Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PKThreeCompartmentModel.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 0.001004/0.001004, allocations: 91.55 kB / 20.19 MB, free: 4.352 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 0.00139/0.00139, allocations: 169.3 kB / 23.5 MB, free: 1.047 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 0.9114/0.9114, allocations: 177.1 MB / 203.8 MB, free: 5.641 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 1.585/1.585, allocations: 273.5 MB / 0.5213 GB, free: 14.77 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.Examples.PKThreeCompartmentModel,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKThreeCompartmentModel") translateModel(Pharmacolibrary.Examples.PKThreeCompartmentModel,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKThreeCompartmentModel") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.152e-06/1.152e-06, allocations: 0 / 0.647 GB, free: 38.68 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 1.188e-05/1.304e-05, allocations: 2.875 kB / 0.647 GB, free: 38.68 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKThreeCompartmentModel): time 0.002163/0.002177, allocations: 2.681 MB / 0.6496 GB, free: 36.93 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.0007769/0.002953, allocations: 0.6666 MB / 0.6502 GB, free: 36.49 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 8.917e-05/0.003043, allocations: 6.156 kB / 0.6502 GB, free: 36.48 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 0.0001089/0.003151, allocations: 37.81 kB / 0.6503 GB, free: 36.46 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0001699/0.003321, allocations: 100.6 kB / 0.6504 GB, free: 36.43 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001789/0.0035, allocations: 81.83 kB / 0.6505 GB, free: 36.38 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0002593/0.003759, allocations: 386.5 kB / 0.6508 GB, free: 36.19 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001241/0.003884, allocations: 53.98 kB / 0.6509 GB, free: 36.16 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001637/0.004047, allocations: 192.7 kB / 0.6511 GB, free: 36.09 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001333/0.004181, allocations: 114.5 kB / 0.6512 GB, free: 36.05 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 3.596e-05/0.004216, allocations: 25.91 kB / 0.6512 GB, free: 36.05 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 3.345e-05/0.00425, allocations: 28.53 kB / 0.6512 GB, free: 36.05 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 3.973e-05/0.00429, allocations: 61.94 kB / 0.6513 GB, free: 36.01 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 9.176e-05/0.004381, allocations: 117.8 kB / 0.6514 GB, free: 35.96 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0002091/0.004591, allocations: 223.5 kB / 0.6516 GB, free: 35.86 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 1.844e-06/0.004592, allocations: 5.5 kB / 0.6516 GB, free: 35.86 MB / 0.5262 GB Notification: Performance of FrontEnd: time 7.52e-07/0.004593, allocations: 0 / 0.6516 GB, free: 35.86 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 5.35e-06/0.004599, allocations: 0 / 0.6516 GB, free: 35.86 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: 58 * Number of variables: 58 Notification: Performance of Generate backend data structure: time 0.0006014/0.0052, allocations: 0.7016 MB / 0.6523 GB, free: 35.23 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 3.341e-05/0.005233, allocations: 11.25 kB / 0.6523 GB, free: 35.23 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 7.591e-05/0.005309, allocations: 51.44 kB / 0.6524 GB, free: 35.21 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001749/0.005484, allocations: 196.4 kB / 0.6525 GB, free: 35.03 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.69e-05/0.005501, allocations: 21.69 kB / 0.6526 GB, free: 35.02 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 3.687e-05/0.005538, allocations: 26.97 kB / 0.6526 GB, free: 35.02 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002599/0.005798, allocations: 277.6 kB / 0.6529 GB, free: 34.84 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.635e-05/0.005814, allocations: 14.42 kB / 0.6529 GB, free: 34.83 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.731e-05/0.005831, allocations: 12.19 kB / 0.6529 GB, free: 34.82 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.466e-06/0.00584, allocations: 4 kB / 0.6529 GB, free: 34.82 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000182/0.006022, allocations: 208.8 kB / 0.6531 GB, free: 34.71 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005903/0.006612, allocations: 0.5659 MB / 0.6536 GB, free: 34.32 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0002078/0.00682, allocations: 239.9 kB / 0.6539 GB, free: 34.16 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 9.378e-05/0.006914, allocations: 146.2 kB / 0.654 GB, free: 34.04 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.127e-05/0.006925, allocations: 5.812 kB / 0.654 GB, free: 34.04 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002328/0.007158, allocations: 446.8 kB / 0.6544 GB, free: 33.67 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=42): time 1.753e-06/0.00716, allocations: 1.125 kB / 0.6544 GB, free: 33.67 MB / 0.5262 GB Notification: Performance of matching and sorting (n=45): time 0.001137/0.008296, allocations: 1.246 MB / 0.6557 GB, free: 32.8 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 4.453e-05/0.008341, allocations: 300.9 kB / 0.6559 GB, free: 32.46 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000128/0.008469, allocations: 231.2 kB / 0.6562 GB, free: 32.27 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 2.498e-05/0.008494, allocations: 38.5 kB / 0.6562 GB, free: 32.24 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 5.594e-05/0.00855, allocations: 