Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.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 0.0009996/0.0009996, allocations: 77.83 kB / 20.66 MB, free: 3.82 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 0.001015/0.001015, allocations: 177 kB / 24.07 MB, free: 424 kB / 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 1.024/1.024, allocations: 177.1 MB / 204.5 MB, free: 5.484 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 1.642/1.642, allocations: 273.5 MB / 0.522 GB, free: 14.55 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.DevModels.SingleDoseDiffusion,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion") translateModel(Pharmacolibrary.DevModels.SingleDoseDiffusion,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 2.014e-06/2.014e-06, allocations: 1.312 kB / 0.6482 GB, free: 38.54 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.326e-05/2.528e-05, allocations: 2.312 kB / 0.6482 GB, free: 38.54 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.SingleDoseDiffusion): time 0.002799/0.002825, allocations: 2.888 MB / 0.651 GB, free: 36.66 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.0009518/0.003777, allocations: 0.7351 MB / 0.6517 GB, free: 36.17 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 8.75e-05/0.003864, allocations: 4.344 kB / 0.6517 GB, free: 36.17 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 6.41e-05/0.003928, allocations: 38.52 kB / 0.6517 GB, free: 36.15 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.000235/0.004163, allocations: 114 kB / 0.6518 GB, free: 36.1 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002124/0.004375, allocations: 95.72 kB / 0.6519 GB, free: 36.05 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0003024/0.004678, allocations: 411.7 kB / 0.6523 GB, free: 35.84 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.000257/0.004935, allocations: 222.2 kB / 0.6525 GB, free: 35.71 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002182/0.005153, allocations: 245.9 kB / 0.6528 GB, free: 35.61 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001955/0.005349, allocations: 150.2 kB / 0.6529 GB, free: 35.57 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 4.551e-05/0.005394, allocations: 35.97 kB / 0.653 GB, free: 35.57 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 3.771e-05/0.005432, allocations: 35.38 kB / 0.653 GB, free: 35.57 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 4.942e-05/0.005481, allocations: 72.77 kB / 0.6531 GB, free: 35.52 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 9.676e-05/0.005578, allocations: 132.1 kB / 0.6532 GB, free: 35.46 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0002448/0.005823, allocations: 267.9 kB / 0.6534 GB, free: 35.34 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 3.026e-06/0.005826, allocations: 0 / 0.6534 GB, free: 35.34 MB / 0.5262 GB Notification: Performance of FrontEnd: time 1.212e-06/0.005827, allocations: 0 / 0.6534 GB, free: 35.34 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 4.789e-06/0.005832, allocations: 1.031 kB / 0.6534 GB, free: 35.34 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: 65 * Number of variables: 65 Notification: Performance of Generate backend data structure: time 0.0006463/0.006478, allocations: 0.6632 MB / 0.6541 GB, free: 34.77 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 3.756e-05/0.006516, allocations: 10.94 kB / 0.6541 GB, free: 34.77 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 7.457e-05/0.00659, allocations: 53.88 kB / 0.6541 GB, free: 34.75 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.000179/0.006769, allocations: 209.7 kB / 0.6543 GB, free: 34.56 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.568e-05/0.006795, allocations: 19.88 kB / 0.6544 GB, free: 34.55 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 5.08e-05/0.006846, allocations: 36.02 kB / 0.6544 GB, free: 34.54 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003604/0.007206, allocations: 342.4 kB / 0.6547 GB, free: 34.33 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.507e-05/0.007221, allocations: 3.938 kB / 0.6547 GB, free: 34.32 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.212e-05/0.007243, allocations: 15.12 kB / 0.6547 GB, free: 34.32 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.474e-06/0.007251, allocations: 8.062 kB / 0.6548 GB, free: 34.32 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001554/0.007406, allocations: 144.5 kB / 0.6549 GB, free: 34.28 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0008529/0.008259, allocations: 0.7942 MB / 0.6557 GB, free: 33.71 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0003242/0.008583, allocations: 155.2 kB / 0.6558 GB, free: 33.63 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 8.968e-05/0.008673, allocations: 81.03 kB / 0.6559 GB, free: 33.58 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 2.358e-05/0.008697, allocations: 4.938 kB / 0.6559 GB, free: 33.58 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002407/0.008937, allocations: 232 kB / 0.6561 GB, free: 33.41 MB / 0.5262 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.0001331/0.00907, allocations: 42.64 kB / 0.6562 GB, free: 33.39 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=30): time 2.785e-06/0.009073, allocations: 1.781 kB / 0.6562 GB, free: 33.39 MB / 0.5262 GB Notification: Performance of matching and sorting (n=31): time 0.000952/0.01003, allocations: 0.6591 MB / 0.6568 GB, free: 32.97 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 4.79e-05/0.01007, allocations: 136.9 kB / 0.6569 GB, free: 32.81 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001092/0.01018, allocations: 238.1 kB / 0.6572 GB, free: 32.62 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 1.881e-05/0.0102, allocations: 32.48 kB / 0.6572 GB, free: 32.58 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 6.748e-05/0.01027, allocations: 212.3 kB / 0.6574 GB, free: 32.39 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 5.066e-05/0.01032, allocations: 115.1 kB / 0.6575 GB, free: 32.3 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 7.35e-05/0.01039, allocations: 73.36 kB / 0.6576 GB, free: 32.25 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 6.676e-05/0.01046, allocations: 0.5062 MB / 0.6581 GB, free: 31.75 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 9.19e-05/0.01055, allocations: 125.3 kB / 0.6582 GB, free: 31.66 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001223/0.01067, allocations: 262.6 kB / 0.6584 GB, free: 31.39 