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 0.001486/0.001486, allocations: 117.9 kB / 17.13 MB, free: 5.781 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 0.0015/0.0015, allocations: 194.1 kB / 20.08 MB, free: 2.871 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 1.444/1.444, allocations: 225.6 MB / 248.5 MB, free: 3.605 MB / 190.1 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 0.07091/0.07091, allocations: 12.41 MB / 315.8 MB, free: 376 kB / 238.1 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: translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container") translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container") [Timeout 660] "Warning: Ignoring unknown experiment annotation option: Algorithm = \"dassl\" Notification: Performance of FrontEnd - loaded program: time 0.001949/0.001949, allocations: 68.09 kB / 440.7 MB, free: 36.5 MB / 350.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.07639/0.07834, allocations: 54.92 MB / 495.6 MB, free: 7.648 MB / 350.1 MB Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.009319/0.08766, allocations: 8.519 MB / 0.4923 GB, free: 0.582 MB / 350.1 MB Notification: Performance of NFInst.instExpressions: time 0.0009332/0.08859, allocations: 0.8185 MB / 0.4931 GB, free: 15.76 MB / 366.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.0002365/0.08883, allocations: 40 kB / 0.4932 GB, free: 15.72 MB / 366.1 MB Notification: Performance of NFTyping.typeComponents: time 0.0002996/0.08913, allocations: 146.8 kB / 0.4933 GB, free: 15.58 MB / 366.1 MB Notification: Performance of NFTyping.typeBindings: time 0.0004373/0.08957, allocations: 214 kB / 0.4935 GB, free: 15.37 MB / 366.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.0003895/0.08996, allocations: 191.8 kB / 0.4937 GB, free: 15.18 MB / 366.1 MB Notification: Performance of NFFlatten.flatten: time 0.000878/0.09084, allocations: 0.8453 MB / 0.4945 GB, free: 14.33 MB / 366.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.0005774/0.09141, allocations: 374.6 kB / 0.4949 GB, free: 13.94 MB / 366.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.0003761/0.09179, allocations: 366.7 kB / 0.4952 GB, free: 13.58 MB / 366.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.0004911/0.09228, allocations: 426 kB / 0.4956 GB, free: 13.16 MB / 366.1 MB Notification: Performance of NFPackage.collectConstants: time 0.0001575/0.09244, allocations: 120 kB / 0.4957 GB, free: 13.05 MB / 366.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.0001606/0.0926, allocations: 116 kB / 0.4959 GB, free: 12.93 MB / 366.1 MB Notification: Performance of NFScalarize.scalarize: time 0.000195/0.09279, allocations: 231.3 kB / 0.4961 GB, free: 12.71 MB / 366.1 MB Notification: Performance of NFVerifyModel.verify: time 0.0004406/0.09323, allocations: 485.6 kB / 0.4965 GB, free: 12.23 MB / 366.1 MB Notification: Performance of NFConvertDAE.convert: time 0.001199/0.09443, allocations: 1.167 MB / 0.4977 GB, free: 11.06 MB / 366.1 MB Notification: Performance of FrontEnd - DAE generated: time 3.376e-06/0.09444, allocations: 0 / 0.4977 GB, free: 11.06 MB / 366.1 MB Notification: Performance of FrontEnd: time 1.092e-06/0.09444, allocations: 0 / 0.4977 GB, free: 11.06 MB / 366.1 MB Notification: Performance of Transformations before backend: time 1.059e-05/0.09445, allocations: 0 / 0.4977 GB, free: 11.06 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 0.001825/0.09627, allocations: 1.149 MB / 0.4988 GB, free: 9.855 MB / 366.1 MB Notification: Performance of prepare preOptimizeDAE: time 3.251e-05/0.09631, allocations: 8.031 kB / 0.4988 GB, free: 9.848 MB / 366.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001546/0.09646, allocations: 100.3 kB / 0.4989 GB, free: 9.75 MB / 366.