382.1 MB Notification: Performance of matching and sorting (n=59): time 0.005146/0.1507, allocations: 2.172 MB / 0.5056 GB, free: 9.496 MB / 382.1 MB Notification: Performance of inlineWhenForInitialization (initialization): time 6.564e-05/0.1508, allocations: 89.67 kB / 0.5057 GB, free: 9.391 MB / 382.1 MB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004029/0.1512, allocations: 369.4 kB / 0.506 GB, free: 9.023 MB / 382.1 MB Notification: Performance of collectPreVariables (initialization): time 3.984e-05/0.1512, allocations: 41.69 kB / 0.5061 GB, free: 8.977 MB / 382.1 MB Notification: Performance of collectInitialEqns (initialization): time 0.0003244/0.1516, allocations: 455.7 kB / 0.5065 GB, free: 8.523 MB / 382.1 MB Notification: Performance of collectInitialBindings (initialization): time 0.0002056/0.1518, allocations: 234 kB / 0.5067 GB, free: 8.293 MB / 382.1 MB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002497/0.152, allocations: 142.6 kB / 0.5069 GB, free: 8.145 MB / 382.1 MB Notification: Performance of setup shared object (initialization): time 0.0001978/0.1522, allocations: 354.8 kB / 0.5072 GB, free: 7.789 MB / 382.1 MB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0004004/0.1526, allocations: 248.8 kB / 0.5075 GB, free: 7.547 MB / 382.1 MB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005862/0.1532, allocations: 484.9 kB / 0.5079 GB, free: 6.953 MB / 382.1 MB Notification: Performance of analyzeInitialSystem (initialization): time 0.006065/0.1593, allocations: 1.696 MB / 0.5096 GB, free: 5.137 MB / 382.1 MB Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.436e-06/0.1593, allocations: 11.94 kB / 0.5096 GB, free: 5.125 MB / 382.1 MB Notification: Performance of matching and sorting (n=107) (initialization): time 0.00126/0.1605, allocations: 0.7951 MB / 0.5104 GB, free: 4.32 MB / 382.1 MB Notification: Performance of prepare postOptimizeDAE: time 2.501e-05/0.1606, allocations: 12 kB / 0.5104 GB, free: 4.309 MB / 382.1 MB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.303e-05/0.1606, allocations: 8.906 kB / 0.5104 GB, free: 4.301 MB / 382.1 MB Notification: Performance of postOpt tearingSystem (initialization): time 2.943e-05/0.1606, allocations: 12 kB / 0.5104 GB, free: 4.289 MB / 382.1 MB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006676/0.1613, allocations: 191.7 kB / 0.5106 GB, free: 4.102 MB / 382.1 MB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.26e-05/0.1613, allocations: 19.92 kB / 0.5106 GB, free: 4.082 MB / 382.1 MB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002955/0.1616, allocations: 24 kB / 0.5106 GB, free: 4.059 MB / 382.1 MB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.812e-05/0.1616, allocations: 40 kB / 0.5107 GB, free: 4.02 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 0.0005081/0.1622, allocations: 284.2 kB / 0.5109 GB, free: 3.734 MB / 382.1 MB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001002/0.1623, allocations: 51.67 kB / 0.511 GB, free: 3.684 MB / 382.1 MB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001608/0.1624, allocations: 64.91 kB / 0.511 GB, free: 3.617 MB / 382.1 MB Notification: Performance of postOpt inlineArrayEqn (simulation): time 9.798e-06/0.1624, allocations: 11.98 kB / 0.5111 GB, free: 3.605 MB / 382.1 MB Notification: Performance of postOpt constantLinearSystem (simulation): time 6.232e-06/0.1624, allocations: 0 / 0.5111 GB, free: 3.605 MB / 382.1 MB Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.912e-06/0.1624, allocations: 11.86 kB / 0.5111 GB, free: 3.594 MB / 382.1 MB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001163/0.1636, allocations: 0.7593 MB / 0.5118 GB, free: 2.785 MB / 382.1 MB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.545e-06/0.1636, allocations: 0 / 0.5118 GB, free: 2.785 MB / 382.1 MB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005466/0.1641, allocations: 103.9 kB / 0.5119 GB, free: 2.684 MB / 382.1 MB