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0002629/0.01094, allocations: 421 kB / 0.6588 GB, free: 31.04 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.545e-06/0.01094, allocations: 3.594 kB / 0.6588 GB, free: 31.04 MB / 0.5262 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0003307/0.01127, allocations: 389.5 kB / 0.6592 GB, free: 30.81 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 4.186e-05/0.01131, allocations: 65.94 kB / 0.6593 GB, free: 30.74 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.983e-06/0.01132, allocations: 2.812 kB / 0.6593 GB, free: 30.74 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.336e-05/0.01133, allocations: 5.719 kB / 0.6593 GB, free: 30.74 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002214/0.01155, allocations: 99.14 kB / 0.6594 GB, free: 30.73 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.412e-06/0.01156, allocations: 4.281 kB / 0.6594 GB, free: 30.73 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001046/0.01166, allocations: 21.69 kB / 0.6594 GB, free: 30.72 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.075e-05/0.01169, allocations: 9.875 kB / 0.6594 GB, free: 30.72 MB / 0.5262 GB Warning: Assuming fixed start value for the following 8 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 artery.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real tissueCompartment.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real RBC.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real RBC.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real RBC.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real RBC.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: 13 ($PRE.RBC.Cmin,RBC.Cmin,$PRE.RBC.Cmax,RBC.Cmax,$PRE.RBC.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,RBC.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition2,$whenCondition1,$whenCondition3) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (47): * Single equations (assignments): 45 * Array equations: 0 * Algorithm blocks: 2 * 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 0.0001833/0.01187, allocations: 250 kB / 0.6597 GB, free: 30.5 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.848e-05/0.01191, allocations: 34.19 kB / 0.6597 GB, free: 30.48 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0003002/0.01221, allocations: 295.4 kB / 0.66 GB, free: 30.33 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.127e-06/0.01221, allocations: 7.172 kB / 0.66 GB, free: 30.33 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 1.743e-06/0.01221, allocations: 0 / 0.66 GB, free: 30.33 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.999e-06/0.01222, allocations: 3.938 kB / 0.66 GB, free: 30.32 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004883/0.01271, allocations: 0.5888 MB / 0.6606 GB, free: 29.91 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.134e-06/0.01271, allocations: 3.938 kB / 0.6606 GB, free: 29.91 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001646/0.01287, allocations: 44.16 kB / 0.6606 GB, free: 29.91 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 4.207e-06/0.01288, allocations: 3.719 kB / 0.6606 GB, free: 29.91 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.654e-05/0.01289, allocations: 10.08 kB / 0.6606 GB, free: 29.9 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.775e-06/0.0129, allocations: 1.344 kB / 0.6606 GB, free: 29.9 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.443e-06/0.0129, allocations: 1.438 kB / 0.6606 GB, free: 29.9 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004203/0.01332, allocations: 0.5195 MB / 0.6611 GB, free: 29.55 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 2.668e-05/0.01334, allocations: 19.91 kB / 0.6611 GB, free: 29.54 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.208e-05/0.01338, allocations: 13.05 kB / 0.6612 GB, free: 29.53 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 9.682e-05/0.01347, allocations: 9.562 kB / 0.6612 GB, free: 29.53 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.225e-05/0.01354, allocations: 23.12 kB / 0.6612 GB, free: 29.52 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.413e-05/0.01355, allocations: 11.59 kB / 0.6612 GB, free: 29.52 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 6.187e-05/0.01361, allocations: 160.5 kB / 0.6614 GB, free: 29.4 MB / 0.5262 GB Notification: Performance of sort global known variables: time 7e-08/0.01361, allocations: 0.9062 kB / 0.6614 GB, free: 29.4 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0002497/0.01386, allocations: 83.44 kB / 0.6614 GB, free: 29.39 MB / 0.5262 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 8 (singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,artery.M,artery.AUC,tissueCompartment.M,tissueCompartment.AUC,RBC.C,RBC.AUC) * Number of discrete variables: 8 ($whenCondition3,$whenCondition1,$whenCondition2,singleDose.pulse.T_start,singleDose.pulse.count,RBC.Cmax,RBC.Cmin,RBC.rising) * Number of discrete states: 6 (singleDose.pulse.count,RBC.Cmin,$whenCondition2,RBC.Cmax,$whenCondition1,RBC.rising) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (28): * Single equations (assignments): 25 * Array equations: 0 * Algorithm blocks: 1 * 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 0.0001123/0.01397, allocations: 116.5 kB / 0.6615 GB, free: 29.29 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0003018/0.01428, allocations: 368.5 kB / 0.6619 GB, free: 29.04 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 2.334e-06/0.01428, allocations: 2.188 kB / 0.6619 GB, free: 29.04 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0001243/0.0144, allocations: 176.4 kB / 0.6621 GB, free: 28.91 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003224/0.01472, allocations: 81.11 kB / 0.6621 GB, free: 28.89 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001469/0.01619, allocations: 0.8405 MB / 0.663 GB, free: 28.35 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 5.612e-05/0.01625, allocations: 99.16 kB / 0.6631 GB, free: 28.27 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 0.0001049/0.01635, allocations: 36.05 kB / 0.6631 GB, free: 28.26 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001897/0.01654, allocations: 152.6 kB / 0.6632 GB, free: 28.18 MB / 0.5262 GB Notification: Performance of SimCode: time 1.332e-06/0.01655, allocations: 0 / 0.6632 GB, free: 28.18 MB / 0.5262 GB Notification: Performance of Templates: time 0.006986/0.02353, allocations: 4.514 MB / 0.6676 GB, free: 27.77 MB / 0.5262 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 5.487740857060999]