Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Pharmacokinetic.Models.PK_2C.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 0.0008939/0.0008939, allocations: 92.22 kB / 19.65 MB, free: 276 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 0.0009331/0.0009331, allocations: 169 kB / 23.02 MB, free: 1.547 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 0.9795/0.9795, allocations: 177.1 MB / 203.4 MB, free: 5.633 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 1.638/1.638, allocations: 273.5 MB / 0.5209 GB, free: 14.74 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.Pharmacokinetic.Models.PK_2C,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Pharmacokinetic.Models.PK_2C") translateModel(Pharmacolibrary.Pharmacokinetic.Models.PK_2C,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Pharmacokinetic.Models.PK_2C") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 2.084e-06/2.084e-06, allocations: 0 / 0.647 GB, free: 38.57 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.693e-05/2.902e-05, allocations: 4.984 kB / 0.647 GB, free: 38.57 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Pharmacokinetic.Models.PK_2C): time 0.003969/0.003998, allocations: 2.712 MB / 0.6496 GB, free: 36.8 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.001345/0.005344, allocations: 0.6788 MB / 0.6503 GB, free: 36.36 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001255/0.005469, allocations: 5.844 kB / 0.6503 GB, free: 36.35 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 0.0001545/0.005624, allocations: 40.59 kB / 0.6503 GB, free: 36.33 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0002683/0.005892, allocations: 105.9 kB / 0.6505 GB, free: 36.29 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002925/0.006184, allocations: 79.41 kB / 0.6505 GB, free: 36.25 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0003638/0.006548, allocations: 365.2 kB / 0.6509 GB, free: 36.07 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001849/0.006733, allocations: 57.53 kB / 0.6509 GB, free: 36.04 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002481/0.006981, allocations: 191 kB / 0.6511 GB, free: 35.96 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0003073/0.007288, allocations: 121.3 kB / 0.6512 GB, free: 35.93 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 5.533e-05/0.007344, allocations: 24.06 kB / 0.6513 GB, free: 35.93 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 5.759e-05/0.007401, allocations: 23.5 kB / 0.6513 GB, free: 35.93 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 5.734e-05/0.007459, allocations: 53.64 kB / 0.6513 GB, free: 35.89 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 0.0001358/0.007595, allocations: 108.5 kB / 0.6514 GB, free: 35.85 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.000304/0.007899, allocations: 207.8 kB / 0.6516 GB, free: 35.75 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 8.536e-06/0.007907, allocations: 0 / 0.6516 GB, free: 35.75 MB / 0.5262 GB Notification: Performance of FrontEnd: time 1.713e-06/0.007909, allocations: 1.375 kB / 0.6516 GB, free: 35.75 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 5.901e-06/0.007915, allocations: 0 / 0.6516 GB, free: 35.75 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: 49 * Number of variables: 49 Notification: Performance of Generate backend data structure: time 0.0008661/0.008781, allocations: 0.6768 MB / 0.6523 GB, free: 35.16 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 4.219e-05/0.008823, allocations: 9.188 kB / 0.6523 GB, free: 35.16 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001017/0.008925, allocations: 47.56 kB / 0.6523 GB, free: 35.14 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002607/0.009185, allocations: 207.2 kB / 0.6525 GB, free: 34.96 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.466e-05/0.00921, allocations: 17.12 kB / 0.6526 GB, free: 34.95 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 6.013e-05/0.00927, allocations: 27.36 kB / 0.6526 GB, free: 34.93 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004178/0.009688, allocations: 263.7 kB / 0.6528 GB, free: 34.76 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 2.145e-05/0.009709, allocations: 5.688 kB / 0.6528 GB, free: 34.76 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.591e-05/0.009735, allocations: 7.812 kB / 0.6528 GB, free: 34.76 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.335e-05/0.009749, allocations: 6.062 kB / 0.6529 GB, free: 34.76 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000265/0.01001, allocations: 161.8 kB / 0.653 GB, free: 34.67 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001054/0.01107, allocations: 0.7478 MB / 0.6537 GB, free: 34.1 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0003193/0.01139, allocations: 178.8 kB / 0.6539 GB, free: 33.98 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001542/0.01154, allocations: 112 kB / 0.654 GB, free: 33.9 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.627e-05/0.01156, allocations: 6.844 kB / 0.654 GB, free: 33.9 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003092/0.01187, allocations: 324.8 kB / 0.6543 GB, free: 33.63 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=33): time 2.064e-06/0.01187, allocations: 2.625 kB / 0.6543 GB, free: 33.63 MB / 0.5262 GB Notification: Performance of matching and sorting (n=35): time 0.001548/0.01342, allocations: 0.9434 MB / 0.6553 GB, free: 32.97 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 5.972e-05/0.01348, allocations: 216.7 kB / 0.6555 GB, free: 32.72 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002658/0.01374, allocations: 286.5 kB / 0.6557 GB, free: 32.52 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 3.34e-05/0.01378, allocations: 34.14 kB / 0.6558 GB, free: 32.48 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 9.457e-05/0.01387, allocations: 198.1 kB / 0.656 GB, free: 32.3 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 8.573e-05/0.01396, allocations: 116.2 kB / 0.6561 GB, free: 32.21 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001276/0.01408, allocations: 81.34 kB / 0.6561 GB, free: 32.16 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 7.063e-05/0.01415, allocations: 0.514 MB / 0.6566 GB, free: 31.66 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002006/0.01436, allocations: 155.5 kB / 0.6568 GB, free: 31.53 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002382/0.01459, allocations: 298.8 kB / 0.6571 GB, free: 31.23 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0005293/0.01512, allocations: 0.5253 MB / 0.6576 GB, free: 30.75 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.106e-06/0.01513, allocations: 