182.1 kB / 0.6564 GB, free: 32.07 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 7.439e-05/0.008624, allocations: 151.6 kB / 0.6565 GB, free: 31.95 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 9.973e-05/0.008724, allocations: 92.02 kB / 0.6566 GB, free: 31.89 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 5.956e-05/0.008783, allocations: 0.5131 MB / 0.6571 GB, free: 31.39 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001576/0.008941, allocations: 201.4 kB / 0.6573 GB, free: 31.23 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001954/0.009136, allocations: 350.5 kB / 0.6576 GB, free: 30.89 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0004492/0.009586, allocations: 0.6567 MB / 0.6583 GB, free: 30.29 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.745e-06/0.009588, allocations: 2.344 kB / 0.6583 GB, free: 30.29 MB / 0.5262 GB Notification: Performance of matching and sorting (n=66) (initialization): time 0.0004128/0.01, allocations: 0.5882 MB / 0.6589 GB, free: 29.91 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 3.209e-05/0.01003, allocations: 120.3 kB / 0.659 GB, free: 29.78 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.402e-06/0.01004, allocations: 2.812 kB / 0.659 GB, free: 29.78 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.465e-05/0.01005, allocations: 8.562 kB / 0.659 GB, free: 29.78 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002195/0.01027, allocations: 104.1 kB / 0.6591 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.077e-05/0.01028, allocations: 5.562 kB / 0.6591 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001112/0.0104, allocations: 22.73 kB / 0.6591 GB, free: 29.76 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.94e-05/0.01042, allocations: 20.78 kB / 0.6591 GB, free: 29.75 MB / 0.5262 GB Warning: Assuming fixed start value for the following 14 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 peripheral.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real peripheral2.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real peripheral.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real peripheral.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real central.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real central.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real peripheral2.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real peripheral2.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real peripheral2.rising:DISCRETE(fixed = true protected = true ) type: Boolean central.rising:DISCRETE(fixed = true protected = true ) type: Boolean peripheral.rising:DISCRETE(fixed = true protected = true ) type: Boolean Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 13 * Number of states: 0 () * Number of discrete variables: 29 ($PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.peripheral2.Cmin,peripheral2.Cmin,$PRE.peripheral2.Cmax,peripheral2.Cmax,$PRE.peripheral2.rising,$PRE.central.rising,$PRE.peripheral.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,peripheral2.rising,central.rising,peripheral.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,$whenCondition7,$whenCondition6,$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 (62): * Single equations (assignments): 58 * Array equations: 0 * Algorithm blocks: 4 * 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 0.0001709/0.01059, allocations: 345.8 kB / 0.6595 GB, free: 29.45 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 4.125e-05/0.01063, allocations: 51.8 kB / 0.6595 GB, free: 29.43 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.526e-05/0.01066, allocations: 34.69 kB / 0.6595 GB, free: 29.4 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.548e-06/0.01067, allocations: 0 / 0.6595 GB, free: 29.4 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 9.92e-07/0.01067, allocations: 0 / 0.6595 GB, free: 29.4 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 2.096e-05/0.01069, allocations: 22.41 kB / 0.6596 GB, free: 29.39 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.776e-05/0.01073, allocations: 16.44 kB / 0.6596 GB, free: 29.38 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.3e-05/0.0108, allocations: 17.5 kB / 0.6596 GB, free: 29.38 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.748e-05/0.01087, allocations: 41.28 kB / 0.6596 GB, free: 29.36 MB / 0.5262 GB Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.0005083/0.01138, allocations: 0.6371 MB / 0.6603 GB, free: 28.95 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.0005384/0.01191, allocations: 0.9639 MB / 0.6612 GB, free: 28.25 MB / 0.5262 GB Notification: Performance of postOpt setEvaluationStage (simulation): time 0.0001428/0.01206, allocations: 213.8 kB / 0.6614 GB, free: 28.11 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 5.311e-05/0.01211, allocations: 166.2 kB / 0.6616 GB, free: 27.98 MB / 0.5262 GB Notification: Performance of Backend: time 3.81e-07/0.01211, allocations: 0 / 0.6616 GB, free: 27.98 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0004645/0.01257, allocations: 0.5906 MB / 0.6621 GB, free: 27.48 MB / 0.5262 GB Notification: Performance of SimCode: time 0.001363/0.01394, allocations: 1.668 MB / 0.6638 GB, free: 26.06 MB / 0.5262 GB Notification: Performance of Templates: time 0.00573/0.01967, allocations: 4.661 MB / 0.6683 GB, free: 25.69 MB / 0.5262 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKThreeCompartmentModel.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKThreeCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKThreeCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKThreeCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKThreeCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKThreeCompartmentModel -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKThreeCompartmentModel.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 4.642681885976344]