Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_2C_IVMidazolam.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 0.001018/0.001018, allocations: 84.53 kB / 19.93 MB, free: 4.605 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 0.0009454/0.0009454, allocations: 173.9 kB / 23.21 MB, free: 1.328 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 0.9609/0.9609, allocations: 177.1 MB / 203.5 MB, free: 5.742 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 1.62/1.62, allocations: 273.5 MB / 0.5209 GB, free: 15 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.PK_2C_IVMidazolam,tolerance=1e-08,outputFormat="empty",numberOfIntervals=43200,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_2C_IVMidazolam") translateModel(Pharmacolibrary.Examples.PK_2C_IVMidazolam,tolerance=1e-08,outputFormat="empty",numberOfIntervals=43200,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_2C_IVMidazolam") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.824e-06/1.824e-06, allocations: 0 / 0.7558 GB, free: 10.74 MB / 0.5887 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.007e-05/2.189e-05, allocations: 2.281 kB / 0.7558 GB, free: 10.74 MB / 0.5887 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_2C_IVMidazolam): time 0.002703/0.002725, allocations: 2.521 MB / 0.7582 GB, free: 8.23 MB / 0.5887 GB Notification: Performance of NFInst.instExpressions: time 0.001487/0.004212, allocations: 1.173 MB / 0.7594 GB, free: 7.062 MB / 0.5887 GB Notification: Performance of NFInst.updateImplicitVariability: time 9.813e-05/0.00431, allocations: 4 kB / 0.7594 GB, free: 7.059 MB / 0.5887 GB Notification: Performance of NFTyping.typeComponents: time 0.0002951/0.004605, allocations: 220.4 kB / 0.7596 GB, free: 6.844 MB / 0.5887 GB Notification: Performance of NFTyping.typeBindings: time 0.0003406/0.004945, allocations: 243.4 kB / 0.7598 GB, free: 6.637 MB / 0.5887 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001779/0.005123, allocations: 136.2 kB / 0.76 GB, free: 6.504 MB / 0.5887 GB Notification: Performance of NFFlatten.flatten: time 0.0002991/0.005423, allocations: 431.1 kB / 0.7604 GB, free: 6.082 MB / 0.5887 GB Notification: Performance of NFFlatten.resolveConnections: time 8.783e-05/0.00551, allocations: 51.08 kB / 0.7604 GB, free: 6.035 MB / 0.5887 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001727/0.005683, allocations: 231.4 kB / 0.7606 GB, free: 5.809 MB / 0.5887 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001812/0.005864, allocations: 187.6 kB / 0.7608 GB, free: 5.625 MB / 0.5887 GB Notification: Performance of NFPackage.collectConstants: time 3.13e-05/0.005895, allocations: 28 kB / 0.7608 GB, free: 5.598 MB / 0.5887 GB Notification: Performance of NFFlatten.collectFunctions: time 0.0001052/0.006001, allocations: 63.92 kB / 0.7609 GB, free: 5.535 MB / 0.5887 GB Notification: Performance of NFScalarize.scalarize: time 7.803e-05/0.006079, allocations: 79.67 kB / 0.761 GB, free: 5.457 MB / 0.5887 GB Notification: Performance of NFVerifyModel.verify: time 8.303e-05/0.006162, allocations: 111.7 kB / 0.7611 GB, free: 5.348 MB / 0.5887 GB Notification: Performance of NFConvertDAE.convert: time 0.000306/0.006468, allocations: 374.8 kB / 0.7614 GB, free: 4.98 MB / 0.5887 GB Notification: Performance of FrontEnd - DAE generated: time 1.333e-06/0.006469, allocations: 0 / 0.7614 GB, free: 4.98 MB / 0.5887 GB Notification: Performance of FrontEnd: time 1.553e-06/0.006471, allocations: 3.984 kB / 0.7614 GB, free: 4.977 MB / 0.5887 GB Notification: Performance of Transformations before backend: time 3.917e-06/0.006475, allocations: 8 kB / 0.7614 GB, free: 4.969 MB / 0.5887 GB Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 46 * Number of variables: 46 Notification: Performance of Generate