Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.conf.json loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.0009445/0.0009445, allocations: 92.2 kB / 20.19 MB, free: 4.363 MB / 18.57 MB " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.0009741/0.0009741, allocations: 173 kB / 23.49 MB, free: 1.059 MB / 18.57 MB " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 0.9585/0.9585, allocations: 177.1 MB / 203.8 MB, free: 5.633 MB / 186.7 MB " [Timeout remaining time 179] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/package.mo", uses=false) [Timeout 180] "[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/Examples/package.order:0:0-0:0:readonly] Warning: The package.order file does not list all .mo files and directories (containing package.mo) present in its directory. Missing names are: Paracetamol_Experiment Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/package.mo): time 1.577/1.577, allocations: 273.5 MB / 0.5213 GB, free: 14.86 MB / 458.7 MB " [Timeout remaining time 178] Using package Pharmacolibrary with version 25.09 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/package.mo) Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo) Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo) Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo) Running command: translateModel(Pharmacolibrary.DevModels.PKTwoCompartmentModel,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel") translateModel(Pharmacolibrary.DevModels.PKTwoCompartmentModel,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.333e-06/1.333e-06, allocations: 0 / 0.6462 GB, free: 39.23 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 1.305e-05/1.439e-05, allocations: 2.312 kB / 0.6462 GB, free: 39.22 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModel): time 0.002543/0.002557, allocations: 2.389 MB / 0.6485 GB, free: 37.67 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.0009397/0.003497, allocations: 0.6113 MB / 0.6491 GB, free: 37.27 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 9.462e-05/0.003592, allocations: 2.219 kB / 0.6491 GB, free: 37.27 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 6.776e-05/0.003659, allocations: 29.7 kB / 0.6492 GB, free: 37.25 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.000213/0.003872, allocations: 80.11 kB / 0.6492 GB, free: 37.21 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001914/0.004064, allocations: 63.83 kB / 0.6493 GB, free: 37.18 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.000316/0.00438, allocations: 301.9 kB / 0.6496 GB, free: 37.05 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001414/0.004521, allocations: 52 kB / 0.6496 GB, free: 37.02 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002045/0.004726, allocations: 154.1 kB / 0.6498 GB, free: 36.96 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001525/0.004878, allocations: 90.14 kB / 0.6499 GB, free: 36.93 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 4.39e-05/0.004922, allocations: 23 kB / 0.6499 GB, free: 36.93 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 3.73e-05/0.004959, allocations: 22.69 kB / 0.6499 GB, free: 36.93 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 3.901e-05/0.004998, allocations: 46.41 kB / 0.6499 GB, free: 36.9 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 0.0001025/0.005101, allocations: 88.12 kB / 0.65 GB, free: 36.86 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0002343/0.005335, allocations: 181.9 kB / 0.6502 GB, free: 36.78 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 2.013e-06/0.005337, allocations: 0 / 0.6502 GB, free: 36.78 MB / 0.5262 GB Notification: Performance of FrontEnd: time 6.92e-07/0.005338, allocations: 1.312 kB / 0.6502 GB, free: 36.78 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 4.318e-06/0.005342, allocations: 0 / 0.6502 GB, free: 36.78 MB / 0.5262 GB Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 45 * Number of variables: 45 Notification: Performance of Generate backend data structure: time 0.0006812/0.006023, allocations: 0.6159 MB / 0.6508 GB, free: 36.22 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 3.859e-05/0.006062, allocations: 10.94 kB / 0.6508 GB, free: 36.22 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 9.097e-05/0.006153, allocations: 37.89 kB / 0.6509 GB, free: 36.2 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001117/0.006265, allocations: 152.9 kB / 0.651 GB, free: 36.04 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.06e-05/0.006285, allocations: 11.94 kB / 0.651 GB, free: 36.04 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 4.511e-05/0.00633, allocations: 32.61 kB / 0.651 GB, free: 36.02 