Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.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 0.001143/0.001143, allocations: 85.17 kB / 19.87 MB, free: 4.617 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 0.001156/0.001156, allocations: 169 kB / 23.27 MB, free: 1.223 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 0.9488/0.9488, allocations: 177.1 MB / 203.7 MB, free: 5.516 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 1.585/1.585, allocations: 273.5 MB / 0.5212 GB, free: 14.77 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.PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin")
translateModel(Pharmacolibrary.Examples.PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.793e-06/1.793e-06, allocations: 0 / 0.6474 GB, free: 38.57 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.203e-05/2.383e-05, allocations: 4.906 kB / 0.6474 GB, free: 38.56 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKPG_1C_Gentamicin): time 0.002474/0.002498, allocations: 2.476 MB / 0.6498 GB, free: 36.96 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001052/0.003549, allocations: 0.9235 MB / 0.6507 GB, free: 36.37 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.27e-05/0.003632, allocations: 2.188 kB / 0.6507 GB, free: 36.37 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0003522/0.003984, allocations: 109 kB / 0.6508 GB, free: 36.33 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001172/0.004101, allocations: 91.66 kB / 0.6509 GB, free: 36.29 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003155/0.004417, allocations: 143.5 kB / 0.6511 GB, free: 36.22 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002475/0.004664, allocations: 291.5 kB / 0.6513 GB, free: 36.1 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001211/0.004786, allocations: 43.17 kB / 0.6514 GB, free: 36.07 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001458/0.004931, allocations: 147.2 kB / 0.6515 GB, free: 36.01 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001256/0.005057, allocations: 87.03 kB / 0.6516 GB, free: 35.98 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.903e-05/0.005086, allocations: 25.25 kB / 0.6516 GB, free: 35.98 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001676/0.005254, allocations: 162.8 kB / 0.6518 GB, free: 35.93 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 6.317e-05/0.005317, allocations: 60.03 kB / 0.6518 GB, free: 35.89 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 6.726e-05/0.005384, allocations: 81.73 kB / 0.6519 GB, free: 35.86 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002857/0.00567, allocations: 330.9 kB / 0.6522 GB, free: 35.71 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.645e-06/0.005672, allocations: 4.625 kB / 0.6522 GB, free: 35.71 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 9.42e-07/0.005673, allocations: 0 / 0.6522 GB, free: 35.71 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 3.827e-06/0.005677, allocations: 0 / 0.6522 GB, free: 35.71 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: 40
 * Number of variables: 40
Notification: Performance of Generate backend data structure: time 0.0005588/0.006236, allocations: 0.7077 MB / 0.6529 GB, free: 35.07 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.856e-05/0.006274, allocations: 10.91 kB / 0.6529 GB, free: 35.07 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.000194/0.006469, allocations: 116.1 kB / 0.653 GB, free: 35.04 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001562/0.006625, allocations: 206.7 kB / 0.6532 GB, free: 34.84 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.815e-05/0.006643, allocations: 13.62 kB / 0.6533 GB, free: 34.84 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.767e-05/0.00667, allocations: 26.59 kB / 0.6533 GB, free: 34.83 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002104/0.006881, allocations: 233.9 kB / 0.6535 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.324e-05/0.006894, allocations: 3.344 kB / 0.6535 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.202e-05/0.006906, allocations: 6.375 kB / 0.6535 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.484e-06/0.006914, allocations: 3.406 kB / 0.6535 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001039/0.007017, allocations: 148.6 kB / 0.6537 GB, free: 34.56 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004897/0.007507, allocations: 468.3 kB / 0.6541 GB, free: 34.22 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001647/0.007672, allocations: 198.7 kB / 0.6543 GB, free: 34.07 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 5.952e-05/0.007731, allocations: 133.3 kB / 0.6544 GB, free: 33.95 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 9.799e-06/0.007741, allocations: 3.375 kB / 0.6544 GB, free: 33.95 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.00018/0.007921, allocations: 279.3 kB / 0.6547 GB, free: 33.72 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 1.743e-06/0.007923, allocations: 3.938 kB / 0.6547 GB, free: 33.71 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.0008831/0.008806, allocations: 0.9819 MB / 0.6557 GB, free: 32.95 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.363e-05/0.00885, allocations: 194.5 kB / 0.6558 GB, free: 32.72 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001988/0.009048, allocations: 309.4 kB / 0.6561 GB, free: 32.51 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.726e-05/0.009066, allocations: 36.3 kB / 0.6562 GB, free: 32.48 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 7.816e-05/0.009144, allocations: 213 kB / 0.6564 GB, free: 32.29 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 4.834e-05/0.009192, allocations: 88.72 kB / 0.6565 GB, free: 32.22 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.261e-05/0.009265, allocations: 70.64 kB / 0.6565 GB, free: 32.17 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 7.018e-05/0.009335, allocations: 0.5235 MB / 0.657 GB, free: 31.66 