Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody.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 0.001262/0.001262, allocations: 87.55 kB / 20.19 MB, free: 4.352 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 0.001579/0.001579, allocations: 169 kB / 23.5 MB, free: 1.047 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 1.074/1.074, allocations: 177.1 MB / 203.8 MB, free: 5.645 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 1.598/1.598, allocations: 273.5 MB / 0.5213 GB, free: 14.88 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.PBPK_OralDoseGUTWholeBody,tolerance=1e-06,outputFormat="empty",numberOfIntervals=3600,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody") translateModel(Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody,tolerance=1e-06,outputFormat="empty",numberOfIntervals=3600,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.603e-06/1.603e-06, allocations: 0 / 0.647 GB, free: 38.64 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.286e-05/2.447e-05, allocations: 4.062 kB / 0.647 GB, free: 38.64 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody): time 0.007814/0.007839, allocations: 8.434 MB / 0.6552 GB, free: 33.12 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.003729/0.01157, allocations: 1.722 MB / 0.6569 GB, free: 31.93 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.00064/0.01221, allocations: 13.84 kB / 0.6569 GB, free: 31.93 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 0.0004556/0.01266, allocations: 200.2 kB / 0.6571 GB, free: 31.82 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.001081/0.01374, allocations: 500 kB / 0.6576 GB, free: 31.46 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0008356/0.01458, allocations: 365.8 kB / 0.6579 GB, free: 31.26 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.001929/0.01651, allocations: 1.779 MB / 0.6597 GB, free: 30.3 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.002676/0.01919, allocations: 2.452 MB / 0.6621 GB, free: 28.88 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.003377/0.02256, allocations: 1.826 MB / 0.6639 GB, free: 28.13 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.00328/0.02584, allocations: 1.481 MB / 0.6653 GB, free: 27.77 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 0.001001/0.02684, allocations: 306.3 kB / 0.6656 GB, free: 27.77 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 0.0007612/0.0276, allocations: 307.1 kB / 0.6659 GB, free: 27.77 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 0.0005111/0.02811, allocations: 0.6701 MB / 0.6665 GB, free: 27.34 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 0.001962/0.03008, allocations: 0.9156 MB / 0.6674 GB, free: 26.91 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.003165/0.03324, allocations: 1.816 MB / 0.6692 GB, free: 26.04 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 6.492e-06/0.03325, allocations: 1.406 kB / 0.6692 GB, free: 26.04 MB / 0.5262 GB Notification: Performance of FrontEnd: time 1.333e-06/0.03325, allocations: 4 kB / 0.6692 GB, free: 26.03 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 6.17e-05/0.03331, allocations: 0 / 0.6692 GB, free: 26.03 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: 307 * Number of variables: 307 Notification: Performance of Generate backend data structure: time 0.005717/0.03903, allocations: 1.762 MB / 0.6709 GB, free: 25.01 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 5.909e-05/0.03909, allocations: 9.438 kB / 0.6709 GB, free: 25.01 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0008555/0.03994, allocations: 240.3 kB / 0.6712 GB, free: 24.89 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.001572/0.04151, allocations: 0.7389 MB / 0.6719 GB, free: 24.43 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 7.475e-05/0.04159, allocations: 96.02 kB / 0.672 GB, free: 24.38 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.0003688/0.04196, allocations: 142.5 kB / 0.6721 GB, free: 24.33 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.004861/0.04682, allocations: 2.282 MB / 0.6744 GB, free: 23.55 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 4.603e-05/0.04686, allocations: 11.48 kB / 0.6744 GB, free: 23.54 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001754/0.04704, allocations: 51.31 kB / 0.6744 GB, free: 23.5 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.347e-05/0.04706, allocations: 28.31 kB / 0.6744 GB, free: 23.5 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002178/0.04924, allocations: 1.472 MB / 0.6759 GB, free: 23.31 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.005841/0.05508, allocations: 4.626 MB / 0.6804 GB, free: 19.81 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.00114/0.05622, allocations: 0.741 MB / 0.6811 GB, free: 19.53 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.000751/0.05697, allocations: 488.8 kB / 0.6816 GB, free: 19.35 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 5.609e-05/0.05703, allocations: 28 kB / 0.6816 GB, free: 19.34 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.001073/0.0581, allocations: 0.8816 MB / 0.6825 GB, free: 18.79 MB / 0.5262 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.003425/0.06153, allocations: 1.563 MB / 0.684 GB, free: 18.26 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=113): time 3.617e-06/0.06153, allocations: 0 / 0.684 GB, free: 18.26 MB / 0.5262 GB Notification: Performance of matching and sorting (n=113): time 0.003122/0.06465, allocations: 1.774 MB / 0.6857 GB, free: 17.55 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 3.054e-05/0.06468, allocations: 63.97 kB / 0.6858 GB, free: 17.48 