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 0.0009946/0.0009946, allocations: 104.3 kB / 19.71 MB, free: 440 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 0.001135/0.001135, allocations: 216 kB / 23 MB, free: 2.977 MB / 13.93 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 1.034/1.034, allocations: 230.6 MB / 256.8 MB, free: 9.605 MB / 202.7 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 1.653/1.653, allocations: 334.2 MB / 0.6323 GB, free: 7.961 MB / 442.7 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: Pharmacolibrary requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed. Notification: Performance of FrontEnd - loaded program: time 0.00171/0.00171, allocations: 71.89 kB / 0.8678 GB, free: 7.25 MB / 0.573 GB Notification: Performance of FrontEnd - Absyn->SCode: time 0.2105/0.2122, allocations: 112.8 MB / 0.978 GB, free: 6.172 MB / 0.6824 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Lithium2): time 0.003927/0.2162, allocations: 3.761 MB / 0.9816 GB, free: 2.391 MB / 0.6824 GB Notification: Performance of NFInst.instExpressions: time 0.001083/0.2173, allocations: 0.7055 MB / 0.9823 GB, free: 1.684 MB / 0.6824 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001079/0.2174, allocations: 4 kB / 0.9823 GB, free: 1.68 MB / 0.6824 GB Notification: Performance of NFTyping.typeComponents: time 0.0001346/0.2175, allocations: 35.64 kB / 0.9824 GB, free: 1.645 MB / 0.6824 GB Notification: Performance of NFTyping.typeBindings: time 0.0001879/0.2177, allocations: 107.1 kB / 0.9825 GB, free: 1.539 MB / 0.6824 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002953/0.218, allocations: 95.81 kB / 0.9826 GB, free: 1.445 MB / 0.6824 GB Notification: Performance of NFFlatten.flatten: time 0.0003164/0.2183, allocations: 362.2 kB / 0.9829 GB, free: 1.09 MB / 0.6824 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001546/0.2185, allocations: 53.33 kB / 0.9829 GB, free: 1.035 MB / 0.6824 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001331/0.2186, allocations: 127.6 kB / 0.9831 GB, free: 0.9102 MB / 0.6824 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0002027/0.2188, allocations: 131.3 kB / 0.9832 GB, free: 0.7812 MB / 0.6824 GB Notification: Performance of NFPackage.collectConstants: time 3.947e-05/0.2188, allocations: 28 kB / 0.9832 GB, free: 0.7539 MB / 0.6824 GB Notification: Performance of NFFlatten.collectFunctions: time 3.374e-05/0.2189, allocations: 28 kB / 0.9832 GB, free: 0.7266 MB / 0.6824 GB Notification: Performance of NFScalarize.scalarize: time 4.364e-05/0.2189, allocations: 59.77 kB / 0.9833 GB, free: 0.668 MB / 0.6824 GB Notification: Performance of NFVerifyModel.verify: time 9.983e-05/0.219, allocations: 135.4 kB / 0.9834 GB, free: 0.5352 MB / 0.6824 GB Notification: Performance of NFConvertDAE.convert: time 0.0002527/0.2193, allocations: 294.9 kB / 0.9837 GB, free: 252 kB / 0.6824 GB Notification: Performance of FrontEnd - DAE generated: time 4.328e-06/0.2193, allocations: 3.938 kB / 0.9837 GB, free: 248 kB / 0.6824 GB Notification: Performance of FrontEnd: time 2.345e-06/0.2193, allocations: 3.938 kB / 0.9837 GB, free: 244 kB / 0.6824 GB Notification: Performance of Transformations before backend: time 7.334e-06/0.2193, allocations: 4 kB / 0.9837 GB, free: 240 kB / 0.6824 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 0.0007118/0.22, allocations: 0.5881 MB / 0.9843 GB, free: 15.59 MB / 0.698 GB Notification: Performance of prepare preOptimizeDAE: time 3.841e-05/0.22, allocations: 10.11 kB / 0.9843 GB, free: 15.59 MB / 0.698 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 5.269e-05/0.2201, allocations: 32.75 kB / 0.9843 GB, free: 15.55 MB / 0.698 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002172/0.2203, allocations: 208.2 kB / 0.9845 GB, free: 15.33 MB / 0.698 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.306e-05/0.2203, allocations: 16.38 kB / 0.9846 GB, free: 15.31 MB / 0.698 GB Notification: Performance of preOpt expandDerOperator (simulation): time 4.54e-05/0.2204, allocations: 31.95 kB / 0.9846 GB, free: 15.28 MB / 0.698 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003324/0.2207, allocations: 291.9 kB / 0.9849 GB, free: 14.96 MB / 0.698 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.493e-05/0.2207, allocations: 0 / 0.9849 GB, free: 14.96 MB / 0.698 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.856e-05/0.2207, allocations: 12 kB / 0.9849 GB, free: 14.95 MB / 0.698 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.181e-06/0.2207, allocations: 8 kB / 0.9849 GB, free: 14.95 MB / 0.698 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002752/0.221, allocations: 235.1 kB / 0.9851 GB, free: 14.71 MB / 0.698 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006781/0.2217, allocations: 0.5948 MB / 0.9857 GB, free: 14.07 MB / 0.698 GB Notification: Performance of preOpt comSubExp (simulation): time 0.000387/0.2221, allocations: 256.5 kB / 0.9859 GB, free: 13.8 MB / 0.698 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001519/0.2222, allocations: 156.5 kB / 0.9861 GB, free: 13.64 MB / 0.698 GB Notification: Performance of preOpt evalFunc (simulation): time 2.098e-05/0.2222, allocations: 8.219 kB / 0.9861 GB, free: 13.63 MB / 0.698 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003117/0.2226, allocations: 375.2 kB / 0.9864 GB, free: 13.21 MB / 0.698 GB Notification: Performance of pre-optimization done (n=34): time 1.473e-06/0.2226, allocations: 0 / 0.9864 GB, free: 13.21 MB / 0.698 GB Notification: Performance of matching and sorting (n=36): time 0.001243/0.2238, allocations: 1.117 MB / 0.9875 GB, free: 12.01 MB / 0.698 GB Notification: Performance of inlineWhenForInitialization (initialization): time 7.649e-05/0.2239, allocations: 229.5 kB / 0.9878 GB, free: 11.73 MB / 0.698 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001564/0.224, allocations: 232.9 kB / 0.988 GB, free: 11.5 MB / 0.698 GB Notification: Performance of collectPreVariables (initialization): time 2.243e-05/0.2241, allocations: 37.7 kB / 0.988 GB, free: 11.46 MB / 0.698 GB Notification: Performance of collectInitialEqns (initialization): time 7.296e-05/0.2241, allocations: 140.9 kB / 0.9882 GB, free: 11.31 MB / 0.698 GB Notification: Performance of collectInitialBindings (initialization): time 6.254e-05/0.2242, allocations: 126.9 kB / 0.9883 GB, free: 11.19 MB / 0.698 GB Notification: Performance of simplifyInitialFunctions (initialization): time 7.015e-05/0.2243, allocations: 65.7 kB / 0.9883 GB, free: 11.12 MB / 0.698 GB Notification: Performance of setup shared object (initialization): time 9.299e-05/0.2243, allocations: 342.8 kB / 0.9887 GB, free: 10.77 MB / 0.698 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001919/0.2245, allocations: 211 kB / 0.9889 GB, free: 10.55 MB / 0.698 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003017/0.2248, allocations: 313.2 kB / 0.9892 GB, free: 10.18 MB / 0.698 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0007731/0.2256, allocations: 0.7977 MB / 0.9899 GB, free: 9.277 MB / 0.698 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.204e-06/0.2256, allocations: 0 / 0.9899 GB, free: 9.277 MB / 0.698 GB Notification: Performance of matching and sorting (n=54) (initialization): time 0.0005151/0.2261, allocations: 0.5714 MB / 0.9905 GB, free: 8.664 MB / 0.698 GB Notification: Performance of prepare postOptimizeDAE: time 4.429e-05/0.2262, allocations: 93.09 kB / 0.9906 GB, free: 8.555 MB / 0.698 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.214e-06/0.2262, allocations: 4.344 kB / 0.9906 GB, free: 8.551 MB / 0.698 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.528e-05/0.2262, allocations: 8 kB / 0.9906 GB, free: 8.543 MB / 0.698 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001682/0.2264, allocations: 83.83 kB / 0.9907 GB, free: 8.461 MB / 0.698 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.396e-06/0.2264, allocations: 7.938 kB / 0.9907 GB, free: 8.453 MB / 0.698 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001167/0.2265, allocations: 19.98 kB / 0.9907 GB, free: 8.434 MB / 0.698 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.816e-05/0.2265, allocations: 20 kB / 0.9907 GB, free: 8.414 MB / 0.698 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 0.0002035/0.2267, allocations: 250.2 kB / 0.991 GB, free: 8.148 MB / 