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 0.001469/0.001469, allocations: 80.94 kB / 19.94 MB, free: 4.547 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 0.001233/0.001233, allocations: 173 kB / 23.36 MB, free: 1.133 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 0.9837/0.9837, allocations: 177.1 MB / 203.8 MB, free: 5.473 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 1.592/1.592, allocations: 273.5 MB / 0.5213 GB, free: 14.65 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 2.054e-06/2.054e-06, allocations: 0 / 0.5954 GB, free: 2.73 MB / 0.5105 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.429e-05/2.634e-05, allocations: 6.25 kB / 0.5954 GB, free: 2.723 MB / 0.5105 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKPG_1C_Gentamicin): time 0.003924/0.003951, allocations: 2.482 MB / 0.5978 GB, free: 260 kB / 0.5105 GB
Notification: Performance of NFInst.instExpressions: time 0.001688/0.005638, allocations: 0.9407 MB / 0.5988 GB, free: 15.32 MB / 0.5261 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001401/0.005778, allocations: 7.938 kB / 0.5988 GB, free: 15.31 MB / 0.5261 GB
Notification: Performance of NFTyping.typeComponents: time 0.0004515/0.00623, allocations: 111.2 kB / 0.5989 GB, free: 15.21 MB / 0.5261 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001901/0.00642, allocations: 85.62 kB / 0.5989 GB, free: 15.14 MB / 0.5261 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0004867/0.006907, allocations: 146.2 kB / 0.5991 GB, free: 15 MB / 0.5261 GB
Notification: Performance of NFFlatten.flatten: time 0.0004326/0.007339, allocations: 288.7 kB / 0.5994 GB, free: 14.77 MB / 0.5261 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001718/0.007511, allocations: 51.02 kB / 0.5994 GB, free: 14.71 MB / 0.5261 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002866/0.007798, allocations: 147.6 kB / 0.5996 GB, free: 14.57 MB / 0.5261 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002021/0.008, allocations: 83.72 kB / 0.5996 GB, free: 14.49 MB / 0.5261 GB
Notification: Performance of NFPackage.collectConstants: time 4.135e-05/0.008041, allocations: 20 kB / 0.5996 GB, free: 14.47 MB / 0.5261 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0002608/0.008302, allocations: 159.3 kB / 0.5998 GB, free: 14.31 MB / 0.5261 GB
Notification: Performance of NFScalarize.scalarize: time 8.723e-05/0.008389, allocations: 67.7 kB / 0.5999 GB, free: 14.25 MB / 0.5261 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001035/0.008493, allocations: 83.77 kB / 0.5999 GB, free: 14.16 MB / 0.5261 GB
Notification: Performance of NFConvertDAE.convert: time 0.0005067/0.008999, allocations: 334.8 kB / 0.6003 GB, free: 13.84 MB / 0.5261 GB
Notification: Performance of FrontEnd - DAE generated: time 5.13e-06/0.009004, allocations: 0 / 0.6003 GB, free: 13.84 MB / 0.5261 GB
Notification: Performance of FrontEnd: time 1.402e-06/0.009006, allocations: 0 / 0.6003 GB, free: 13.84 MB / 0.5261 GB
Notification: Performance of Transformations before backend: time 8.295e-06/0.009014, allocations: 0 / 0.6003 GB, free: 13.84 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 0.0009331/0.009947, allocations: 0.5728 MB / 0.6008 GB, free: 13.21 MB / 0.5261 GB
Notification: Performance of prepare preOptimizeDAE: time 3.853e-05/0.009986, allocations: 12.03 kB / 0.6008 GB, free: 13.2 MB / 0.5261 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.000294/0.01028, allocations: 100.8 kB / 0.6009 GB, free: 13.11 MB / 0.5261 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002475/0.01053, allocations: 192.8 kB / 0.6011 GB, free: 12.89 MB / 0.5261 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.336e-05/0.01055, allocations: 12.38 kB / 0.6011 GB, free: 12.88 MB / 0.5261 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.188e-05/0.01059, allocations: 16.38 kB / 0.6011 GB, free: 12.87 MB / 0.5261 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003134/0.01091, allocations: 240.2 kB / 0.6014 GB, free: 12.61 MB / 0.5261 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.72e-05/0.01092, allocations: 7.984 kB / 0.6014 GB, free: 12.6 MB / 0.5261 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.685e-05/0.01094, allocations: 4 kB / 0.6014 GB, free: 12.6 MB / 0.5261 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.175e-06/0.01095, allocations: 4 kB / 0.6014 GB, free: 12.59 MB / 0.5261 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001687/0.01112, allocations: 144.9 kB / 0.6015 GB, free: 12.44 MB / 0.5261 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006036/0.01172, allocations: 331 kB / 0.6018 GB, free: 12.1 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002373/0.01196, allocations: 231.4 kB / 0.6021 GB, free: 11.84 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 9.824e-05/0.01206, allocations: 122 kB / 0.6022 GB, free: 11.7 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.161e-05/0.01207, allocations: 7.984 kB / 0.6022 GB, free: 11.7 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002397/0.01231, allocations: 267.2 kB / 0.6024 GB, free: 11.39 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=26): time 2.064e-06/0.01231, allocations: 0 / 0.6024 GB, free: 11.39 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=27): time 0.001126/0.01344, allocations: 0.9167 MB / 0.6033 GB, free: 10.35 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 9.414e-05/0.01353, allocations: 195.9 kB / 0.6035 GB, free: 10.12 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001972/0.01373, allocations: 225 kB / 0.6037 GB, free: 9.891 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 2.913e-05/0.01376, allocations: 33.7 kB / 0.6038 GB, free: 9.852 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 