Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.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 0.001318/0.001318, allocations: 77.09 kB / 20.66 MB, free: 3.844 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 0.00163/0.00163, allocations: 169 kB / 24.06 MB, free: 456 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 0.9278/0.9278, allocations: 177.1 MB / 204.5 MB, free: 5.504 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 1.545/1.545, allocations: 273.5 MB / 0.522 GB, free: 14.7 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.PKOneCompartmentModel,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel")
translateModel(Pharmacolibrary.Examples.PKOneCompartmentModel,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.122e-06/1.122e-06, allocations: 0 / 0.6482 GB, free: 38.39 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 9.267e-06/1.039e-05, allocations: 6.25 kB / 0.6482 GB, free: 38.39 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKOneCompartmentModel): time 0.00184/0.001851, allocations: 2.047 MB / 0.6502 GB, free: 37.05 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0005928/0.002443, allocations: 0.5392 MB / 0.6507 GB, free: 36.7 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 6.399e-05/0.002507, allocations: 6.062 kB / 0.6507 GB, free: 36.7 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001032/0.002611, allocations: 21.41 kB / 0.6507 GB, free: 36.68 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001117/0.002722, allocations: 51 kB / 0.6508 GB, free: 36.66 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001321/0.002855, allocations: 43.89 kB / 0.6508 GB, free: 36.64 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002001/0.003055, allocations: 195.9 kB / 0.651 GB, free: 36.59 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 9.472e-05/0.003149, allocations: 36.19 kB / 0.651 GB, free: 36.55 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001141/0.003263, allocations: 101.7 kB / 0.6511 GB, free: 36.51 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 9.252e-05/0.003356, allocations: 57.53 kB / 0.6512 GB, free: 36.5 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.42e-05/0.00338, allocations: 13.91 kB / 0.6512 GB, free: 36.5 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 1.7e-05/0.003397, allocations: 15.88 kB / 0.6512 GB, free: 36.5 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 3.011e-05/0.003427, allocations: 30.67 kB / 0.6512 GB, free: 36.47 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 5.174e-05/0.003479, allocations: 56.33 kB / 0.6513 GB, free: 36.45 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001406/0.00362, allocations: 121.9 kB / 0.6514 GB, free: 36.39 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 1.703e-06/0.003621, allocations: 0 / 0.6514 GB, free: 36.39 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 5.01e-07/0.003622, allocations: 0 / 0.6514 GB, free: 36.39 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.509e-06/0.003626, allocations: 0 / 0.6514 GB, free: 36.39 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: 26
 * Number of variables: 26
Notification: Performance of Generate backend data structure: time 0.0004277/0.004054, allocations: 0.5161 MB / 0.6519 GB, free: 35.9 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.212e-05/0.004086, allocations: 9.406 kB / 0.6519 GB, free: 35.9 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.654e-05/0.004133, allocations: 28.38 kB / 0.6519 GB, free: 35.89 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001185/0.004251, allocations: 158.3 kB / 0.6521 GB, free: 35.73 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.476e-05/0.004266, allocations: 6.5 kB / 0.6521 GB, free: 35.73 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.578e-05/0.004292, allocations: 17.41 kB / 0.6521 GB, free: 35.72 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001376/0.004429, allocations: 135.4 kB / 0.6522 GB, free: 35.63 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.029e-05/0.00444, allocations: 3.938 kB / 0.6523 GB, free: 35.63 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 9.538e-06/0.004449, allocations: 1.906 kB / 0.6523 GB, free: 35.63 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.18e-06/0.004454, allocations: 2.375 kB / 0.6523 GB, free: 35.63 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 8.773e-05/0.004542, allocations: 82.31 kB / 0.6523 GB, free: 35.59 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0003375/0.00488, allocations: 379.4 kB / 0.6527 GB, free: 35.28 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001142/0.004994, allocations: 112.8 kB / 0.6528 GB, free: 35.2 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 3.901e-05/0.005033, allocations: 68 kB / 0.6529 GB, free: 35.15 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 7.965e-06/0.005041, allocations: 1.906 kB / 0.6529 GB, free: 35.15 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001268/0.005168, allocations: 189.8 kB / 0.6531 GB, free: 35 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 1.623e-06/0.005169, allocations: 1.406 kB / 0.6531 GB, free: 35 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0005395/0.005709, allocations: 0.5396 MB / 0.6536 GB, free: 34.6 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.563e-05/0.005744, allocations: 139.6 kB / 0.6537 GB, free: 34.44 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 7.086e-05/0.005815, allocations: 198.1 kB / 0.6539 GB, free: 34.26 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.285e-05/0.005828, allocations: 33.64 kB / 0.6539 GB, free: 34.23 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 4.178e-05/0.00587, allocations: 156.8 kB / 0.6541 GB, free: 34.08 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 3.214e-05/0.005902, allocations: 71.59 kB / 0.6542 GB, free: 34.02 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.212e-05/0.005954, allocations: 57.89 kB / 0.6542 GB, free: 33.98 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 5.869e-05/0.006013, allocations: 0.4986 MB / 0.6547 GB, free: 33.48 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 5.153e-05/0.006064, allocations: 97.64 kB / 