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003126/0.006643, allocations: 219.5 kB / 0.6513 GB, free: 35.88 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.844e-05/0.006662, allocations: 1.531 kB / 0.6513 GB, free: 35.88 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.084e-05/0.006682, allocations: 6.906 kB / 0.6513 GB, free: 35.88 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.007e-05/0.006692, allocations: 5.906 kB / 0.6513 GB, free: 35.88 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002135/0.006906, allocations: 148.6 kB / 0.6514 GB, free: 35.8 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.00072/0.007626, allocations: 0.5046 MB / 0.6519 GB, free: 35.43 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0002463/0.007872, allocations: 181.3 kB / 0.6521 GB, free: 35.3 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001101/0.007982, allocations: 106.8 kB / 0.6522 GB, free: 35.22 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.421e-05/0.007997, allocations: 3.438 kB / 0.6522 GB, free: 35.22 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002669/0.008263, allocations: 324.5 kB / 0.6525 GB, free: 34.96 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=31): time 2.014e-06/0.008265, allocations: 0 / 0.6525 GB, free: 34.96 MB / 0.5262 GB Notification: Performance of matching and sorting (n=33): time 0.001207/0.009472, allocations: 0.9078 MB / 0.6534 GB, free: 34.31 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 5.213e-05/0.009524, allocations: 216 kB / 0.6536 GB, free: 34.06 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001232/0.009648, allocations: 219 kB / 0.6538 GB, free: 33.88 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 2.33e-05/0.009671, allocations: 37.45 kB / 0.6538 GB, free: 33.84 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 5.548e-05/0.009726, allocations: 174.3 kB / 0.654 GB, free: 33.68 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 6.608e-05/0.009793, allocations: 106.9 kB / 0.6541 GB, free: 33.6 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 8.932e-05/0.009882, allocations: 69.02 kB / 0.6542 GB, free: 33.55 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 6.016e-05/0.009942, allocations: 0.5071 MB / 0.6547 GB, free: 33.05 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001489/0.01009, allocations: 152.7 kB / 0.6548 GB, free: 32.93 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.000173/0.01026, allocations: 262.2 kB / 0.6551 GB, free: 32.66 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0003989/0.01066, allocations: 491.2 kB / 0.6555 GB, free: 32.23 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.515e-06/0.01067, allocations: 1.312 kB / 0.6555 GB, free: 32.23 MB / 0.5262 GB Notification: Performance of matching and sorting (n=48) (initialization): time 0.0005192/0.01118, allocations: 446.4 kB / 0.6559 GB, free: 31.94 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 4.16e-05/0.01123, allocations: 92.7 kB / 0.656 GB, free: 31.84 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.538e-06/0.01124, allocations: 6.281 kB / 0.656 GB, free: 31.84 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.917e-05/0.01125, allocations: 3.938 kB / 0.656 GB, free: 31.84 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002795/0.01153, allocations: 79.91 kB / 0.6561 GB, free: 31.83 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.506e-06/0.01154, allocations: 5.719 kB / 0.6561 GB, free: 31.83 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000144/0.01169, allocations: 18.75 kB / 0.6561 GB, free: 31.82 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.458e-05/0.01171, allocations: 13.19 kB / 0.6562 GB, free: 31.82 MB / 0.5262 GB Warning: Assuming fixed start value for the following 10 variables: periodicDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real periodicDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real intestine.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real blood.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real intestine.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real intestine.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.rising:DISCRETE(fixed = true protected = true ) type: Boolean intestine.rising:DISCRETE(fixed = true protected = true ) type: Boolean Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 9 * Number of states: 0 () * Number of discrete variables: 21 ($PRE.intestine.Cmin,intestine.Cmin,$PRE.intestine.Cmax,intestine.Cmax,$PRE.blood.Cmin,blood.Cmin,$PRE.blood.Cmax,blood.Cmax,$PRE.blood.rising,$PRE.intestine.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,blood.rising,intestine.