0.698 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 2.918e-05/0.2267, allocations: 35.8 kB / 0.991 GB, free: 8.113 MB / 0.698 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.567e-05/0.2268, allocations: 30.97 kB / 0.991 GB, free: 8.086 MB / 0.698 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.685e-06/0.2268, allocations: 4 kB / 0.991 GB, free: 8.082 MB / 0.698 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 6.792e-06/0.2268, allocations: 7.875 kB / 0.991 GB, free: 8.074 MB / 0.698 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.831e-06/0.2268, allocations: 3.984 kB / 0.991 GB, free: 8.07 MB / 0.698 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.4196/0.6464, allocations: 0.7797 MB / 0.9918 GB, free: 26.01 MB / 0.698 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.559e-06/0.6464, allocations: 0 / 0.9918 GB, free: 26.01 MB / 0.698 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002018/0.6466, allocations: 58.45 kB / 0.9919 GB, free: 26.01 MB / 0.698 GB Notification: Performance of postOpt tearingSystem (simulation): time 7.474e-06/0.6466, allocations: 7.094 kB / 0.9919 GB, free: 26.01 MB / 0.698 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.21e-05/0.6467, allocations: 14.52 kB / 0.9919 GB, free: 26.01 MB / 0.698 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.019e-06/0.6467, allocations: 1.625 kB / 0.9919 GB, free: 26.01 MB / 0.698 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.543e-06/0.6467, allocations: 1.375 kB / 0.9919 GB, free: 26.01 MB / 0.698 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0006794/0.6473, allocations: 0.75 MB / 0.9926 GB, free: 25.69 MB / 0.698 GB Notification: Performance of postOpt removeConstants (simulation): time 0.0001051/0.6474, allocations: 45.09 kB / 0.9927 GB, free: 25.69 MB / 0.698 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.08e-05/0.6475, allocations: 14.41 kB / 0.9927 GB, free: 25.69 MB / 0.698 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001097/0.6476, allocations: 19.14 kB / 0.9927 GB, free: 25.69 MB / 0.698 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 8.465e-05/0.6477, allocations: 30.41 kB / 0.9927 GB, free: 25.69 MB / 0.698 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.767e-05/0.6477, allocations: 21.27 kB / 0.9927 GB, free: 25.69 MB / 0.698 GB Notification: Performance of sorting global known variables: time 0.0001025/0.6478, allocations: 164.4 kB / 0.9929 GB, free: 25.61 MB / 0.698 GB Notification: Performance of sort global known variables: time 8e-08/0.6478, allocations: 1.812 kB / 0.9929 GB, free: 25.61 MB / 0.698 GB Notification: Performance of remove unused functions: time 0.0002958/0.6481, allocations: 85.78 kB / 0.993 GB, free: 25.61 MB / 0.698 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 0.0001046/0.6482, allocations: 119.3 kB / 0.9931 GB, free: 25.52 MB / 0.698 GB Notification: Performance of simCode: created initialization part: time 0.0004741/0.6487, allocations: 0.5888 MB / 0.9937 GB, free: 25.17 MB / 0.698 GB Notification: Performance of simCode: created event and clocks part: time 1.953e-06/0.6487, allocations: 4.844 kB / 0.9937 GB, free: 25.17 MB / 0.698 GB Notification: Performance of simCode: created simulation system equations: time 0.0001872/0.6489, allocations: 310.8 kB / 0.994 GB, free: 24.98 MB / 0.698 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003663/0.6492, allocations: 84.11 kB / 0.994 GB, free: 24.98 MB / 0.698 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001009/0.6502, allocations: 1.024 MB / 0.995 GB, free: 24.39 MB / 0.698 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 9.091e-05/0.6503, allocations: 161.3 kB / 0.9952 GB, free: 24.31 MB / 0.698 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 5.609e-05/0.6504, allocations: 24.5 kB / 0.9952 GB, free: 24.3 MB / 0.698 GB Notification: Performance of SimCode: time 8.92e-07/0.6504, allocations: 0 / 0.9952 GB, free: 24.3 MB / 0.698 GB Notification: Performance of Templates: time 0.004655/0.655, allocations: 3.99 MB / 0.9991 GB, free: 23.95 MB / 0.698 GB " [Timeout remaining time 659] 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: 7.633730059955269]