Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Lithium2.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 0.00111/0.00111, allocations: 84.53 kB / 19.93 MB, free: 4.609 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 0.001036/0.001036, allocations: 173.9 kB / 23.21 MB, free: 1.332 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 0.9615/0.9615, allocations: 177.2 MB / 203.5 MB, free: 5.738 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 1.602/1.602, allocations: 273.5 MB / 0.5209 GB, free: 15.03 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_1C_Lithium2,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Lithium2") translateModel(Pharmacolibrary.Examples.PK_1C_Lithium2,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Lithium2") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.613e-06/1.613e-06, allocations: 0 / 0.7568 GB, free: 9.699 MB / 0.5887 GB Notification: Performance of FrontEnd - Absyn->SCode: time 3.198e-05/3.359e-05, allocations: 2.281 kB / 0.7568 GB, free: 9.695 MB / 0.5887 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Lithium2): time 0.004369/0.004402, allocations: 3.776 MB / 0.7605 GB, free: 5.938 MB / 0.5887 GB Notification: Performance of NFInst.instExpressions: time 0.001137/0.005539, allocations: 0.7068 MB / 0.7612 GB, free: 5.234 MB / 0.5887 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001212/0.00566, allocations: 4 kB / 0.7612 GB, free: 5.23 MB / 0.5887 GB Notification: Performance of NFTyping.typeComponents: time 0.0001336/0.005794, allocations: 32.95 kB / 0.7612 GB, free: 5.199 MB / 0.5887 GB Notification: Performance of NFTyping.typeBindings: time 0.0002273/0.006021, allocations: 119.2 kB / 0.7613 GB, free: 5.109 MB / 0.5887 GB Notification: Performance of NFTyping.typeClassSections: time 0.0003242/0.006345, allocations: 99.69 kB / 0.7614 GB, free: 5.012 MB / 0.5887 GB Notification: Performance of NFFlatten.flatten: time 0.000333/0.006678, allocations: 374.1 kB / 0.7618 GB, free: 4.645 MB / 0.5887 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001673/0.006845, allocations: 53.39 kB / 0.7618 GB, free: 4.594 MB / 0.5887 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002084/0.007054, allocations: 187.6 kB / 0.762 GB, free: 4.41 MB / 0.5887 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0002283/0.007282, allocations: 119.5 kB / 0.7621 GB, free: 4.293 MB / 0.5887 GB Notification: Performance of NFPackage.collectConstants: time 4.022e-05/0.007322, allocations: 28 kB / 0.7621 GB, free: 4.266 MB / 0.5887 GB Notification: Performance of NFFlatten.collectFunctions: time 3.472e-05/0.007357, allocations: 32 kB / 0.7622 GB, free: 4.234 MB / 0.5887 GB Notification: Performance of NFScalarize.scalarize: time 4.758e-05/0.007405, allocations: 55.77 kB / 0.7622 GB, free: 4.18 MB / 0.5887 GB Notification: Performance of NFVerifyModel.verify: time 0.0001054/0.00751, allocations: 107.8 kB / 0.7623 GB, free: 4.074 MB / 0.5887 GB Notification: Performance of NFConvertDAE.convert: time 0.0003187/0.007829, allocations: 307.1 kB / 0.7626 GB, free: 3.773 MB / 0.5887 GB Notification: Performance of FrontEnd - DAE generated: time 2.885e-06/0.007831, allocations: 0 / 0.7626 GB, free: 3.773 MB / 0.5887 GB Notification: Performance of FrontEnd: time 1.263e-06/0.007833, allocations: 0 / 0.7626 GB, free: 3.773 MB / 0.5887 GB Notification: Performance of Transformations before backend: time 8.086e-06/0.007841, allocations: 3.984 kB / 0.7626 GB, free: 3.77 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: 48 * Number of variables: 48 Notification: Performance of Generate backend data structure: time 0.0008476/0.008688, allocations: 0.5842 MB / 0.7632 GB, free: 3.133 MB / 0.5887 GB Notification: Performance of prepare preOptimizeDAE: time 5.562e-05/0.008744, allocations: 12.03 kB / 0.7632 GB, free: 3.121 MB / 0.5887 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 7.164e-05/0.008816, allocations: 32.75 kB / 0.7632 GB, free: 3.09 MB / 0.5887 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002438/0.009059, allocations: 206.2 kB / 0.7634 GB, free: 2.863 MB / 0.5887 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.001e-05/0.009079, allocations: 20.38 kB / 0.7634 GB, free: 2.844 MB / 0.5887 GB Notification: Performance of preOpt expandDerOperator (simulation): time 4.823e-05/0.009128, allocations: 23.95 kB / 0.7635 GB, free: 2.82 MB / 0.5887 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003656/0.009493, allocations: 297.1 kB / 0.7638 GB, free: 2.508 MB / 0.5887 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.695e-05/0.00951, allocations: 7.5 kB / 0.7638 GB, free: 2.504 MB / 0.5887 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.101e-05/0.009531, allocations: 15.94 kB / 0.7638 GB, free: 2.488 MB / 0.5887 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.013e-06/0.009538, allocations: 4 kB / 0.7638 GB, free: 2.484 MB / 0.5887 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003054/0.009844, allocations: 242.1 kB / 0.764 GB, free: 2.242 MB / 0.5887 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007812/0.01062, allocations: 