0.6548 GB, free: 33.4 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 7.385e-05/0.006138, allocations: 190.7 kB / 0.655 GB, free: 33.2 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.000156/0.006294, allocations: 311.5 kB / 0.6553 GB, free: 32.92 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.252e-06/0.006295, allocations: 0 / 0.6553 GB, free: 32.92 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002082/0.006504, allocations: 296.2 kB / 0.6555 GB, free: 32.72 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.628e-05/0.00653, allocations: 60.75 kB / 0.6556 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.43e-06/0.006535, allocations: 3.875 kB / 0.6556 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 9.177e-06/0.006544, allocations: 7.734 kB / 0.6556 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001218/0.006666, allocations: 47.47 kB / 0.6557 GB, free: 32.65 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 4.598e-06/0.006671, allocations: 3.156 kB / 0.6557 GB, free: 32.65 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.146e-05/0.006742, allocations: 19.08 kB / 0.6557 GB, free: 32.64 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.214e-05/0.006754, allocations: 7.438 kB / 0.6557 GB, free: 32.64 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 6 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
         central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" 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
         central.rising:DISCRETE(fixed = true protected = true )  type: Boolean
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 7
 * Number of states: 0 ()
 * Number of discrete variables: 13 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,central.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (30):
 * Single equations (assignments): 28
 * 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 0.0001153/0.00687, allocations: 226.1 kB / 0.6559 GB, free: 32.43 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.529e-05/0.006895, allocations: 25.22 kB / 0.6559 GB, free: 32.42 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 2.71e-05/0.006922, allocations: 20.39 kB / 0.6559 GB, free: 32.41 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.056e-06/0.006925, allocations: 6.188 kB / 0.656 GB, free: 32.4 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.033e-06/0.006927, allocations: 0 / 0.656 GB, free: 32.4 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.167e-06/0.006931, allocations: 0.5938 kB / 0.656 GB, free: 32.4 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003005/0.007232, allocations: 0.4901 MB / 0.6564 GB, free: 32 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.443e-06/0.007233, allocations: 1.406 kB / 0.6564 GB, free: 32 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001162/0.00735, allocations: 35.62 kB / 0.6565 GB, free: 32 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.006e-06/0.007353, allocations: 0.5625 kB / 0.6565 GB, free: 32 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.324e-05/0.007366, allocations: 9.281 kB / 0.6565 GB, free: 32 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.106e-06/0.007369, allocations: 3.75 kB / 0.6565 GB, free: 32 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.112e-06/0.00737, allocations: 0.5625 kB / 0.6565 GB, free: 32 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003162/0.007686, allocations: 438.8 kB / 0.6569 GB, free: 31.68 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.35e-05/0.0077, allocations: 11.81 kB / 0.6569 GB, free: 31.67 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.149e-05/0.007721, allocations: 14.06 kB / 0.6569 GB, free: 31.66 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.883e-05/0.00779, allocations: 11.2 kB / 0.6569 GB, free: 31.66 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.245e-05/0.007832, allocations: 18.05 kB / 0.657 GB, free: 31.66 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.045e-05/0.007843, allocations: 8.406 kB / 0.657 GB, free: 31.65 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 3.902e-05/0.007882, allocations: 149.3 kB / 0.6571 GB, free: 31.53 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 7e-08/0.007882, allocations: 0 / 0.6571 GB, free: 31.53 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0001836/0.008066, allocations: 46.97 kB / 0.6571 GB, free: 31.53 MB / 0.5262 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,central.C,central.AUC,elim.MExc)
 * Number of discrete variables: 8 ($whenCondition1,$whenCondition2,$whenCondition3,singleDose.pulse.T_start,singleDose.pulse.count,central.Cmax,central.Cmin,central.rising)
 * Number of discrete states: 6 (singleDose.pulse.count,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (18):
 * Single equations (assignments): 15
 * 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 6.485e-05/0.00813, allocations: 118.4 kB / 0.6573 GB, free: 31.43 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0001844/0.008315, allocations: 301.7 kB / 0.6576 GB, free: 31.18 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 9.52e-07/0.008316, allocations: 2.562 kB / 0.6576 GB, free: 31.18 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 7.963e-05/0.008395, allocations: 148.2 kB / 0.6577 GB, free: 31.07 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002377/0.008633, allocations: 50.84 kB / 0.6577 GB, free: 31.05 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001216/0.009849, allocations: 0.5728 MB / 0.6583 GB, free: 30.68 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.126e-05/0.0099, allocations: 80.88 kB / 0.6584 GB, free: 30.6 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 6.166e-05/0.009962, allocations: 17.11 kB / 0.6584 GB, free: 30.6 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001517/0.01011, allocations: 113.6 kB / 0.6585 GB, free: 30.53 MB / 0.5262 GB
Notification: Performance of SimCode: time 1.002e-06/0.01011, allocations: 4.562 kB / 0.6585 GB, free: 30.53 MB / 0.5262 GB
Notification: Performance of Templates: time 0.004362/0.01448, allocations: 2.744 MB / 0.6612 GB, free: 30.29 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.650769346859306]