backend data structure: time 0.0006888/0.007163, allocations: 0.6854 MB / 0.7621 GB, free: 4.234 MB / 0.5887 GB Notification: Performance of prepare preOptimizeDAE: time 2.287e-05/0.007186, allocations: 11.97 kB / 0.7621 GB, free: 4.223 MB / 0.5887 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 4.64e-05/0.007233, allocations: 40.7 kB / 0.7622 GB, free: 4.184 MB / 0.5887 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002129/0.007446, allocations: 241.6 kB / 0.7624 GB, free: 3.926 MB / 0.5887 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.465e-05/0.00746, allocations: 20.36 kB / 0.7624 GB, free: 3.906 MB / 0.5887 GB Notification: Performance of preOpt expandDerOperator (simulation): time 2.873e-05/0.007489, allocations: 28.33 kB / 0.7624 GB, free: 3.879 MB / 0.5887 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003133/0.007802, allocations: 292 kB / 0.7627 GB, free: 3.566 MB / 0.5887 GB Notification: Performance of preOpt findStateOrder (simulation): time 9.929e-06/0.007812, allocations: 8 kB / 0.7627 GB, free: 3.559 MB / 0.5887 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.279e-05/0.007825, allocations: 4 kB / 0.7627 GB, free: 3.555 MB / 0.5887 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.081e-06/0.007831, allocations: 8 kB / 0.7627 GB, free: 3.547 MB / 0.5887 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002595/0.008091, allocations: 235.6 kB / 0.763 GB, free: 3.305 MB / 0.5887 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005419/0.008632, allocations: 0.5869 MB / 0.7635 GB, free: 2.684 MB / 0.5887 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0003315/0.008964, allocations: 288.5 kB / 0.7638 GB, free: 2.371 MB / 0.5887 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001487/0.009113, allocations: 165 kB / 0.764 GB, free: 2.191 MB / 0.5887 GB Notification: Performance of preOpt evalFunc (simulation): time 1.384e-05/0.009126, allocations: 4 kB / 0.764 GB, free: 2.188 MB / 0.5887 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000302/0.009428, allocations: 410.9 kB / 0.7644 GB, free: 1.73 MB / 0.5887 GB Notification: Performance of pre-optimization done (n=36): time 1.242e-06/0.00943, allocations: 0 / 0.7644 GB, free: 1.73 MB / 0.5887 GB Notification: Performance of matching and sorting (n=38): time 0.001299/0.01073, allocations: 1.192 MB / 0.7655 GB, free: 456 kB / 0.5887 GB Notification: Performance of inlineWhenForInitialization (initialization): time 9.595e-05/0.01082, allocations: 251.2 kB / 0.7658 GB, free: 148 kB / 0.5887 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003005/0.01113, allocations: 432.5 kB / 0.7662 GB, free: 15.71 MB / 0.6043 GB Notification: Performance of collectPreVariables (initialization): time 2.266e-05/0.01115, allocations: 33.7 kB / 0.7662 GB, free: 15.67 MB / 0.6043 GB Notification: Performance of collectInitialEqns (initialization): time 7.976e-05/0.01123, allocations: 176.9 kB / 0.7664 GB, free: 15.5 MB / 0.6043 GB Notification: Performance of collectInitialBindings (initialization): time 6.38e-05/0.01129, allocations: 119 kB / 0.7665 GB, free: 15.38 MB / 0.6043 GB Notification: Performance of simplifyInitialFunctions (initialization): time 6.716e-05/0.01136, allocations: 73.69 kB / 0.7666 GB, free: 15.3 MB / 0.6043 GB Notification: Performance of setup shared object (initialization): time 9.469e-05/0.01145, allocations: 358.8 kB / 0.7669 GB, free: 14.94 MB / 0.6043 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001969/0.01165, allocations: 207.4 kB / 0.7671 GB, free: 14.72 MB / 0.6043 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002259/0.01188, allocations: 322.9 kB / 0.7674 GB, free: 14.34 MB / 0.6043 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0007923/0.01267, allocations: 0.7909 MB / 0.7682 