0.5949 MB / 0.7646 GB, free: 1.609 MB / 0.5887 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0004558/0.01108, allocations: 264.2 kB / 0.7648 GB, free: 1.336 MB / 0.5887 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001708/0.01125, allocations: 160.4 kB / 0.765 GB, free: 1.164 MB / 0.5887 GB Notification: Performance of preOpt evalFunc (simulation): time 2.827e-05/0.01128, allocations: 8.234 kB / 0.765 GB, free: 1.156 MB / 0.5887 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003701/0.01165, allocations: 363.6 kB / 0.7654 GB, free: 0.75 MB / 0.5887 GB Notification: Performance of pre-optimization done (n=34): time 1.964e-06/0.01165, allocations: 0 / 0.7654 GB, free: 0.75 MB / 0.5887 GB Notification: Performance of matching and sorting (n=36): time 0.001437/0.01309, allocations: 1.105 MB / 0.7664 GB, free: 15.55 MB / 0.6043 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0003453/0.01343, allocations: 221.6 kB / 0.7666 GB, free: 15.29 MB / 0.6043 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001803/0.01361, allocations: 225.8 kB / 0.7669 GB, free: 15.06 MB / 0.6043 GB Notification: Performance of collectPreVariables (initialization): time 2.915e-05/0.01364, allocations: 41.7 kB / 0.7669 GB, free: 15.01 MB / 0.6043 GB Notification: Performance of collectInitialEqns (initialization): time 8.537e-05/0.01373, allocations: 144.8 kB / 0.767 GB, free: 14.86 MB / 0.6043 GB Notification: Performance of collectInitialBindings (initialization): time 6.648e-05/0.0138, allocations: 123 kB / 0.7672 GB, free: 14.74 MB / 0.6043 GB Notification: Performance of simplifyInitialFunctions (initialization): time 7.732e-05/0.01387, allocations: 69.69 kB / 0.7672 GB, free: 14.67 MB / 0.6043 GB Notification: Performance of setup shared object (initialization): time 0.0001135/0.01399, allocations: 346.7 kB / 0.7675 GB, free: 14.32 MB / 0.6043 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.000208/0.01419, allocations: 207 kB / 0.7677 GB, free: 14.1 MB / 0.6043 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002469/0.01444, allocations: 316.8 kB / 0.768 GB, free: 13.73 MB / 0.6043 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0007964/0.01524, allocations: 0.7932 MB / 0.7688 GB, free: 12.83 MB / 0.6043 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.144e-06/0.01524, allocations: 0 / 0.7688 GB, free: 12.83 MB / 0.6043 GB Notification: Performance of matching and sorting (n=54) (initialization): time 0.0005558/0.0158, allocations: 0.5797 MB / 0.7694 GB, free: 12.21 MB / 0.6043 GB Notification: Performance of prepare postOptimizeDAE: time 5.675e-05/0.01585, allocations: 93.09 kB / 0.7695 GB, free: 12.1 MB / 0.6043 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.582e-06/0.01586, allocations: 4 kB / 0.7695 GB, free: 12.1 MB / 0.6043 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.387e-05/0.01587, allocations: 4.344 kB / 0.7695 GB, free: 12.09 MB / 0.6043 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001773/0.01605, allocations: 79.89 kB / 0.7696 GB, free: 12.02 MB / 0.6043 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.087e-05/0.01606, allocations: 7.938 kB / 0.7696 GB, free: 12.01 MB / 0.6043 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001145/0.01618, allocations: 27.92 kB / 0.7696 GB, free: 11.98 MB / 0.6043 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.694e-05/0.01619, allocations: 16 kB / 0.7696 GB, free: 11.96 MB / 0.6043 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 periodicDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real periodicDose.absorptionLumen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real periodicDose.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 periodicDose.absorptionLumen.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real periodicDose.absorptionLumen.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real periodicDose.absorptionLumen.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: 12 * Number of states: 0 () * Number of discrete variables: 21 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.periodicDose.absorptionLumen.Cmin,periodicDose.absorptionLumen.Cmin,$PRE.periodicDose.absorptionLumen.Cmax,periodicDose.absorptionLumen.Cmax,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,$PRE.periodicDose.absorptionLumen.rising,$PRE.central.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,periodicDose.absorptionLumen.