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 0.0009833/0.0009833, allocations: 80.94 kB / 19.94 MB, free: 4.543 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 0.001102/0.001102, allocations: 177 kB / 23.36 MB, free: 1.129 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 1.017/1.017, allocations: 177.2 MB / 203.8 MB, free: 5.469 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 1.648/1.648, allocations: 273.5 MB / 0.5213 GB, free: 14.62 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 2.014e-06/2.014e-06, allocations: 3.938 kB / 0.5955 GB, free: 2.648 MB / 0.5105 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.075e-05/2.276e-05, allocations: 5.547 kB / 0.5955 GB, free: 2.645 MB / 0.5105 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKPG_1C_Gentamicin): time 0.003364/0.003386, allocations: 2.52 MB / 0.5979 GB, free: 140 kB / 0.5105 GB
Notification: Performance of NFInst.instExpressions: time 0.001764/0.005151, allocations: 0.9423 MB / 0.5988 GB, free: 15.2 MB / 0.5261 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001327/0.005284, allocations: 7.938 kB / 0.5988 GB, free: 15.19 MB / 0.5261 GB
Notification: Performance of NFTyping.typeComponents: time 0.0004236/0.005707, allocations: 115.7 kB / 0.599 GB, free: 15.08 MB / 0.5261 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001917/0.005899, allocations: 86.55 kB / 0.599 GB, free: 15.02 MB / 0.5261 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0004544/0.006353, allocations: 146.5 kB / 0.5992 GB, free: 14.88 MB / 0.5261 GB
Notification: Performance of NFFlatten.flatten: time 0.0007863/0.00714, allocations: 280.3 kB / 0.5994 GB, free: 14.65 MB / 0.5261 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001572/0.007297, allocations: 47.03 kB / 0.5995 GB, free: 14.6 MB / 0.5261 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002525/0.007549, allocations: 151.6 kB / 0.5996 GB, free: 14.45 MB / 0.5261 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001729/0.007722, allocations: 95.69 kB / 0.5997 GB, free: 14.36 MB / 0.5261 GB
Notification: Performance of NFPackage.collectConstants: time 3.242e-05/0.007755, allocations: 16 kB / 0.5997 GB, free: 14.34 MB / 0.5261 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0002818/0.008036, allocations: 171.3 kB / 0.5999 GB, free: 14.17 MB / 0.5261 GB
Notification: Performance of NFScalarize.scalarize: time 8.399e-05/0.00812, allocations: 59.7 kB / 0.6 GB, free: 14.11 MB / 0.5261 GB
Notification: Performance of NFVerifyModel.verify: time 9.457e-05/0.008215, allocations: 83.77 kB / 0.6 GB, free: 14.03 MB / 0.5261 GB
Notification: Performance of NFConvertDAE.convert: time 0.0004441/0.008659, allocations: 330.8 kB / 0.6004 GB, free: 13.71 MB / 0.5261 GB
Notification: Performance of FrontEnd - DAE generated: time 2.705e-06/0.008662, allocations: 0 / 0.6004 GB, free: 13.71 MB / 0.5261 GB
Notification: Performance of FrontEnd: time 1.082e-06/0.008663, allocations: 4 kB / 0.6004 GB, free: 13.71 MB / 0.5261 GB
Notification: Performance of Transformations before backend: time 6.553e-06/0.008669, allocations: 0 / 0.6004 GB, free: 13.71 MB / 0.5261 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 0.0007004/0.00937, allocations: 0.5805 MB / 0.6009 GB, free: 13.08 MB / 0.5261 GB
Notification: Performance of prepare preOptimizeDAE: time 3.678e-05/0.009407, allocations: 12.03 kB / 0.6009 GB, free: 13.07 MB / 0.5261 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002275/0.009634, allocations: 100.8 kB / 0.601 GB, free: 12.97 MB / 0.5261 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002071/0.009841, allocations: 184.8 kB / 0.6012 GB, free: 12.77 MB / 0.5261 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.883e-05/0.00986, allocations: 12.38 kB / 0.6012 GB, free: 12.75 MB / 0.5261 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.916e-05/0.009889, allocations: 20.38 kB / 0.6012 GB, free: 12.73 MB / 0.5261 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002334/0.01012, allocations: 236.8 kB / 0.6015 GB, free: 12.48 MB / 0.5261 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.548e-05/0.01014, allocations: 3.984 kB / 0.6015 GB, free: 12.47 MB / 0.5261 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.333e-05/0.01015, allocations: 8 kB / 0.6015 GB, free: 12.46 MB / 0.5261 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.053e-06/0.01016, allocations: 4 kB / 0.6015 GB, free: 12.46 MB / 0.5261 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001256/0.01028, allocations: 144.9 kB / 0.6016 GB, free: 12.3 MB / 0.5261 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004731/0.01076, allocations: 330.9 kB / 0.6019 GB, free: 11.96 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001986/0.01096, allocations: 229.7 kB / 0.6022 GB, free: 11.71 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 7.683e-05/0.01103, allocations: 122 kB / 0.6023 GB, free: 11.57 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 9.538e-06/0.01104, allocations: 4 kB / 0.6023 GB, free: 11.57 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002055/0.01125, allocations: 283.1 kB / 0.6025 GB, free: 11.25 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=26): time 1.452e-06/0.01125, allocations: 0 / 0.6025 GB, free: 11.25 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=27): time 0.0009329/0.01218, allocations: 0.9131 MB / 0.6034 GB, free: 10.21 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.551e-05/0.01226, allocations: 191.9 kB / 0.6036 GB, free: 9.984 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001386/0.0124, allocations: 221 kB / 0.6038 GB, free: 9.762 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 2.21e-05/0.01242, allocations: 33.7 kB / 0.6039 GB, free: 9.723 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 