GB, free: 13.45 MB / 0.6043 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.164e-06/0.01267, allocations: 0 / 0.7682 GB, free: 13.45 MB / 0.6043 GB Notification: Performance of matching and sorting (n=56) (initialization): time 0.000535/0.01321, allocations: 0.6005 MB / 0.7688 GB, free: 12.81 MB / 0.6043 GB Notification: Performance of prepare postOptimizeDAE: time 5.182e-05/0.01326, allocations: 93.09 kB / 0.7689 GB, free: 12.7 MB / 0.6043 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.522e-06/0.01326, allocations: 0 / 0.7689 GB, free: 12.7 MB / 0.6043 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.549e-05/0.01328, allocations: 8.312 kB / 0.7689 GB, free: 12.69 MB / 0.6043 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001861/0.01347, allocations: 87.83 kB / 0.769 GB, free: 12.61 MB / 0.6043 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.947e-06/0.01347, allocations: 8 kB / 0.769 GB, free: 12.6 MB / 0.6043 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001188/0.01359, allocations: 20.3 kB / 0.769 GB, free: 12.58 MB / 0.6043 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.02e-05/0.01361, allocations: 16 kB / 0.769 GB, free: 12.56 MB / 0.6043 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: 12 * Number of states: 0 () * Number of discrete variables: 26 ($PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.CTT_MidazolamC.nextTimeEvent,$whenCondition1,CTT_MidazolamC.nextTimeEventScaled,$PRE.CTT_MidazolamC.nextTimeEventScaled,CTT_MidazolamC.nextTimeEvent,$PRE.central.rising,$PRE.peripheral.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,central.rising,peripheral.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,$whenCondition6,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (53): * Single equations (assignments): 50 * 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 0.0002139/0.01383, allocations: 289.3 kB / 0.7693 GB, free: 12.26 MB / 0.6043 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.803e-05/0.01387, allocations: 47.66 kB / 0.7693 GB, free: 12.21 MB / 0.6043 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001649/0.01403, allocations: 129.7 kB / 0.7694 GB, free: 12.08 MB / 0.6043 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.906e-06/0.01403, allocations: 8 kB / 0.7695 GB, free: 12.07 MB / 0.6043 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 2.044e-06/0.01404, allocations: 0 / 0.7695 GB, free: 12.07 MB / 0.6043 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.907e-06/0.01404, allocations: 0 / 0.7695 GB, free: 12.07 MB / 0.6043 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007222/0.01476, allocations: 0.8109 MB / 0.7702 GB, free: 11.2 MB / 0.6043 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.525e-06/0.01476, allocations: 4 kB / 0.7702 GB, free: 11.2 MB / 0.6043 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001552/0.01492, allocations: 59.91 kB / 0.7703 GB, free: 11.14 MB / 0.6043 GB Notification: Performance of postOpt tearingSystem (simulation): time 2.224e-06/0.01492, allocations: 0 / 0.7703 GB, free: 11.14 MB / 0.6043 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.039e-05/0.01494, allocations: 11.98 kB / 0.7703 GB, free: 11.13 MB / 0.6043 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.515e-06/0.01494, allocations: 8 kB / 0.7703 GB, free: 11.12 MB / 0.6043 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 7.52e-07/0.01495, allocations: 0 / 0.7703 GB, free: 11.12 MB / 0.6043 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0007246/0.01567, allocations: 0.8044 MB / 0.7711 GB, free: 10.26 MB / 0.6043 GB Notification: Performance of postOpt removeConstants (simulation): time 3.36e-05/0.0157, allocations: 39.75 kB / 0.7711 GB, free: 10.22 MB / 0.6043 