Notification: Performance of postOpt tearingSystem (simulation): time 6.823e-06/0.1642, allocations: 4 kB / 0.5119 GB, free: 2.68 MB / 382.1 MB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.698e-05/0.1642, allocations: 19.98 kB / 0.5119 GB, free: 2.66 MB / 382.1 MB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.15e-06/0.1642, allocations: 4 kB / 0.5119 GB, free: 2.656 MB / 382.1 MB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.153e-06/0.1642, allocations: 0 / 0.5119 GB, free: 2.656 MB / 382.1 MB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00132/0.1655, allocations: 0.9363 MB / 0.5128 GB, free: 1.699 MB / 382.1 MB Notification: Performance of postOpt removeConstants (simulation): time 0.000105/0.1656, allocations: 120.8 kB / 0.513 GB, free: 1.562 MB / 382.1 MB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.156e-05/0.1657, allocations: 16 kB / 0.513 GB, free: 1.547 MB / 382.1 MB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002581/0.166, allocations: 8 kB / 0.513 GB, free: 1.539 MB / 382.1 MB Notification: Performance of postOpt findZeroCrossings (simulation): time 7.297e-05/0.166, allocations: 40.5 kB / 0.513 GB, free: 1.5 MB / 382.1 MB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.839e-05/0.1661, allocations: 16.11 kB / 0.513 GB, free: 1.484 MB / 382.1 MB Notification: Performance of sorting global known variables: time 0.0003135/0.1664, allocations: 243.1 kB / 0.5133 GB, free: 1.25 MB / 382.1 MB Notification: Performance of sort global known variables: time 7e-08/0.1664, allocations: 0 / 0.5133 GB, free: 1.25 MB / 382.1 MB Notification: Performance of remove unused functions: time 0.0005826/0.167, allocations: 156 kB / 0.5134 GB, free: 1.098 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 0.2235/0.3905, allocations: 1.491 MB / 0.5149 GB, free: 30.15 MB / 382.1 MB Notification: Performance of simCode: created initialization part: time 0.0008829/0.3914, allocations: 0.5518 MB / 0.5154 GB, free: 30.15 MB / 382.1 MB Notification: Performance of simCode: created event and clocks part: time 3.216e-06/0.3914, allocations: 0.7812 kB / 0.5154 GB, free: 30.15 MB / 382.1 MB Notification: Performance of simCode: created simulation system equations: time 0.0002916/0.3917, allocations: 244.9 kB / 0.5156 GB, free: 30.15 MB / 382.1 MB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000559/0.3922, allocations: 67.92 kB / 0.5157 GB, free: 30.15 MB / 382.1 MB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.007757/0.4, allocations: 5.863 MB / 0.5214 GB, free: 27.4 MB / 382.1 MB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005759/0.4006, allocations: 0.9411 MB / 0.5224 GB, free: 26.69 MB / 382.1 MB Notification: Performance of simCode: alias equations: time 0.0003498/0.4009, allocations: 62.48 kB / 0.5224 GB, free: 26.68 MB / 382.1 MB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003439/0.4013, allocations: 284.2 kB / 0.5227 GB, free: 26.67 MB / 382.1 MB Notification: Performance of SimCode: time 2.074e-06/0.4013, allocations: 0 / 0.5227 GB, free: 26.67 MB / 382.1 MB Notification: Performance of buildModelFMU: Generate the FMI files: time 0.05721/0.4585, allocations: 11.08 MB / 0.5335 GB, free: 23.93 MB / 382.1 MB Notification: Performance of buildModelFMU: Generate platform static: time 8.83/9.288, allocations: 13.67 kB / 0.5335 GB, free: 23.92 MB / 382.1 MB " [Timeout remaining time 651] (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 & /home/hudson/saved_omc/OMSimulator/install/bin/OMSimulator --tempDir=temp_BioChem_BioChem_Examples_CircadianOscillator_Container_fmu --startTime=0 --stopTime=150 --stepSize=150 --timeout=50 --tolerance=1e-06 BioChem_BioChem_Examples_CircadianOscillator_Container.fmu > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1) [Timeout 52.5] [Calling sys.exit(0), Time elapsed: 11.828477054834366] Failed to read output from testmodel.py, exit status != 0: 9.364303883630782 9.38068281 9.24511773 Calling exit ...