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 0.001271/0.001271, allocations: 92.2 kB / 20.19 MB, free: 4.359 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 0.0009488/0.0009488, allocations: 173 kB / 23.49 MB, free: 1.059 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 0.95/0.95, allocations: 177.1 MB / 203.8 MB, free: 5.652 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 1.574/1.574, allocations: 273.5 MB / 0.5213 GB, free: 14.81 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 2.345e-06/2.345e-06, allocations: 0 / 0.6462 GB, free: 39.08 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.41e-05/2.644e-05, allocations: 5.125 kB / 0.6462 GB, free: 39.08 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKOneCompartmentModel): time 0.00239/0.002416, allocations: 2.054 MB / 0.6482 GB, free: 37.74 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0008592/0.003276, allocations: 0.5408 MB / 0.6487 GB, free: 37.38 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.226e-05/0.003358, allocations: 2.156 kB / 0.6487 GB, free: 37.38 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001132/0.003471, allocations: 18.86 kB / 0.6487 GB, free: 37.37 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001474/0.003618, allocations: 58.38 kB / 0.6488 GB, free: 37.34 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001914/0.00381, allocations: 46.05 kB / 0.6488 GB, free: 37.32 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002471/0.004057, allocations: 195.8 kB / 0.649 GB, free: 37.26 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001253/0.004182, allocations: 29.75 kB / 0.6491 GB, free: 37.24 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001444/0.004327, allocations: 103.9 kB / 0.6492 GB, free: 37.2 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001073/0.004434, allocations: 59.41 kB / 0.6492 GB, free: 37.18 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 3.124e-05/0.004465, allocations: 15.31 kB / 0.6492 GB, free: 37.18 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.158e-05/0.004487, allocations: 16.72 kB / 0.6492 GB, free: 37.18 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 3.252e-05/0.004519, allocations: 27.83 kB / 0.6493 GB, free: 37.16 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 8.082e-05/0.0046, allocations: 60.19 kB / 0.6493 GB, free: 37.13 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001781/0.004778, allocations: 118.2 kB / 0.6494 GB, free: 37.07 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.665e-06/0.004781, allocations: 1.5 kB / 0.6494 GB, free: 37.07 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 8.32e-07/0.004782, allocations: 0.9375 kB / 0.6494 GB, free: 37.07 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.799e-06/0.004787, allocations: 3.938 kB / 0.6494 GB, free: 37.07 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 0.0005812/0.005368, allocations: 0.5169 MB / 0.65 GB, free: 36.58 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.956e-05/0.005407, allocations: 12.44 kB / 0.65 GB, free: 36.58 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.333e-05/0.005471, allocations: 26.8 kB / 0.65 GB, free: 36.57 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002195/0.00569, allocations: 169.1 kB / 0.6502 GB, free: 36.41 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.353e-05/0.005704, allocations: 4 kB / 0.6502 GB, free: 36.41 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.479e-05/0.005738, allocations: 24.84 kB / 0.6502 GB, free: 36.4 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001864/0.005925, allocations: 144.4 kB / 0.6503 GB, free: 36.3 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.407e-05/0.005939, allocations: 10.2 kB / 0.6503 GB, free: 36.3 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.482e-05/0.005954, allocations: 7.328 kB / 0.6503 GB, free: 36.29 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.617e-06/0.005962, allocations: 3.531 kB / 0.6503 GB, free: 36.29 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001075/0.00607, allocations: 80.19 kB / 0.6504 GB, free: 36.26 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004689/0.006539, allocations: 398.8 kB / 0.6508 GB, free: 35.93 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001547/0.006693, allocations: 116.8 kB / 0.6509 GB, free: 35.85 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 5.687e-05/0.00675, allocations: 68.53 kB / 0.651 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.067e-05/0.006761, allocations: 3.656 kB / 0.651 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001725/0.006933, allocations: 197.5 kB / 0.6512 GB, free: 35.64 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 1.763e-06/0.006935, allocations: 3.938 kB / 0.6512 GB, free: 35.63 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0007477/0.007683, allocations: 0.5759 MB / 0.6517 GB, free: 35.21 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.899e-05/0.007722, allocations: 137.6 kB / 0.6519 GB, free: 35.05 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.157e-05/0.007813, allocations: 202.1 kB / 0.6521 GB, free: 34.88 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.478e-05/0.007828, allocations: 35.88 kB / 0.6521 GB, free: 34.84 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 4.965e-05/0.007878, allocations: 159 kB / 0.6522 GB, free: 34.69 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 3.309e-05/0.007911, allocations: 63.11 kB / 0.6523 GB, free: 34.64 