6.395e-05/0.01248, allocations: 133 kB / 0.604 GB, free: 9.586 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 5.165e-05/0.01253, allocations: 87.3 kB / 0.6041 GB, free: 9.5 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.751e-05/0.01261, allocations: 69.84 kB / 0.6041 GB, free: 9.426 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 9.655e-05/0.01271, allocations: 346.7 kB / 0.6045 GB, free: 9.078 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001159/0.01282, allocations: 163.2 kB / 0.6046 GB, free: 8.891 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001274/0.01295, allocations: 235.7 kB / 0.6049 GB, free: 8.605 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002998/0.01325, allocations: 0.4966 MB / 0.6053 GB, free: 8.023 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.365e-06/0.01325, allocations: 4.031 kB / 0.6053 GB, free: 8.02 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0003625/0.01362, allocations: 453.3 kB / 0.6058 GB, free: 7.527 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 5.818e-05/0.01367, allocations: 118.8 kB / 0.6059 GB, free: 7.387 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.326e-06/0.01368, allocations: 7.469 kB / 0.6059 GB, free: 7.383 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.197e-05/0.01369, allocations: 4 kB / 0.6059 GB, free: 7.379 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0004742/0.01417, allocations: 63.89 kB / 0.606 GB, free: 7.316 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 5.731e-06/0.01417, allocations: 8.125 kB / 0.606 GB, free: 7.309 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.339e-05/0.01426, allocations: 19.98 kB / 0.606 GB, free: 7.289 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.118e-05/0.0143, allocations: 43.94 kB / 0.606 GB, free: 7.246 MB / 0.5261 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 0.0001886/0.01449, allocations: 239.3 kB / 0.6063 GB, free: 6.98 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001065/0.01459, allocations: 79.86 kB / 0.6063 GB, free: 6.902 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.713e-05/0.01463, allocations: 30.95 kB / 0.6064 GB, free: 6.875 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.565e-06/0.01463, allocations: 0 / 0.6064 GB, free: 6.875 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.118e-06/0.01464, allocations: 7.875 kB / 0.6064 GB, free: 6.867 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.037e-06/0.01464, allocations: 4 kB / 0.6064 GB, free: 6.863 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004549/0.0151, allocations: 0.5809 MB / 0.6069 GB, free: 6.23 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.984e-06/0.0151, allocations: 0 / 0.6069 GB, free: 6.23 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000149/0.01525, allocations: 43.91 kB / 0.607 GB, free: 6.188 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 4.659e-06/0.01525, allocations: 15.86 kB / 0.607 GB, free: 6.172 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.594e-05/0.01527, allocations: 12 kB / 0.607 GB, free: 6.16 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.364e-06/0.01527, allocations: 0 / 0.607 GB, free: 6.16 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.143e-06/0.01527, allocations: 0 / 0.607 GB, free: 6.16 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004709/0.01574, allocations: 0.677 MB / 0.6077 GB, free: 5.41 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.724e-05/0.01577, allocations: 19.86 kB / 0.6077 GB, free: 5.391 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.027e-05/0.0158, allocations: 8 kB / 0.6077 GB, free: 5.383 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.143e-05/0.01588, allocations: 11.98 kB / 0.6077 GB, free: 5.371 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.429e-05/0.01594, allocations: 19.97 kB / 0.6077 GB, free: 5.352 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.146e-05/0.01598, allocations: 55.86 kB / 0.6078 GB, free: 5.297 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 6.53e-05/0.01604, allocations: 74.78 kB / 0.6078 GB, free: 5.227 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 6e-08/0.01604, allocations: 0 / 0.6078 GB, free: 5.227 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.0002608/0.0163, allocations: 72 kB / 0.6079 GB, free: 5.156 MB / 0.5261 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 0.0002308/0.01653, allocations: 135.6 kB / 0.608 GB, free: 5.02 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.0003992/0.01693, allocations: 0.5608 MB / 0.6086 GB, free: 4.367 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 7.694e-06/0.01694, allocations: 8.125 kB / 0.6086 GB, free: 4.359 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001807/0.01712, allocations: 335.3 kB / 0.6089 GB, free: 3.977 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000264/0.01739, allocations: 56.45 kB / 0.609 GB, free: 3.922 MB / 0.5261 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001427/0.01881, allocations: 0.7566 MB / 0.6097 GB, free: 3.117 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 7.862e-05/0.01889, allocations: 100.3 kB / 0.6098 GB, free: 3 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 8.418e-05/0.01898, allocations: 17.94 kB / 0.6098 GB, free: 2.98 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001741/0.01915, allocations: 123.3 kB / 0.6099 GB, free: 2.859 MB / 0.5261 GB
Notification: Performance of SimCode: time 7.71e-07/0.01915, allocations: 4 kB / 0.6099 GB, free: 2.855 MB / 0.5261 GB
Notification: Performance of Templates: time 0.4097/0.4289, allocations: 5.143 MB / 0.615 GB, free: 52.75 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 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.952375805005431]