Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.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 0.001008/0.001008, allocations: 80.88 kB / 19.94 MB, free: 4.547 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 0.001024/0.001024, allocations: 181 kB / 23.36 MB, free: 1.133 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 1.024/1.024, allocations: 177.1 MB / 203.8 MB, free: 5.488 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 1.646/1.646, allocations: 273.5 MB / 0.5213 GB, free: 14.7 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.PKTwoCompartmentModelOral,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral") translateModel(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.493e-06/1.493e-06, allocations: 0 / 0.5954 GB, free: 2.75 MB / 0.5105 GB Notification: Performance of FrontEnd - Absyn->SCode: time 1.144e-05/1.294e-05, allocations: 2.312 kB / 0.5954 GB, free: 2.746 MB / 0.5105 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral): time 0.002402/0.002415, allocations: 2.452 MB / 0.5978 GB, free: 324 kB / 0.5105 GB Notification: Performance of NFInst.instExpressions: time 0.0008592/0.003274, allocations: 0.6116 MB / 0.5984 GB, free: 15.71 MB / 0.5261 GB Notification: Performance of NFInst.updateImplicitVariability: time 8.156e-05/0.003356, allocations: 8 kB / 0.5984 GB, free: 15.7 MB / 0.5261 GB Notification: Performance of NFTyping.typeComponents: time 5.39e-05/0.00341, allocations: 23.72 kB / 0.5985 GB, free: 15.68 MB / 0.5261 GB Notification: Performance of NFTyping.typeBindings: time 0.0001944/0.003604, allocations: 82.72 kB / 0.5985 GB, free: 15.62 MB / 0.5261 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001793/0.003784, allocations: 59.86 kB / 0.5986 GB, free: 15.56 MB / 0.5261 GB Notification: Performance of NFFlatten.flatten: time 0.0002355/0.004019, allocations: 303.8 kB / 0.5989 GB, free: 15.31 MB / 0.5261 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001205/0.004139, allocations: 46.72 kB / 0.5989 GB, free: 15.27 MB / 0.5261 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001713/0.004311, allocations: 159.7 kB / 0.5991 GB, free: 15.11 MB / 0.5261 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001266/0.004437, allocations: 87.7 kB / 0.5992 GB, free: 15.02 MB / 0.5261 GB Notification: Performance of NFPackage.collectConstants: time 3.091e-05/0.004468, allocations: 28 kB / 0.5992 GB, free: 15 MB / 0.5261 GB Notification: Performance of NFFlatten.collectFunctions: time 2.403e-05/0.004492, allocations: 20 kB / 0.5992 GB, free: 14.98 MB / 0.5261 GB Notification: Performance of NFScalarize.scalarize: time 4.024e-05/0.004533, allocations: 47.83 kB / 0.5993 GB, free: 14.93 MB / 0.5261 GB Notification: Performance of NFVerifyModel.verify: time 7.498e-05/0.004608, allocations: 91.81 kB / 0.5993 GB, free: 14.84 MB / 0.5261 GB Notification: Performance of NFConvertDAE.convert: time 0.0001786/0.004786, allocations: 171.4 kB / 0.5995 GB, free: 14.67 MB / 0.5261 GB Notification: Performance of FrontEnd - DAE generated: time 3.186e-06/0.004789, allocations: 3.984 kB / 0.5995 GB, free: 14.67 MB / 0.5261 GB Notification: Performance of FrontEnd: time 6.31e-07/0.00479, allocations: 0 / 0.5995 GB, free: 14.67 MB / 0.5261 GB Notification: Performance of Transformations before backend: time 3.326e-06/0.004793, allocations: 0 / 0.5995 GB, free: 14.67 MB / 0.5261 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 0.0008264/0.00562, allocations: 0.497 MB / 0.6 GB, free: 14.13 MB / 0.5261 GB Notification: Performance of prepare preOptimizeDAE: time 2.736e-05/0.005647, allocations: 8.031 kB / 0.6 GB, free: 14.12 MB / 0.5261 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 4.71e-05/0.005694, allocations: 32.91 kB / 0.6 GB, free: 14.09 MB / 0.5261 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001543/0.005848, allocations: 149.4 kB / 0.6002 GB, free: 13.92 MB / 0.5261 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.829e-05/0.005867, allocations: 16.38 kB / 0.6002 GB, free: 13.9 MB / 0.5261 GB Notification: Performance of preOpt expandDerOperator (simulation): time 2.913e-05/0.005896, allocations: 20.38 kB / 0.6002 GB, free: 13.88 MB / 0.5261 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001992/0.006095, allocations: 211 kB / 0.6004 GB, free: 13.66 MB / 0.5261 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.558e-05/0.006111, allocations: 11.94 kB / 0.6004 GB, free: 13.64 MB / 0.5261 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.153e-05/0.006122, allocations: 4 kB / 0.6004 GB, free: 13.64 MB / 0.5261 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.082e-06/0.006128, allocations: 8 kB / 0.6004 GB, free: 13.63 MB / 0.5261 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001167/0.006245, allocations: 129.2 kB / 0.6006 GB, free: 13.5 MB / 0.5261 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004387/0.006684, allocations: 