0.7812 kB / 0.6576 GB, free: 30.75 MB / 0.5262 GB Notification: Performance of matching and sorting (n=54) (initialization): time 0.0006937/0.01582, allocations: 0.4923 MB / 0.6581 GB, free: 30.43 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 6.956e-05/0.01589, allocations: 93.45 kB / 0.6582 GB, free: 30.33 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.34e-05/0.0159, allocations: 4.219 kB / 0.6582 GB, free: 30.33 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 3.4e-05/0.01594, allocations: 4.25 kB / 0.6582 GB, free: 30.33 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003842/0.01632, allocations: 88 kB / 0.6583 GB, free: 30.32 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.612e-05/0.01634, allocations: 4.938 kB / 0.6583 GB, free: 30.32 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002684/0.01661, allocations: 22.17 kB / 0.6583 GB, free: 30.31 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.761e-05/0.01665, allocations: 21.98 kB / 0.6583 GB, free: 30.3 MB / 0.5262 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.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 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 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: 13 * 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,$PRE.peripheral.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,$PRE.central.rising,peripheral.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,central.rising,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1,$whenCondition5) * 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 0.000388/0.01704, allocations: 289.3 kB / 0.6586 GB, free: 30.04 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 8.429e-05/0.01712, allocations: 39.95 kB / 0.6586 GB, free: 30.03 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.504e-05/0.0172, allocations: 33.61 kB / 0.6586 GB, free: 30 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.953e-06/0.01721, allocations: 2.812 kB / 0.6587 GB, free: 30 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 1.205e-05/0.01722, allocations: 0 / 0.6587 GB, free: 30 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.756e-06/0.01723, allocations: 5.234 kB / 0.6587 GB, free: 30 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001206/0.01843, allocations: 0.7546 MB / 0.6594 GB, free: 29.46 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.23e-06/0.01844, allocations: 1.344 kB / 0.6594 GB, free: 29.46 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000293/0.01873, allocations: 51.58 kB / 0.6594 GB, free: 29.46 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 5.982e-06/0.01874, allocations: 1.344 kB / 0.6594 GB, free: 29.46 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.012e-05/0.01877, allocations: 12.11 kB / 0.6595 GB, free: 29.46 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 7.434e-06/0.01878, allocations: 5.375 kB / 0.6595 GB, free: 29.45 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.585e-06/0.01878, allocations: 0 / 0.6595 GB, free: 29.45 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0007417/0.01952, allocations: 0.6741 MB / 0.6601 GB, free: 28.98 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 6.297e-05/0.01958, allocations: 25.78 kB / 0.6601 GB, free: 28.97 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.922e-05/0.01964, allocations: 13.62 kB / 0.6602 GB, free: 28.96 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000194/0.01984, allocations: 15.88 kB / 0.6602 GB, free: 28.96 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001209/0.01996, allocations: 30.11 kB / 0.6602 GB, free: 28.95 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.074e-05/0.01999, allocations: 12.47 kB / 0.6602 GB, free: 28.95 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 0.0001596/0.02015, allocations: 193.6 kB / 0.6604 GB, free: 28.82 MB / 0.5262 GB Notification: Performance of sort global known variables: time 1.2e-07/0.02015, allocations: 0 / 0.6604 GB, free: 28.82 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0005059/0.02065, allocations: 85.88 kB / 0.6605 GB, free: 28.81 MB / 0.5262 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.variableDose.TotalCumulativeMass,peripheral.C,peripheral.AUC) * Number of discrete variables: 13 ($whenCondition5,$whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,central.Cmax,central.Cmin,central.rising,periodicDose.pulse.T_start,periodicDose.pulse.count,peripheral.Cmax,peripheral.Cmin,peripheral.rising) * Number of discrete states: 11 (periodicDose.pulse.count,peripheral.Cmin,$whenCondition4,peripheral.Cmax,$whenCondition3,peripheral.rising,central.Cmin,$whenCondition2,central.Cmax,$whenCondition1,central.rising) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (29): * Single equations (assignments): 25 * 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 0.000139/0.02079, allocations: 121.7 kB / 0.6606 GB, free: 28.71 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0005669/0.02136, allocations: 0.5078 MB / 0.6611 GB, free: 28.31 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 2.344e-06/0.02136, allocations: 1.406 kB / 0.6611 GB, free: 28.31 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0002313/0.02159, allocations: 273.2 kB / 0.6614 GB, free: 28.09 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006064/0.0222, allocations: 94.08 kB / 0.6614 GB, free: 28.07 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002455/0.02465, allocations: 0.8764 MB / 0.6623 GB, free: 27.5 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 6.992e-05/0.02472, allocations: 88.7 kB / 0.6624 GB, free: 27.43 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 0.0001422/0.02487, allocations: 36.3 kB / 0.6624 GB, free: 27.43 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 7.549e-05/0.02494, allocations: 26.72 kB / 0.6624 GB, free: 27.42 MB / 0.5262 GB Notification: Performance of SimCode: time 1.312e-06/0.02494, allocations: 0 / 0.6624 GB, free: 27.42 MB / 0.5262 GB Notification: Performance of Templates: time 0.006874/0.03182, allocations: 4.356 MB / 0.6667 GB, free: 27.04 MB / 0.5262 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.Pharmacokinetic.Models.PK_2C.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.Pharmacokinetic.Models.PK_2C.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Pharmacokinetic.Models.PK_2C.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Pharmacokinetic.Models.PK_2C.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Pharmacokinetic.Models.PK_2C.sim & ./Pharmacolibrary_Pharmacolibrary.Pharmacokinetic.Models.PK_2C -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Pharmacokinetic.Models.PK_2C.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 5.0280333259142935]