Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_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 0.0009114/0.0009114, allocations: 80.75 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 0.001503/0.001503, allocations: 181 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 0.9321/0.9321, allocations: 177.1 MB / 203.8 MB, free: 5.477 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 1.708/1.708, allocations: 273.5 MB / 0.5213 GB, free: 14.71 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.Pharmacogenomics.Patient_PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin")
translateModel(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.633e-06/1.633e-06, allocations: 0 / 0.5955 GB, free: 2.723 MB / 0.5105 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.477e-05/2.64e-05, allocations: 5.828 kB / 0.5955 GB, free: 2.719 MB / 0.5105 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin): time 0.004026/0.004052, allocations: 2.577 MB / 0.598 GB, free: 160 kB / 0.5105 GB
Notification: Performance of NFInst.instExpressions: time 0.001211/0.005263, allocations: 0.9447 MB / 0.5989 GB, free: 15.21 MB / 0.5261 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.523e-05/0.005349, allocations: 0 / 0.5989 GB, free: 15.21 MB / 0.5261 GB
Notification: Performance of NFTyping.typeComponents: time 0.0003508/0.005699, allocations: 128.6 kB / 0.599 GB, free: 15.09 MB / 0.5261 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001333/0.005833, allocations: 84.16 kB / 0.5991 GB, free: 15.04 MB / 0.5261 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003126/0.006145, allocations: 150.2 kB / 0.5993 GB, free: 14.89 MB / 0.5261 GB
Notification: Performance of NFFlatten.flatten: time 0.0002806/0.006426, allocations: 293.6 kB / 0.5995 GB, free: 14.64 MB / 0.5261 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001278/0.006554, allocations: 47.38 kB / 0.5996 GB, free: 14.6 MB / 0.5261 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001654/0.006719, allocations: 155.6 kB / 0.5997 GB, free: 14.45 MB / 0.5261 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001481/0.006867, allocations: 95.69 kB / 0.5998 GB, free: 14.35 MB / 0.5261 GB
Notification: Performance of NFPackage.collectConstants: time 2.791e-05/0.006895, allocations: 20 kB / 0.5998 GB, free: 14.33 MB / 0.5261 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001906/0.007086, allocations: 171.2 kB / 0.6 GB, free: 14.16 MB / 0.5261 GB
Notification: Performance of NFScalarize.scalarize: time 6.337e-05/0.007149, allocations: 63.7 kB / 0.6001 GB, free: 14.1 MB / 0.5261 GB
Notification: Performance of NFVerifyModel.verify: time 7.112e-05/0.00722, allocations: 87.77 kB / 0.6001 GB, free: 14.02 MB / 0.5261 GB
Notification: Performance of NFConvertDAE.convert: time 0.0003386/0.007559, allocations: 346.7 kB / 0.6005 GB, free: 13.68 MB / 0.5261 GB
Notification: Performance of FrontEnd - DAE generated: time 3.998e-06/0.007563, allocations: 0 / 0.6005 GB, free: 13.68 MB / 0.5261 GB
Notification: Performance of FrontEnd: time 1.282e-06/0.007564, allocations: 0 / 0.6005 GB, free: 13.68 MB / 0.5261 GB
Notification: Performance of Transformations before backend: time 6.091e-06/0.00757, allocations: 0 / 0.6005 GB, free: 13.68 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 0.0006125/0.008183, allocations: 0.5806 MB / 0.601 GB, free: 13.05 MB / 0.5261 GB
Notification: Performance of prepare preOptimizeDAE: time 3.044e-05/0.008213, allocations: 8.031 kB / 0.6011 GB, free: 13.04 MB / 0.5261 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.000212/0.008425, allocations: 100.8 kB / 0.6011 GB, free: 12.94 MB / 0.5261 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001829/0.008608, allocations: 200.4 kB / 0.6013 GB, free: 12.73 MB / 0.5261 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.912e-05/0.008627, allocations: 16.38 kB / 0.6014 GB, free: 12.71 MB / 0.5261 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.826e-05/0.008656, allocations: 24.31 kB / 0.6014 GB, free: 12.69 MB / 0.5261 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002348/0.00889, allocations: 236.8 kB / 0.6016 GB, free: 12.43 MB / 0.5261 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.228e-05/0.008903, allocations: 3.953 kB / 0.6016 GB, free: 12.43 MB / 0.5261 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.481e-05/0.008918, allocations: 8 kB / 0.6016 GB, free: 12.42 MB / 0.5261 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.711e-06/0.008923, allocations: 4 kB / 0.6016 GB, free: 12.41 MB / 0.5261 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001187/0.009042, allocations: 144.9 kB / 0.6018 GB, free: 12.26 MB / 0.5261 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004553/0.009497, allocations: 330.6 kB / 0.6021 GB, free: 11.92 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002097/0.009707, allocations: 227.5 kB / 0.6023 GB, free: 11.67 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001124/0.009819, allocations: 126 kB / 0.6024 GB, free: 11.53 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.055e-05/0.00983, allocations: 4 kB / 0.6024 GB, free: 11.52 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002114/0.01004, allocations: 275.3 kB / 0.6027 GB, free: 11.21 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=26): time 1.833e-06/0.01004, allocations: 0 / 0.6027 GB, free: 11.21 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=27): time 0.001045/0.01109, allocations: 0.9094 MB / 0.6036 GB, free: 10.18 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001017/0.01119, allocations: 203.8 kB / 0.6038 GB, free: 9.934 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002121/0.0114, allocations: 237 kB / 0.604 GB, free: 9.695 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 2.917e-05/0.01143, allocations: 33.7 kB / 0.604 GB, free: 9.656 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 8.743e-05/0.01152, allocations: 129 kB / 0.6041 GB, free: 9.52 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 7.249e-05/0.01159, allocations: 91.23 kB / 0.6042 GB, free: 9.43 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.643e-05/0.01169, allocations: 65.77 kB / 0.6043 GB, free: 9.363 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 