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.352e-05/0.007964, allocations: 50.69 kB / 0.6523 GB, free: 34.61 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 5.485e-05/0.008019, allocations: 0.4958 MB / 0.6528 GB, free: 34.11 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.431e-05/0.008104, allocations: 112.4 kB / 0.6529 GB, free: 34.02 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 9.476e-05/0.008198, allocations: 195.1 kB / 0.6531 GB, free: 33.82 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002137/0.008412, allocations: 328.6 kB / 0.6534 GB, free: 33.52 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.473e-06/0.008413, allocations: 1.375 kB / 0.6534 GB, free: 33.52 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002628/0.008676, allocations: 310.4 kB / 0.6537 GB, free: 33.32 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 3.042e-05/0.008707, allocations: 63.44 kB / 0.6538 GB, free: 33.25 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.442e-06/0.008713, allocations: 4.812 kB / 0.6538 GB, free: 33.25 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.459e-05/0.008728, allocations: 2.219 kB / 0.6538 GB, free: 33.25 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001482/0.008876, allocations: 50.81 kB / 0.6539 GB, free: 33.25 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.624e-06/0.008883, allocations: 6.281 kB / 0.6539 GB, free: 33.24 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.705e-05/0.008961, allocations: 11.72 kB / 0.6539 GB, free: 33.24 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.488e-05/0.008975, allocations: 15.06 kB / 0.6539 GB, free: 33.23 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 0.0001606/0.009136, allocations: 220.3 kB / 0.6541 GB, free: 33.03 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.861e-05/0.009165, allocations: 31.34 kB / 0.6541 GB, free: 33.02 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.007e-05/0.009195, allocations: 19.05 kB / 0.6541 GB, free: 33.01 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.306e-06/0.009198, allocations: 1.969 kB / 0.6541 GB, free: 33.01 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.171e-06/0.009204, allocations: 3.938 kB / 0.6541 GB, free: 33 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.518e-06/0.009209, allocations: 3.938 kB / 0.6542 GB, free: 33 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003717/0.00958, allocations: 0.5211 MB / 0.6547 GB, free: 32.58 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.134e-06/0.009583, allocations: 0 / 0.6547 GB, free: 32.58 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001135/0.009696, allocations: 32.92 kB / 0.6547 GB, free: 32.57 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.266e-06/0.009699, allocations: 1.469 kB / 0.6547 GB, free: 32.57 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.675e-05/0.009716, allocations: 11.92 kB / 0.6547 GB, free: 32.57 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.813e-06/0.009718, allocations: 1.281 kB / 0.6547 GB, free: 32.57 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.192e-06/0.009719, allocations: 0 / 0.6547 GB, free: 32.57 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003088/0.01003, allocations: 451.2 kB / 0.6551 GB, free: 32.24 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.799e-05/0.01005, allocations: 22.19 kB / 0.6552 GB, free: 32.23 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.569e-05/0.01007, allocations: 7.531 kB / 0.6552 GB, free: 32.23 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.022e-05/0.01014, allocations: 9.156 kB / 0.6552 GB, free: 32.23 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.761e-05/0.0102, allocations: 18.91 kB / 0.6552 GB, free: 32.22 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.083e-05/0.01021, allocations: 9.875 kB / 0.6552 GB, free: 32.22 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 4.501e-05/0.01026, allocations: 150.4 kB / 0.6553 GB, free: 32.1 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 8e-08/0.01026, allocations: 0 / 0.6553 GB, free: 32.1 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002024/0.01046, allocations: 47.84 kB / 0.6554 GB, free: 32.09 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 8.654e-05/0.01054, allocations: 116.1 kB / 0.6555 GB, free: 32 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002467/0.01079, allocations: 321.5 kB / 0.6558 GB, free: 31.74 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.993e-06/0.01079, allocations: 0 / 0.6558 GB, free: 31.74 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 9.073e-05/0.01088, allocations: 150.7 kB / 0.656 GB, free: 31.62 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002671/0.01115, allocations: 52.08 kB / 0.656 GB, free: 31.61 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0014/0.01255, allocations: 0.6115 MB / 0.6566 GB, free: 31.21 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 9.908e-05/0.01265, allocations: 111.1 kB / 0.6567 GB, free: 31.13 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.213e-05/0.01271, allocations: 23.17 kB / 0.6567 GB, free: 31.12 MB / 0.5262 GB
Notification: Performance of SimCode: time 1.442e-06/0.01271, allocations: 0 / 0.6567 GB, free: 31.12 MB / 0.5262 GB
Notification: Performance of Templates: time 0.004318/0.01703, allocations: 2.284 MB / 0.659 GB, free: 30.95 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 > Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 6.272848712047562]