7.595e-05/0.01383, allocations: 129 kB / 0.6039 GB, free: 9.719 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 6.703e-05/0.0139, allocations: 87.3 kB / 0.604 GB, free: 9.633 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.708e-05/0.01399, allocations: 65.84 kB / 0.604 GB, free: 9.562 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 0.0001121/0.0141, allocations: 342.7 kB / 0.6044 GB, free: 9.219 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001422/0.01424, allocations: 171.2 kB / 0.6045 GB, free: 9.023 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001583/0.0144, allocations: 239.7 kB / 0.6048 GB, free: 8.734 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003745/0.01477, allocations: 0.4967 MB / 0.6052 GB, free: 8.152 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.036e-06/0.01478, allocations: 0 / 0.6052 GB, free: 8.152 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0004325/0.01521, allocations: 453.8 kB / 0.6057 GB, free: 7.66 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 6.855e-05/0.01528, allocations: 118.8 kB / 0.6058 GB, free: 7.52 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.594e-06/0.01529, allocations: 8.188 kB / 0.6058 GB, free: 7.512 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.489e-05/0.0153, allocations: 4 kB / 0.6058 GB, free: 7.508 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001775/0.01548, allocations: 47.92 kB / 0.6058 GB, free: 7.461 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.175e-05/0.01549, allocations: 15.86 kB / 0.6059 GB, free: 7.445 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001229/0.01561, allocations: 12 kB / 0.6059 GB, free: 7.434 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.187e-05/0.01568, allocations: 51.92 kB / 0.6059 GB, free: 7.383 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 0.0002195/0.0159, allocations: 242.9 kB / 0.6062 GB, free: 7.117 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001283/0.01603, allocations: 79.86 kB / 0.6062 GB, free: 7.039 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.219e-05/0.01607, allocations: 26.95 kB / 0.6063 GB, free: 7.016 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.038e-06/0.01608, allocations: 4 kB / 0.6063 GB, free: 7.012 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.925e-06/0.01608, allocations: 0 / 0.6063 GB, free: 7.012 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.211e-06/0.01609, allocations: 3.938 kB / 0.6063 GB, free: 7.008 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005532/0.01664, allocations: 0.5903 MB / 0.6068 GB, free: 6.359 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.604e-06/0.01664, allocations: 0 / 0.6068 GB, free: 6.359 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001555/0.0168, allocations: 31.98 kB / 0.6069 GB, free: 6.328 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.216e-06/0.0168, allocations: 0 / 0.6069 GB, free: 6.328 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.297e-05/0.01682, allocations: 15.92 kB / 0.6069 GB, free: 6.312 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.925e-06/0.01683, allocations: 3.938 kB / 0.6069 GB, free: 6.312 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.02e-07/0.01683, allocations: 3.938 kB / 0.6069 GB, free: 6.309 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005906/0.01742, allocations: 0.6692 MB / 0.6075 GB, free: 5.566 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.425e-05/0.01745, allocations: 23.84 kB / 0.6076 GB, free: 5.543 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.182e-05/0.0175, allocations: 8 kB / 0.6076 GB, free: 5.535 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001459/0.01764, allocations: 16 kB / 0.6076 GB, free: 5.52 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.3e-05/0.0177, allocations: 23.95 kB / 0.6076 GB, free: 5.496 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 6.158e-05/0.01777, allocations: 47.94 kB / 0.6077 GB, free: 5.449 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 9.443e-05/0.01786, allocations: 82.75 kB / 0.6077 GB, free: 5.371 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 1e-07/0.01786, allocations: 0 / 0.6077 GB, free: 5.371 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.0003724/0.01823, allocations: 72 kB / 0.6078 GB, free: 5.301 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 0.000232/0.01846, allocations: 136 kB / 0.6079 GB, free: 5.164 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.00052/0.01898, allocations: 0.5567 MB / 0.6085 GB, free: 4.512 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 6.742e-06/0.01899, allocations: 4 kB / 0.6085 GB, free: 4.508 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 0.0007689/0.01976, allocations: 331.3 kB / 0.6088 GB, free: 4.129 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004091/0.02017, allocations: 67.89 kB / 0.6089 GB, free: 4.066 MB / 0.5261 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001863/0.02203, allocations: 0.7443 MB / 0.6096 GB, free: 3.27 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 8.146e-05/0.02211, allocations: 100.3 kB / 0.6097 GB, free: 3.152 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 9.794e-05/0.02221, allocations: 25.56 kB / 0.6097 GB, free: 3.129 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002035/0.02241, allocations: 119.3 kB / 0.6098 GB, free: 3.012 MB / 0.5261 GB
Notification: Performance of SimCode: time 8.11e-07/0.02242, allocations: 0 / 0.6098 GB, free: 3.012 MB / 0.5261 GB
Notification: Performance of Templates: time 0.4204/0.4428, allocations: 5.092 MB / 0.6148 GB, free: 52.82 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: 4.775091975927353]