Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.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 0.0009549/0.0009549, allocations: 89.08 kB / 19.42 MB, free: 492 kB / 13.93 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 0.001204/0.001204, allocations: 169 kB / 22.73 MB, free: 1.824 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 1.035/1.035, allocations: 177.1 MB / 203.1 MB, free: 5.66 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 1.665/1.665, allocations: 273.5 MB / 0.5205 GB, free: 14.84 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.PKTwoCompartmentModel,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel") translateModel(Pharmacolibrary.Examples.PKTwoCompartmentModel,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 2.555e-06/2.555e-06, allocations: 0 / 0.6462 GB, free: 38.57 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 3.084e-05/3.339e-05, allocations: 2.312 kB / 0.6462 GB, free: 38.56 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.003994/0.004027, allocations: 2.368 MB / 0.6485 GB, free: 37.03 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.001446/0.005473, allocations: 0.6198 MB / 0.6491 GB, free: 36.62 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001457/0.005618, allocations: 2.312 kB / 0.6491 GB, free: 36.62 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 0.0001509/0.005769, allocations: 25.61 kB / 0.6492 GB, free: 36.6 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0002485/0.006018, allocations: 70.12 kB / 0.6492 GB, free: 36.58 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.000271/0.006289, allocations: 67.48 kB / 0.6493 GB, free: 36.54 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0004098/0.006699, allocations: 290.8 kB / 0.6496 GB, free: 36.42 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001684/0.006867, allocations: 45.42 kB / 0.6496 GB, free: 36.39 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002737/0.007141, allocations: 149.6 kB / 0.6498 GB, free: 36.34 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001824/0.007323, allocations: 85.7 kB / 0.6498 GB, free: 36.31 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 4.798e-05/0.007371, allocations: 21.19 kB / 0.6499 GB, free: 36.31 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 4.818e-05/0.007419, allocations: 20.81 kB / 0.6499 GB, free: 36.31 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 4.879e-05/0.007468, allocations: 44.12 kB / 0.6499 GB, free: 36.28 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 0.0001294/0.007597, allocations: 90.81 kB / 0.65 GB, free: 36.24 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0002693/0.007867, allocations: 175.1 kB / 0.6502 GB, free: 36.16 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 2.354e-06/0.007869, allocations: 0 / 0.6502 GB, free: 36.16 MB / 0.5262 GB Notification: Performance of FrontEnd: time 8.92e-07/0.00787, allocations: 1.281 kB / 0.6502 GB, free: 36.16 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 7.674e-06/0.007878, allocations: 1.688 kB / 0.6502 GB, free: 36.16 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: 42 * Number of variables: 42 Notification: Performance of Generate backend data structure: time 0.0008305/0.008708, allocations: 0.6049 MB / 0.6508 GB, free: 35.6 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 4.274e-05/0.008751, allocations: 9.562 kB / 0.6508 GB, free: 35.6 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 9.227e-05/0.008843, allocations: 37.98 kB / 0.6508 GB, free: 35.59 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002373/0.00908, allocations: 174.8 kB / 0.651 GB, free: 35.42 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.325e-05/0.009114, allocations: 16.38 kB / 0.651 GB, free: 35.41 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 5.788e-05/0.009172, allocations: 27.89 kB / 0.651 GB, free: 35.4 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003535/0.009525, allocations: 207 kB / 0.6512 GB, free: 35.27 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 2.095e-05/0.009546, allocations: 6.312 kB / 0.6512 GB, free: 35.27 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.274e-05/0.009569, allocations: 5.656 kB / 0.6512 GB, free: 35.26 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.217e-05/0.009581, allocations: 9.188 kB / 0.6512 GB, free: 35.26 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002382/0.009819, allocations: 148.2 kB / 0.6514 GB, free: 35.18 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0008192/0.01064, allocations: 487.3 kB / 0.6518 GB, free: 34.82 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0003033/0.01094, allocations: 173 kB / 0.652 GB, free: 34.7 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001351/0.01108, allocations: 108.3 kB / 0.6521 GB, free: 34.62 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.839e-05/0.0111, allocations: 4.281 kB / 0.6521 GB, free: 34.62 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003061/0.0114, allocations: 317.6 kB / 0.6524 GB, free: 34.36 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=31): time 2.185e-06/0.0114, allocations: 0 / 0.6524 GB, free: 34.36 MB / 0.5262 GB Notification: Performance of matching and sorting (n=33): time 0.001406/0.01281, allocations: 0.9123 MB / 0.6533 GB, free: 33.71 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 6.297e-05/0.01287, allocations: 221.6 kB / 0.6535 GB, free: 33.46 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001537/0.01303, allocations: 221.9 kB / 0.6537 GB, free: 33.27 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 2.628e-05/0.01305, allocations: 35.91 kB / 0.6538 GB, free: 33.24 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 6.474e-05/0.01312, allocations: 169.5 kB / 0.6539 GB, free: 33.08 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 7.451e-05/0.01319, allocations: 111 kB / 0.654 GB, free: 33 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 9.9e-05/0.01329, allocations: 67.61 kB / 0.6541 GB, free: 32.95 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 7.909e-05/0.01337, allocations: 0.5073 MB / 0.6546 GB, free: 32.45 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001637/0.01353, allocations: 148.5 kB / 0.6547 GB, free: 32.33 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001929/0.01373, allocations: 