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003137/0.065, allocations: 471.2 kB / 0.6862 GB, free: 17.16 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 0.0001194/0.06512, allocations: 47.17 kB / 0.6863 GB, free: 17.11 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 0.0001545/0.06527, allocations: 0.4893 MB / 0.6868 GB, free: 16.67 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 0.0002452/0.06552, allocations: 437.3 kB / 0.6872 GB, free: 16.29 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0004958/0.06601, allocations: 421.6 kB / 0.6876 GB, free: 16.02 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 9.083e-05/0.0661, allocations: 0.5654 MB / 0.6881 GB, free: 15.46 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0007688/0.06687, allocations: 0.5537 MB / 0.6887 GB, free: 14.96 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.000816/0.06769, allocations: 0.8812 MB / 0.6895 GB, free: 13.92 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.001612/0.0693, allocations: 1.472 MB / 0.691 GB, free: 12.3 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.628e-06/0.0693, allocations: 4 kB / 0.691 GB, free: 12.29 MB / 0.5262 GB Notification: Performance of matching and sorting (n=166) (initialization): time 0.002185/0.07149, allocations: 1.767 MB / 0.6927 GB, free: 10.51 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 3.178e-05/0.07152, allocations: 38.39 kB / 0.6927 GB, free: 10.46 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.017e-05/0.07153, allocations: 11.94 kB / 0.6927 GB, free: 10.45 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 2.233e-05/0.07155, allocations: 16 kB / 0.6928 GB, free: 10.44 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001302/0.07286, allocations: 0.5887 MB / 0.6933 GB, free: 9.852 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.856e-05/0.07287, allocations: 23.92 kB / 0.6934 GB, free: 9.828 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0007504/0.07362, allocations: 39.98 kB / 0.6934 GB, free: 9.789 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.000147/0.07377, allocations: 151.7 kB / 0.6935 GB, free: 9.641 MB / 0.5262 GB Warning: Assuming fixed start value for the following 17 variables: singleDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real singleDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real venous.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real lungs.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real arterial.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real adipose.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real bone.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real brain.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real heart.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real muscle.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real skin.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real gut.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real spleen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real liver.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real kidney.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real gonads.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real rest.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 34 * Number of states: 0 () * Number of discrete variables: 5 (singleDose.pulse.count,$PRE.singleDose.pulse.count,singleDose.pulse.T_start,$PRE.singleDose.pulse.T_start,$whenCondition1) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (165): * Single equations (assignments): 164 * Array equations: 0 * Algorithm blocks: 1 * 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 0.0004123/0.07418, allocations: 295.2 kB / 0.6938 GB, free: 9.348 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002652/0.07445, allocations: 107.5 kB / 0.6939 GB, free: 9.242 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.002249/0.0767, allocations: 1.731 MB / 0.6956 GB, free: 7.574 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.717e-06/0.07671, allocations: 3.984 kB / 0.6956 GB, free: 7.57 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.046e-06/0.07671, allocations: 0 / 0.6956 GB, free: 7.57 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 6.228e-05/0.07677, allocations: 59.52 kB / 0.6957 GB, free: 7.512 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001366/0.07691, allocations: 31.95 kB / 0.6957 GB, free: 7.48 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005244/0.07743, allocations: 31.92 kB / 0.6957 GB, free: 7.449 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001157/0.07755, allocations: 72.8 kB / 0.6958 GB, free: 7.375 MB / 0.5262 GB Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.003887/0.08144, allocations: 1.387 MB / 0.6972 GB, free: 5.988 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.00245/0.08389, allocations: 2.003 MB / 0.6991 GB, free: 3.961 MB / 0.5262 GB Notification: Performance of postOpt setEvaluationStage (simulation): time 0.0006228/0.08451, allocations: 493.2 kB / 0.6996 GB, free: 3.473 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 0.0001931/0.0847, allocations: 334.8 kB / 0.6999 GB, free: 3.145 MB / 0.5262 GB Notification: Performance of Backend: time 6.72e-07/0.0847, allocations: 0 / 0.6999 GB, free: 3.145 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.001513/0.08622, allocations: 1.12 MB / 0.701 GB, free: 2 MB / 0.5262 GB Notification: Performance of SimCode: time 0.003415/0.08963, allocations: 3.593 MB / 0.7045 GB, free: 14.45 MB / 0.5418 GB Notification: Performance of Templates: time 0.02706/0.1167, allocations: 28.83 MB / 0.7327 GB, free: 1.883 MB / 0.5574 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 5.275963959982619]