0.0001253/0.01181, allocations: 346.7 kB / 0.6046 GB, free: 9.016 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001316/0.01194, allocations: 167.2 kB / 0.6048 GB, free: 8.824 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001565/0.0121, allocations: 235.7 kB / 0.605 GB, free: 8.539 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003878/0.01249, allocations: 0.5044 MB / 0.6055 GB, free: 7.949 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.825e-06/0.01249, allocations: 0 / 0.6055 GB, free: 7.949 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0004705/0.01296, allocations: 450 kB / 0.6059 GB, free: 7.457 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 7.721e-05/0.01304, allocations: 122.8 kB / 0.606 GB, free: 7.312 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.013e-06/0.01305, allocations: 4.188 kB / 0.606 GB, free: 7.309 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.731e-05/0.01306, allocations: 4 kB / 0.6061 GB, free: 7.305 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002502/0.01331, allocations: 63.91 kB / 0.6061 GB, free: 7.242 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.292e-06/0.01332, allocations: 3.938 kB / 0.6061 GB, free: 7.238 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001172/0.01344, allocations: 19.98 kB / 0.6061 GB, free: 7.219 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.54e-05/0.0135, allocations: 51.94 kB / 0.6062 GB, free: 7.168 MB / 0.5261 GB
Warning: Assuming fixed start value for the following 6 variables:
         dose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         dose.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.dose.pulse.count,$PRE.dose.pulse.T_start,CYP2C19.status,SLC22A2.status,central.rising,dose.pulse.count,dose.pulse.T_start,$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 0.000232/0.01373, allocations: 242.3 kB / 0.6064 GB, free: 6.906 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000131/0.01387, allocations: 83.84 kB / 0.6065 GB, free: 6.824 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.791e-05/0.01391, allocations: 34.95 kB / 0.6065 GB, free: 6.789 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.447e-06/0.01392, allocations: 0 / 0.6065 GB, free: 6.789 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.117e-06/0.01392, allocations: 3.938 kB / 0.6065 GB, free: 6.785 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.568e-06/0.01393, allocations: 4 kB / 0.6065 GB, free: 6.781 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005856/0.01451, allocations: 0.5863 MB / 0.6071 GB, free: 6.137 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.735e-06/0.01451, allocations: 0 / 0.6071 GB, free: 6.137 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002093/0.01472, allocations: 43.97 kB / 0.6072 GB, free: 6.094 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 5.199e-06/0.01473, allocations: 3.938 kB / 0.6072 GB, free: 6.09 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.292e-05/0.01475, allocations: 11.98 kB / 0.6072 GB, free: 6.078 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.354e-06/0.01475, allocations: 0 / 0.6072 GB, free: 6.078 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.943e-06/0.01476, allocations: 3.938 kB / 0.6072 GB, free: 6.074 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00062/0.01538, allocations: 0.6724 MB / 0.6078 GB, free: 5.332 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.528e-05/0.01541, allocations: 27.8 kB / 0.6079 GB, free: 5.305 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.107e-05/0.01545, allocations: 12 kB / 0.6079 GB, free: 5.293 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001213/0.01557, allocations: 15.98 kB / 0.6079 GB, free: 5.277 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.859e-05/0.01564, allocations: 19.97 kB / 0.6079 GB, free: 5.258 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.828e-05/0.0157, allocations: 47.92 kB / 0.6079 GB, free: 5.211 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 0.0001004/0.0158, allocations: 86.77 kB / 0.608 GB, free: 5.129 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 1.7e-07/0.0158, allocations: 0 / 0.608 GB, free: 5.129 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.000293/0.01609, allocations: 76 kB / 0.6081 GB, free: 5.055 MB / 0.5261 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (dose.TotalCumulativeMass,dose.variableDose.TotalCumulativeMass,central.C,central.AUC,elim.MExc)
 * Number of discrete variables: 10 ($whenCondition1,$whenCondition2,$whenCondition3,dose.pulse.T_start,dose.pulse.count,central.Cmax,central.Cmin,central.rising,SLC22A2.status,CYP2C19.status)
 * Number of discrete states: 8 (dose.pulse.count,SLC22A2.status,CYP2C19.status,central.Cmin,$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 0.0002107/0.0163, allocations: 132.3 kB / 0.6082 GB, free: 4.918 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.0003536/0.01666, allocations: 0.5606 MB / 0.6088 GB, free: 4.262 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 7.074e-06/0.01666, allocations: 4 kB / 0.6088 GB, free: 4.258 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001704/0.01683, allocations: 328.1 kB / 0.6091 GB, free: 3.879 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002648/0.0171, allocations: 76.19 kB / 0.6092 GB, free: 3.812 MB / 0.5261 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001405/0.0185, allocations: 0.7648 MB / 0.6099 GB, free: 2.996 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 6.448e-05/0.01857, allocations: 96.31 kB / 0.61 GB, free: 2.883 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 8.052e-05/0.01865, allocations: 29.34 kB / 0.61 GB, free: 2.855 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001631/0.01881, allocations: 119.3 kB / 0.6101 GB, free: 2.738 MB / 0.5261 GB
Notification: Performance of SimCode: time 1.563e-06/0.01881, allocations: 0 / 0.6101 GB, free: 2.738 MB / 0.5261 GB
Notification: Performance of Templates: time 0.362/0.3808, allocations: 5.303 MB / 0.6153 GB, free: 52.9 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin -abortSlowSimulation -alarm=240 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.936705046799034]