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003338/0.09679, allocations: 311 kB / 0.4992 GB, free: 9.406 MB / 366.1 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 7.815e-05/0.09687, allocations: 74.38 kB / 0.4993 GB, free: 9.332 MB / 366.1 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001402/0.09701, allocations: 104.3 kB / 0.4994 GB, free: 9.23 MB / 366.1 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.001535/0.09855, allocations: 0.8725 MB / 0.5002 GB, free: 8.348 MB / 366.1 MB Notification: Performance of preOpt findStateOrder (simulation): time 2.763e-05/0.09857, allocations: 192 / 0.5002 GB, free: 8.348 MB / 366.1 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.855e-05/0.09865, allocations: 43.94 kB / 0.5003 GB, free: 8.305 MB / 366.1 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.198e-05/0.09867, allocations: 24 kB / 0.5003 GB, free: 8.281 MB / 366.1 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001181/0.09986, allocations: 0.6286 MB / 0.5009 GB, free: 7.648 MB / 366.1 MB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004675/0.1045, allocations: 2.844 MB / 0.5037 GB, free: 4.723 MB / 366.1 MB Notification: Performance of preOpt comSubExp (simulation): time 0.001055/0.1056, allocations: 0.4987 MB / 0.5042 GB, free: 4.207 MB / 366.1 MB Notification: Performance of preOpt resolveLoops (simulation): time 0.0004285/0.106, allocations: 275 kB / 0.5044 GB, free: 3.934 MB / 366.1 MB Notification: Performance of preOpt evalFunc (simulation): time 4.791e-05/0.1061, allocations: 4.438 kB / 0.5044 GB, free: 3.93 MB / 366.1 MB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.046e-05/0.1061, allocations: 39 kB / 0.5045 GB, free: 3.879 MB / 366.1 MB Notification: Performance of pre-optimization done (n=50): time 1.523e-06/0.1061, allocations: 0 / 0.5045 GB, free: 3.879 MB / 366.1 MB Notification: Performance of matching and sorting (n=59): time 0.005408/0.1115, allocations: 2.191 MB / 0.5066 GB, free: 1.645 MB / 366.1 MB Notification: Performance of inlineWhenForInitialization (initialization): time 6.369e-05/0.1116, allocations: 89.61 kB / 0.5067 GB, free: 1.539 MB / 366.1 MB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003913/0.112, allocations: 365.5 kB / 0.507 GB, free: 1.176 MB / 366.1 MB Notification: Performance of collectPreVariables (initialization): time 3.802e-05/0.112, allocations: 33.69 kB / 0.5071 GB, free: 1.137 MB / 366.1 MB Notification: Performance of collectInitialEqns (initialization): time 0.0003407/0.1123, allocations: 467.6 kB / 0.5075 GB, free: 0.6719 MB / 366.1 MB Notification: Performance of collectInitialBindings (initialization): time 0.0001841/0.1125, allocations: 230 kB / 0.5077 GB, free: 456 kB / 366.1 MB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002029/0.1127, allocations: 142.6 kB / 0.5079 GB, free: 304 kB / 366.1 MB Notification: Performance of setup shared object (initialization): time 0.0002175/0.1129, allocations: 358.8 kB / 0.5082 GB, free: 15.94 MB / 382.1 MB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0004006/0.1133, allocations: 248.8 kB / 0.5085 GB, free: 15.7 MB / 382.1 MB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0006094/0.114, allocations: 480.9 kB / 0.5089 GB, free: 15.11 MB / 382.1 MB Notification: Performance of analyzeInitialSystem (initialization): time 0.006019/0.12, allocations: 1.696 MB / 0.5106 GB, free: 13.29 MB / 382.1 MB Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.035e-06/0.12, allocations: 0 / 0.5106 GB, free: 13.29 MB / 382.1 MB Notification: Performance of matching and sorting (n=107) (initialization): time 0.00132/0.1213, allocations: 0.8074 MB / 0.5114 GB, free: 12.47 MB / 382.1 MB Notification: Performance of prepare postOptimizeDAE: time 1.837e-05/0.1213, allocations: 8.188 kB / 0.5114 GB, free: 12.46 MB / 382.1 MB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.501e-05/0.1213, allocations: 12 kB / 0.5114 GB, free: 12.45 MB / 382.1 MB Notification: Performance of postOpt tearingSystem (initialization): time 3.471e-05/0.1214, allocations: 16 kB / 0.5114 GB, free: 12.44 MB / 382.1 MB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007117/0.1221, allocations: 183.7 kB / 0.5116 GB, free: 12.26 MB / 382.1 MB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.468e-05/0.1221, allocations: 19.92 kB / 0.5116 GB, free: 12.24 MB / 382.1 MB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003231/0.1224, allocations: 28 kB / 0.5116 GB, free: 12.21 MB / 382.1 MB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.949e-05/0.1225, allocations: 32 kB / 0.5117 GB, free: 12.18 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 0.000452/0.1229, allocations: 290 kB / 0.5119 GB, free: 11.89 MB / 382.1 MB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001116/0.123, allocations: 51.61 kB / 0.512 GB, free: 11.84 MB / 