344.4 kB / 0.6009 GB, free: 13.14 MB / 0.5261 GB Notification: Performance of preOpt comSubExp (simulation): time 0.000133/0.006817, allocations: 150 kB / 0.601 GB, free: 12.98 MB / 0.5261 GB Notification: Performance of preOpt resolveLoops (simulation): time 5.624e-05/0.006873, allocations: 96.25 kB / 0.6011 GB, free: 12.87 MB / 0.5261 GB Notification: Performance of preOpt evalFunc (simulation): time 9.779e-06/0.006883, allocations: 4 kB / 0.6011 GB, free: 12.87 MB / 0.5261 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002011/0.007084, allocations: 313.3 kB / 0.6014 GB, free: 12.51 MB / 0.5261 GB Notification: Performance of pre-optimization done (n=30): time 1.723e-06/0.007086, allocations: 0 / 0.6014 GB, free: 12.51 MB / 0.5261 GB Notification: Performance of matching and sorting (n=32): time 0.0007541/0.00784, allocations: 0.7643 MB / 0.6022 GB, free: 11.66 MB / 0.5261 GB Notification: Performance of inlineWhenForInitialization (initialization): time 7.315e-05/0.007913, allocations: 217.6 kB / 0.6024 GB, free: 11.39 MB / 0.5261 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.765e-05/0.00801, allocations: 164.7 kB / 0.6025 GB, free: 11.22 MB / 0.5261 GB Notification: Performance of collectPreVariables (initialization): time 1.907e-05/0.00803, allocations: 33.7 kB / 0.6026 GB, free: 11.18 MB / 0.5261 GB Notification: Performance of collectInitialEqns (initialization): time 5.009e-05/0.00808, allocations: 124.9 kB / 0.6027 GB, free: 11.06 MB / 0.5261 GB Notification: Performance of collectInitialBindings (initialization): time 5.339e-05/0.008133, allocations: 103.1 kB / 0.6028 GB, free: 10.96 MB / 0.5261 GB Notification: Performance of simplifyInitialFunctions (initialization): time 6.642e-05/0.008199, allocations: 69.94 kB / 0.6029 GB, free: 10.88 MB / 0.5261 GB Notification: Performance of setup shared object (initialization): time 8.565e-05/0.008285, allocations: 334.8 kB / 0.6032 GB, free: 10.54 MB / 0.5261 GB Notification: Performance of preBalanceInitialSystem (initialization): time 8.046e-05/0.008366, allocations: 135.3 kB / 0.6033 GB, free: 10.39 MB / 0.5261 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001161/0.008482, allocations: 215 kB / 0.6035 GB, free: 10.13 MB / 0.5261 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0002612/0.008743, allocations: 429.5 kB / 0.6039 GB, free: 9.633 MB / 0.5261 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.814e-06/0.008745, allocations: 0 / 0.6039 GB, free: 9.633 MB / 0.5261 GB Notification: Performance of matching and sorting (n=47) (initialization): time 0.0002572/0.009002, allocations: 364 kB / 0.6043 GB, free: 9.238 MB / 0.5261 GB Notification: Performance of prepare postOptimizeDAE: time 3.889e-05/0.009041, allocations: 89.36 kB / 0.6043 GB, free: 9.133 MB / 0.5261 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.33e-06/0.009046, allocations: 8 kB / 0.6044 GB, free: 9.125 MB / 0.5261 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.204e-05/0.009058, allocations: 4 kB / 0.6044 GB, free: 9.121 MB / 0.5261 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002058/0.009264, allocations: 88.53 kB / 0.6044 GB, free: 9.035 MB / 0.5261 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 4.648e-06/0.009268, allocations: 4 kB / 0.6044 GB, free: 9.031 MB / 0.5261 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.349e-05/0.009352, allocations: 19.98 kB / 0.6045 GB, free: 9.012 MB / 0.5261 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.434e-05/0.009366, allocations: 12 kB / 0.6045 GB, free: 9 MB / 0.5261 GB Warning: Assuming fixed start value for the following 10 variables: central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real peripheral.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real periodicDose1.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real periodicDose1.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" 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 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 peripheral.rising:DISCRETE(fixed = true protected = true ) type: Boolean central.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 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.periodicDose1.pulse.count,$PRE.periodicDose1.pulse.T_start,$PRE.peripheral.rising,$PRE.central.rising,periodicDose1.pulse.count,periodicDose1.pulse.T_start,peripheral.rising,central.rising,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (44): * Single equations (assignments): 41 * 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 0.0001654/0.009532, allocations: 245 kB / 0.6047 GB, free: 8.738 MB / 0.5261 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 2.708e-05/0.009559, allocations: 27.98 kB / 0.6047 GB, free: 8.711 MB / 0.5261 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.127e-05/0.00959, allocations: 21.97 kB / 0.6048 GB, free: 8.688 MB / 0.5261 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.194e-06/0.009592, allocations: 0 / 0.6048 GB, free: 8.688 MB / 0.5261 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 4.028e-06/0.009596, allocations: 3.984 kB / 0.6048 GB, free: 8.684 MB / 0.5261 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.378e-06/0.009601, allocations: 4 kB / 0.6048 GB, free: 8.68 MB / 0.5261 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000372/0.009973, allocations: 497 kB / 0.6052 GB, free: 8.148 MB / 0.5261 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.643e-06/0.009974, allocations: 0 / 0.6052 GB, free: 8.148 MB / 0.5261 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001663/0.01014, allocations: 67.02 kB / 0.6053 GB, free: 8.086 MB / 0.5261 GB Notification: Performance of postOpt tearingSystem (simulation): time 3.346e-06/0.01014, allocations: 4 kB / 0.6053 GB, free: 8.082 MB / 0.5261 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.415e-05/0.01016, allocations: 7.984 kB / 0.6053 GB, free: 8.074 MB / 0.5261 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.633e-06/0.01016, allocations: 7.25 kB / 0.6053 GB, free: 8.07 MB / 0.5261 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.142e-06/0.01016, allocations: 0 / 0.6053 GB, free: 8.07 MB / 0.5261 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002914/0.01045, allocations: 0.4886 MB / 0.6058 GB, free: 7.531 MB / 0.5261 GB Notification: Performance of postOpt removeConstants (simulation): time 1.781e-05/0.01047, allocations: 15.91 kB / 0.6058 GB, free: 7.516 MB / 0.5261 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.562e-05/0.0105, allocations: 8 kB / 0.6058 GB, free: 7.508 MB / 0.5261 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.731e-05/0.01057, allocations: 19.92 kB / 0.6058 GB, free: 7.488 MB / 0.5261 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 5.092e-05/0.01062, allocations: 27.94 kB / 0.6059 GB, free: 7.461 MB / 0.5261 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.185e-05/0.01064, allocations: 12 kB / 0.6059 GB, free: 7.449 MB / 0.5261 GB Notification: Performance of sorting global known variables: time 3.047e-05/0.01067, allocations: 36.81 kB / 0.6059 GB, free: 7.41 MB / 0.5261 GB Notification: Performance of sort global known variables: time 5e-08/0.01067, allocations: 0 / 0.6059 GB, free: 7.41 MB / 0.5261 GB Notification: Performance of remove unused functions: time 0.0001861/0.01085, allocations: 75.94 kB / 0.606 GB, free: 7.336 MB / 0.5261 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 6 (central.C,central.AUC,peripheral.C,peripheral.AUC,periodicDose1.TotalCumulativeMass,periodicDose1.variableDose.TotalCumulativeMass) * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,central.Cmax,central.Cmin,central.rising,peripheral.Cmax,peripheral.Cmin,peripheral.rising,periodicDose1.pulse.T_start,periodicDose1.pulse.count) * Number of discrete states: 11 (periodicDose1.pulse.count,peripheral.Cmin,$whenCondition3,peripheral.Cmax,$whenCondition2,peripheral.rising,central.Cmin,$whenCondition5,central.Cmax,$whenCondition4,central.rising) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (26): * Single equations (assignments): 22 * 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 7.947e-05/0.01093, allocations: 102.2 kB / 0.6061 GB, free: 7.23 MB / 0.5261 GB Notification: Performance of simCode: created initialization part: time 0.0005714/0.0115, allocations: 460.7 kB / 0.6065 GB, free: 6.711 MB / 0.5261 GB Notification: Performance of simCode: created event and clocks part: time 3.206e-06/0.01151, allocations: 0 / 0.6065 GB, free: 6.711 MB / 0.5261 GB Notification: Performance of simCode: created simulation system equations: time 0.0001376/0.01164, allocations: 261.3 kB / 0.6068 GB, free: 6.422 MB / 0.5261 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002335/0.01188, allocations: 70.09 kB / 0.6068 GB, free: 6.359 MB / 0.5261 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001125/0.013, allocations: 0.6547 MB / 0.6075 GB, free: 5.672 MB / 0.5261 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 4.93e-05/0.01305, allocations: 84.92 kB / 0.6076 GB, free: 5.57 MB / 0.5261 GB Notification: Performance of simCode: alias equations: time 7.704e-05/0.01313, allocations: 21.95 kB / 0.6076 GB, free: 5.547 MB / 0.5261 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001486/0.01328, allocations: 127.3 kB / 0.6077 GB, free: 5.422 MB / 0.5261 GB Notification: Performance of SimCode: time 7.72e-07/0.01328, allocations: 0 / 0.6077 GB, free: 5.422 MB / 0.5261 GB Notification: Performance of Templates: time 0.005017/0.01829, allocations: 3.76 MB / 0.6114 GB, free: 1.863 MB / 0.5261 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral -abortSlowSimulation -alarm=240 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 4.8274060850963]