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 9.974e-05/0.009435, allocations: 166.4 kB / 0.6572 GB, free: 31.51 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001156/0.00955, allocations: 258.9 kB / 0.6574 GB, free: 31.25 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002199/0.00977, allocations: 0.5244 MB / 0.6579 GB, free: 30.76 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.583e-06/0.009772, allocations: 0 / 0.6579 GB, free: 30.76 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0003127/0.01008, allocations: 0.5043 MB / 0.6584 GB, free: 30.39 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.047e-05/0.01012, allocations: 118.9 kB / 0.6586 GB, free: 30.27 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.6e-06/0.01013, allocations: 1.438 kB / 0.6586 GB, free: 30.27 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.446e-05/0.01015, allocations: 8.156 kB / 0.6586 GB, free: 30.27 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000133/0.01028, allocations: 56.28 kB / 0.6586 GB, free: 30.26 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 4.368e-06/0.01028, allocations: 2.844 kB / 0.6586 GB, free: 30.26 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.027e-05/0.01036, allocations: 21.98 kB / 0.6586 GB, free: 30.25 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.221e-05/0.01041, allocations: 49.77 kB / 0.6587 GB, free: 30.25 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: 15 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,CYP2C19.status,SLC22A2.status,central.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (34):
 * Single equations (assignments): 30
 * Array equations: 0
 * Algorithm blocks: 4
 * 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 0.0001498/0.01056, allocations: 282.6 kB / 0.659 GB, free: 29.98 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.809e-05/0.01065, allocations: 92.47 kB / 0.659 GB, free: 29.95 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.83e-05/0.01069, allocations: 28.53 kB / 0.6591 GB, free: 29.93 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.967e-06/0.0107, allocations: 8.656 kB / 0.6591 GB, free: 29.93 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.667e-06/0.0107, allocations: 3.844 kB / 0.6591 GB, free: 29.93 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.699e-06/0.0107, allocations: 1.406 kB / 0.6591 GB, free: 29.93 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004393/0.01114, allocations: 0.7007 MB / 0.6598 GB, free: 29.38 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.144e-06/0.01114, allocations: 0 / 0.6598 GB, free: 29.38 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001134/0.01126, allocations: 40.67 kB / 0.6598 GB, free: 29.37 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.818e-06/0.01126, allocations: 1.438 kB / 0.6598 GB, free: 29.37 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.428e-05/0.01128, allocations: 11.17 kB / 0.6598 GB, free: 29.37 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.395e-06/0.01128, allocations: 1.438 kB / 0.6598 GB, free: 29.37 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.082e-06/0.01128, allocations: 0 / 0.6598 GB, free: 29.37 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004094/0.01169, allocations: 0.7433 MB / 0.6605 GB, free: 28.81 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.039e-05/0.01171, allocations: 21.55 kB / 0.6606 GB, free: 28.8 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.524e-05/0.01173, allocations: 15.72 kB / 0.6606 GB, free: 28.79 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.794e-05/0.01181, allocations: 10.33 kB / 0.6606 GB, free: 28.79 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.697e-05/0.01186, allocations: 26.8 kB / 0.6606 GB, free: 28.78 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.272e-05/0.0119, allocations: 47.8 kB / 0.6607 GB, free: 28.78 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 7.392e-05/0.01198, allocations: 204.7 kB / 0.6609 GB, free: 28.64 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 7e-08/0.01198, allocations: 1.062 kB / 0.6609 GB, free: 28.64 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002423/0.01222, allocations: 76.31 kB / 0.6609 GB, free: 28.62 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: 10 ($whenCondition1,$whenCondition2,$whenCondition3,singleDose.pulse.T_start,singleDose.pulse.count,central.Cmax,central.Cmin,central.rising,SLC22A2.status,CYP2C19.status)
 * Number of discrete states: 8 (singleDose.pulse.count,SLC22A2.status,CYP2C19.status,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (22):
 * Single equations (assignments): 17
 * Array equations: 0
 * Algorithm blocks: 3
 * 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 0.0001818/0.0124, allocations: 150.1 kB / 0.6611 GB, free: 28.53 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.000262/0.01266, allocations: 0.565 MB / 0.6616 GB, free: 28.01 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.633e-06/0.01266, allocations: 0 / 0.6616 GB, free: 28.01 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001161/0.01278, allocations: 336.4 kB / 0.662 GB, free: 27.7 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003/0.01308, allocations: 70.66 kB / 0.662 GB, free: 27.69 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001247/0.01433, allocations: 0.8318 MB / 0.6628 GB, free: 27.13 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.961e-05/0.01438, allocations: 100.7 kB / 0.6629 GB, free: 27.05 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 5.356e-05/0.01443, allocations: 20.05 kB / 0.6629 GB, free: 27.05 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001415/0.01457, allocations: 139.8 kB / 0.6631 GB, free: 26.98 MB / 0.5262 GB
Notification: Performance of SimCode: time 7.32e-07/0.01457, allocations: 0 / 0.6631 GB, free: 26.98 MB / 0.5262 GB
Notification: Performance of Templates: time 0.007585/0.02216, allocations: 5.195 MB / 0.6682 GB, free: 26.45 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.001105944160372]