382.1 MB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002023/0.1232, allocations: 72.91 kB / 0.512 GB, free: 11.77 MB / 382.1 MB Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.59e-06/0.1232, allocations: 4 kB / 0.512 GB, free: 11.76 MB / 382.1 MB Notification: Performance of postOpt constantLinearSystem (simulation): time 5.511e-06/0.1232, allocations: 0 / 0.512 GB, free: 11.76 MB / 382.1 MB Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.111e-05/0.1233, allocations: 11.92 kB / 0.5121 GB, free: 11.75 MB / 382.1 MB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001166/0.1244, allocations: 0.7553 MB / 0.5128 GB, free: 10.95 MB / 382.1 MB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.395e-06/0.1244, allocations: 4 kB / 0.5128 GB, free: 10.94 MB / 382.1 MB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0006049/0.125, allocations: 111.9 kB / 0.5129 GB, free: 10.83 MB / 382.1 MB Notification: Performance of postOpt tearingSystem (simulation): time 3.357e-06/0.125, allocations: 0 / 0.5129 GB, free: 10.83 MB / 382.1 MB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.471e-05/0.1251, allocations: 15.98 kB / 0.5129 GB, free: 10.82 MB / 382.1 MB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.364e-06/0.1251, allocations: 4 kB / 0.5129 GB, free: 10.81 MB / 382.1 MB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.72e-07/0.1251, allocations: 0 / 0.5129 GB, free: 10.81 MB / 382.1 MB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001357/0.1264, allocations: 0.9363 MB / 0.5138 GB, free: 9.855 MB / 382.1 MB Notification: Performance of postOpt removeConstants (simulation): time 0.0001503/0.1266, allocations: 124.8 kB / 0.514 GB, free: 9.715 MB / 382.1 MB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.097e-05/0.1267, allocations: 16 kB / 0.514 GB, free: 9.699 MB / 382.1 MB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002788/0.1269, allocations: 12 kB / 0.514 GB, free: 9.688 MB / 382.1 MB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.917e-05/0.127, allocations: 36.5 kB / 0.514 GB, free: 9.652 MB / 382.1 MB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.205e-05/0.127, allocations: 16 kB / 0.514 GB, free: 9.637 MB / 382.1 MB Notification: Performance of sorting global known variables: time 0.0002483/0.1273, allocations: 235.2 kB / 0.5143 GB, free: 9.41 MB / 382.1 MB Notification: Performance of sort global known variables: time 7.1e-08/0.1273, allocations: 0 / 0.5143 GB, free: 9.41 MB / 382.1 MB Notification: Performance of remove unused functions: time 0.0006251/0.1279, allocations: 160 kB / 0.5144 GB, free: 9.254 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 0.0001344/0.128, allocations: 119.6 kB / 0.5145 GB, free: 9.125 MB / 382.1 MB Notification: Performance of simCode: created initialization part: time 0.0009587/0.129, allocations: 0.5482 MB / 0.5151 GB, free: 8.582 MB / 382.1 MB Notification: Performance of simCode: created event and clocks part: time 1.804e-06/0.129, allocations: 192 / 0.5151 GB, free: 8.582 MB / 382.1 MB Notification: Performance of simCode: created simulation system equations: time 0.0004141/0.1294, allocations: 247.1 kB / 0.5153 GB, free: 8.344 MB / 382.1 MB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005034/0.1299, allocations: 65.48 kB / 0.5154 GB, free: 8.277 MB / 382.1 MB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003175/0.1331, allocations: 1.856 MB / 0.5172 GB, free: 6.375 MB / 382.1 MB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0006488/0.1337, allocations: 0.9428 MB / 0.5181 GB, free: 5.406 MB / 382.1 MB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001937/0.1339, allocations: 47.42 kB / 0.5181 GB, free: 5.359 MB / 382.1 MB Notification: Performance of SimCode: time 3.1e-07/0.1339, allocations: 0 / 0.5181 GB, free: 5.359 MB / 382.1 MB Notification: Performance of Templates: time 0.01185/0.1458, allocations: 7.555 MB / 0.5255 GB, free: 13.81 MB / 398.1 MB " [Timeout remaining time 660] make -j1 -f BioChem_BioChem.Examples.CircadianOscillator.Container.makefile [Timeout 660] (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) [Timeout 480] [Calling sys.exit(0), Time elapsed: 6.885295271873474] Failed to read output from testmodel.py, exit status != 0: 0.1532033709809184 0.167246063 0.069859609 Calling exit ...