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 (51): * Single equations (assignments): 48 * 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 0.0002348/0.01643, allocations: 255.8 kB / 0.7699 GB, free: 11.7 MB / 0.6043 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.089e-05/0.01646, allocations: 31.8 kB / 0.7699 GB, free: 11.67 MB / 0.6043 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.899e-05/0.0165, allocations: 30.97 kB / 0.7699 GB, free: 11.64 MB / 0.6043 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.866e-06/0.0165, allocations: 4 kB / 0.7699 GB, free: 11.63 MB / 0.6043 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 3.206e-06/0.0165, allocations: 4 kB / 0.7699 GB, free: 11.63 MB / 0.6043 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.36e-06/0.01651, allocations: 3.984 kB / 0.7699 GB, free: 11.62 MB / 0.6043 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007386/0.01725, allocations: 0.7882 MB / 0.7707 GB, free: 10.78 MB / 0.6043 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.585e-06/0.01725, allocations: 0 / 0.7707 GB, free: 10.78 MB / 0.6043 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001628/0.01741, allocations: 59.89 kB / 0.7708 GB, free: 10.72 MB / 0.6043 GB Notification: Performance of postOpt tearingSystem (simulation): time 3.386e-06/0.01742, allocations: 4 kB / 0.7708 GB, free: 10.71 MB / 0.6043 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.074e-05/0.01744, allocations: 12 kB / 0.7708 GB, free: 10.7 MB / 0.6043 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.865e-06/0.01744, allocations: 3.938 kB / 0.7708 GB, free: 10.7 MB / 0.6043 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.563e-06/0.01744, allocations: 4 kB / 0.7708 GB, free: 10.7 MB / 0.6043 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0006677/0.01811, allocations: 0.7634 MB / 0.7715 GB, free: 9.879 MB / 0.6043 GB Notification: Performance of postOpt removeConstants (simulation): time 7.199e-05/0.01818, allocations: 43.83 kB / 0.7716 GB, free: 9.836 MB / 0.6043 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.457e-05/0.01822, allocations: 12 kB / 0.7716 GB, free: 9.824 MB / 0.6043 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 9.706e-05/0.01831, allocations: 19.92 kB / 0.7716 GB, free: 9.805 MB / 0.6043 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 8.296e-05/0.0184, allocations: 35.94 kB / 0.7716 GB, free: 9.77 MB / 0.6043 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.708e-05/0.01841, allocations: 12 kB / 0.7716 GB, free: 9.758 MB / 0.6043 GB Notification: Performance of sorting global known variables: time 9.911e-05/0.01851, allocations: 169.2 kB / 0.7718 GB, free: 9.598 MB / 0.6043 GB Notification: Performance of sort global known variables: time 6e-08/0.01851, allocations: 0 / 0.7718 GB, free: 9.598 MB / 0.6043 GB Notification: Performance of remove unused functions: time 0.0002237/0.01874, allocations: 80 kB / 0.7719 GB, free: 9.52 MB / 0.6043 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 7 (central.C,central.AUC,elim.MExc,periodicDose.TotalCumulativeMass,periodicDose.absorptionLumen.C,periodicDose.absorptionLumen.AUC,periodicDose.variableDose.TotalCumulativeMass) * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,central.Cmax,central.Cmin,central.rising,periodicDose.absorptionLumen.Cmax,periodicDose.absorptionLumen.Cmin,periodicDose.absorptionLumen.rising,periodicDose.pulse.T_start,periodicDose.pulse.count) * Number of discrete states: 11 (periodicDose.pulse.count,central.Cmin,$whenCondition5,central.Cmax,$whenCondition4,central.rising,periodicDose.absorptionLumen.Cmin,$whenCondition3,periodicDose.absorptionLumen.Cmax,$whenCondition2,periodicDose.absorptionLumen.rising) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (30): * Single equations (assignments): 26 * 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 0.0001215/0.01886, allocations: 123.3 kB / 0.772 GB, free: 9.391 MB / 0.6043 GB Notification: Performance of simCode: created initialization part: time 0.0005147/0.01937, allocations: 0.5733 MB / 0.7726 GB, free: 8.75 MB / 0.6043 GB Notification: Performance of simCode: created event and clocks part: time 2.024e-06/0.01937, allocations: 8.062 kB / 0.7726 GB, free: 8.742 MB / 0.6043 GB Notification: Performance of simCode: created simulation system equations: time 0.0002213/0.01959, allocations: 312.9 kB / 0.7729 GB, free: 8.402 MB / 0.6043 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003584/0.01995, allocations: 96.98 kB / 0.773 GB, free: 8.316 MB / 0.6043 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00112/0.02107, allocations: 0.8513 MB / 0.7738 GB, free: 7.438 MB / 0.6043 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 9.999e-05/0.02117, allocations: 159.7 kB / 0.7739 GB, free: 7.262 MB / 0.6043 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 6.437e-05/0.02124, allocations: 32.5 kB / 0.774 GB, free: 7.23 MB / 0.6043 GB Notification: Performance of SimCode: time 4.81e-07/0.02124, allocations: 0 / 0.774 GB, free: 7.23 MB / 0.6043 GB Notification: Performance of Templates: time 0.004354/0.02559, allocations: 4.001 MB / 0.7779 GB, free: 3.316 MB / 0.6043 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Lithium2.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Lithium2.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Lithium2.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Lithium2.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Lithium2.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Lithium2 > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Lithium2.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 6.761679547838867]