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.791e-05/0.01574, allocations: 12 kB / 0.7712 GB, free: 10.21 MB / 0.6043 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 9.845e-05/0.01584, allocations: 15.98 kB / 0.7712 GB, free: 10.2 MB / 0.6043 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 8.226e-05/0.01592, allocations: 39.59 kB / 0.7712 GB, free: 10.16 MB / 0.6043 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.131e-05/0.01594, allocations: 20.06 kB / 0.7712 GB, free: 10.14 MB / 0.6043 GB Notification: Performance of sorting global known variables: time 0.0001991/0.01614, allocations: 319 kB / 0.7715 GB, free: 9.832 MB / 0.6043 GB Notification: Performance of sort global known variables: time 8e-08/0.01614, allocations: 0 / 0.7715 GB, free: 9.832 MB / 0.6043 GB Notification: Performance of remove unused functions: time 0.0002499/0.01639, allocations: 91.94 kB / 0.7716 GB, free: 9.742 MB / 0.6043 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 2 * Number of states: 7 (periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass,peripheral.C,peripheral.AUC,central.C,central.AUC,elim.MExc) * Number of discrete variables: 16 ($whenCondition1,CTT_MidazolamC.nextTimeEvent,CTT_MidazolamC.nextTimeEventScaled,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,$whenCondition6,periodicDose.pulse.T_start,periodicDose.pulse.count,peripheral.Cmax,peripheral.Cmin,peripheral.rising,central.Cmax,central.Cmin,central.rising) * Number of discrete states: 13 (periodicDose.pulse.count,peripheral.Cmin,$whenCondition6,peripheral.Cmax,$whenCondition5,peripheral.rising,central.Cmin,$whenCondition4,central.Cmax,$whenCondition3,central.rising,CTT_MidazolamC.nextTimeEvent,CTT_MidazolamC.nextTimeEventScaled) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (33): * Single equations (assignments): 27 * Array equations: 0 * Algorithm blocks: 2 * Record equations: 0 * When equations: 4 * 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 0.001138/0.01753, allocations: 458.9 kB / 0.7721 GB, free: 9.492 MB / 0.6043 GB Notification: Performance of simCode: created initialization part: time 0.0005097/0.01804, allocations: 0.6043 MB / 0.7727 GB, free: 8.82 MB / 0.6043 GB Notification: Performance of simCode: created event and clocks part: time 1.893e-06/0.01804, allocations: 0 / 0.7727 GB, free: 8.82 MB / 0.6043 GB Notification: Performance of simCode: created simulation system equations: time 0.0002356/0.01828, allocations: 322 kB / 0.773 GB, free: 8.469 MB / 0.6043 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003314/0.01861, allocations: 100.6 kB / 0.7731 GB, free: 8.375 MB / 0.6043 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001019/0.01963, allocations: 1.018 MB / 0.774 GB, free: 7.324 MB / 0.6043 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.00012/0.01975, allocations: 202.5 kB / 0.7742 GB, free: 7.109 MB / 0.6043 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 6.023e-05/0.01981, allocations: 36.5 kB / 0.7743 GB, free: 7.074 MB / 0.6043 GB Notification: Performance of SimCode: time 5.31e-07/0.01981, allocations: 0 / 0.7743 GB, free: 7.074 MB / 0.6043 GB Notification: Performance of Templates: time 0.004823/0.02463, allocations: 5.022 MB / 0.7792 GB, free: 2.18 MB / 0.6043 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_2C_IVMidazolam.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_2C_IVMidazolam.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_2C_IVMidazolam.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_2C_IVMidazolam.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_2C_IVMidazolam.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_2C_IVMidazolam > Pharmacolibrary_Pharmacolibrary.Examples.PK_2C_IVMidazolam.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 6.957589728059247]