274.1 kB / 0.655 GB, free: 32.05 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0004512/0.01418, allocations: 497.9 kB / 0.6555 GB, free: 31.61 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.268e-06/0.01418, allocations: 1.031 kB / 0.6555 GB, free: 31.61 MB / 0.5262 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0006055/0.01479, allocations: 460.1 kB / 0.6559 GB, free: 31.31 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 4.287e-05/0.01483, allocations: 93.08 kB / 0.656 GB, free: 31.21 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.805e-06/0.01484, allocations: 4.312 kB / 0.656 GB, free: 31.21 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 2.285e-05/0.01486, allocations: 3.375 kB / 0.656 GB, free: 31.21 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003126/0.01517, allocations: 79.5 kB / 0.6561 GB, free: 31.21 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.163e-05/0.01518, allocations: 4.375 kB / 0.6561 GB, free: 31.21 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001581/0.01534, allocations: 16.81 kB / 0.6561 GB, free: 31.2 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.022e-05/0.01537, allocations: 20.69 kB / 0.6561 GB, free: 31.2 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 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 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 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: 10 * Number of states: 0 () * Number of discrete variables: 21 ($PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.peripheral.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,central.rising,peripheral.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 (46): * Single equations (assignments): 43 * 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 0.00024/0.01561, allocations: 291.4 kB / 0.6564 GB, free: 30.93 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 5.873e-05/0.01567, allocations: 38 kB / 0.6564 GB, free: 30.92 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.087e-05/0.01572, allocations: 24.19 kB / 0.6565 GB, free: 30.9 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.438e-06/0.01573, allocations: 3.406 kB / 0.6565 GB, free: 30.9 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 6.673e-06/0.01573, allocations: 0 / 0.6565 GB, free: 30.9 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.63e-06/0.01574, allocations: 0.9375 kB / 0.6565 GB, free: 30.9 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0009178/0.01666, allocations: 0.7251 MB / 0.6572 GB, free: 30.37 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.915e-06/0.01666, allocations: 3.594 kB / 0.6572 GB, free: 30.37 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002744/0.01693, allocations: 49.66 kB / 0.6572 GB, free: 30.36 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 5.951e-06/0.01694, allocations: 1.094 kB / 0.6572 GB, free: 30.36 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.385e-05/0.01697, allocations: 16.09 kB / 0.6572 GB, free: 30.36 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.499e-06/0.01698, allocations: 1.094 kB / 0.6572 GB, free: 30.36 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.424e-06/0.01698, allocations: 0.5625 kB / 0.6572 GB, free: 30.36 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0008078/0.01779, allocations: 0.6545 MB / 0.6579 GB, free: 29.9 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 2.995e-05/0.01782, allocations: 18.64 kB / 0.6579 GB, free: 29.89 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.953e-05/0.01787, allocations: 17.23 kB / 0.6579 GB, free: 29.88 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001464/0.01802, allocations: 12.34 kB / 0.6579 GB, free: 29.88 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 9.658e-05/0.01811, allocations: 27.59 kB / 0.658 GB, free: 29.88 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.464e-05/0.01814, allocations: 14.09 kB / 0.658 GB, free: 29.88 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 8.186e-05/0.01822, allocations: 156.8 kB / 0.6581 GB, free: 29.75 MB / 0.5262 GB Notification: Performance of sort global known variables: time 1.1e-07/0.01822, allocations: 1.375 kB / 0.6581 GB, free: 29.75 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.000399/0.01862, allocations: 74.06 kB / 0.6582 GB, free: 29.74 MB / 0.5262 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 7 (periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass,peripheral.C,peripheral.AUC,central.C,central.AUC,elim.MExc) * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,periodicDose.pulse.T_start,periodicDose.pulse.count,peripheral.Cmax,peripheral.Cmin,peripheral.rising,central.Cmax,central.Cmin,central.rising) * Number of discrete states: 11 (periodicDose.pulse.count,peripheral.Cmin,$whenCondition5,peripheral.Cmax,$whenCondition4,peripheral.rising,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.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 0.0001082/0.01873, allocations: 113.2 kB / 0.6583 GB, free: 29.64 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.000481/0.01921, allocations: 0.4914 MB / 0.6588 GB, free: 29.25 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 2.114e-06/0.01921, allocations: 0 / 0.6588 GB, free: 29.25 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0002263/0.01943, allocations: 277.9 kB / 0.659 GB, free: 29.03 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004809/0.01992, allocations: 60.45 kB / 0.6591 GB, free: 29.01 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002115/0.02203, allocations: 0.7858 MB / 0.6599 GB, free: 28.5 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 5.947e-05/0.02209, allocations: 90.17 kB / 0.66 GB, free: 28.43 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 0.0001077/0.0222, allocations: 18.27 kB / 0.66 GB, free: 28.42 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 7.127e-05/0.02227, allocations: 26.47 kB / 0.66 GB, free: 28.41 MB / 0.5262 GB Notification: Performance of SimCode: time 8.42e-07/0.02227, allocations: 0 / 0.66 GB, free: 28.41 MB / 0.5262 GB Notification: Performance of Templates: time 0.007055/0.02932, allocations: 3.461 MB / 0.6634 GB, free: 28.12 MB / 0.5262 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 5.002975432667881]