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (45): * Single equations (assignments): 42 * Array equations: 0 * Algorithm blocks: 3 * 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 0.0001946/0.01191, allocations: 279.1 kB / 0.6564 GB, free: 31.57 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 5.527e-05/0.01196, allocations: 42.06 kB / 0.6565 GB, free: 31.55 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.963e-05/0.012, allocations: 27.97 kB / 0.6565 GB, free: 31.53 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.765e-06/0.012, allocations: 0 / 0.6565 GB, free: 31.53 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 5.411e-06/0.01201, allocations: 0 / 0.6565 GB, free: 31.53 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.891e-06/0.01201, allocations: 7.312 kB / 0.6565 GB, free: 31.53 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007923/0.01281, allocations: 0.7139 MB / 0.6572 GB, free: 31 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.655e-06/0.01281, allocations: 0 / 0.6572 GB, free: 31 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002614/0.01307, allocations: 50.53 kB / 0.6572 GB, free: 31 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 4.198e-06/0.01308, allocations: 4.719 kB / 0.6572 GB, free: 31 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.931e-05/0.0131, allocations: 14.33 kB / 0.6573 GB, free: 31 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.346e-06/0.01311, allocations: 1.094 kB / 0.6573 GB, free: 31 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.243e-06/0.01311, allocations: 0.5625 kB / 0.6573 GB, free: 31 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0007658/0.01388, allocations: 0.6627 MB / 0.6579 GB, free: 30.53 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 3.312e-05/0.01391, allocations: 13.47 kB / 0.6579 GB, free: 30.52 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.784e-05/0.01396, allocations: 17.11 kB / 0.6579 GB, free: 30.52 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001487/0.0141, allocations: 14.19 kB / 0.658 GB, free: 30.51 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 7.659e-05/0.01418, allocations: 29.98 kB / 0.658 GB, free: 30.5 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.189e-05/0.0142, allocations: 12.56 kB / 0.658 GB, free: 30.5 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 7.045e-05/0.01427, allocations: 158.2 kB / 0.6581 GB, free: 30.38 MB / 0.5262 GB Notification: Performance of sort global known variables: time 1.1e-07/0.01427, allocations: 3.406 kB / 0.6581 GB, free: 30.38 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0003752/0.01465, allocations: 75.34 kB / 0.6582 GB, free: 30.36 MB / 0.5262 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 6 (periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass,intestine.C,intestine.AUC,blood.C,blood.AUC) * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,periodicDose.pulse.T_start,periodicDose.pulse.count,intestine.Cmax,intestine.Cmin,intestine.rising,blood.Cmax,blood.Cmin,blood.rising) * Number of discrete states: 11 (periodicDose.pulse.count,blood.Cmin,$whenCondition3,blood.Cmax,$whenCondition2,blood.rising,intestine.Cmin,$whenCondition5,intestine.Cmax,$whenCondition4,intestine.rising) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (27): * Single equations (assignments): 23 * Array equations: 0 * Algorithm blocks: 2 * Record equations: 0 * When equations: 2 * 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 9.006e-05/0.01474, allocations: 116.4 kB / 0.6583 GB, free: 30.27 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0004373/0.01518, allocations: 0.4908 MB / 0.6588 GB, free: 29.88 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 1.694e-06/0.01518, allocations: 0 / 0.6588 GB, free: 29.88 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.000192/0.01537, allocations: 274.8 kB / 0.6591 GB, free: 29.66 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004432/0.01581, allocations: 68.2 kB / 0.6591 GB, free: 29.64 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00211/0.01792, allocations: 0.7764 MB / 0.6599 GB, free: 29.12 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001004/0.01802, allocations: 131.2 kB / 0.66 GB, free: 29.05 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 8.303e-05/0.01811, allocations: 35.61 kB / 0.6601 GB, free: 29.03 MB / 0.5262 GB Notification: Performance of SimCode: time 6.51e-07/0.01811, allocations: 0 / 0.6601 GB, free: 29.03 MB / 0.5262 GB Notification: Performance of Templates: time 0.005218/0.02333, allocations: 3.146 MB / 0.6631 GB, free: 28.79 MB / 0.5262 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel > Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 6.181329732062295]