Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PKPG_Gentamicin_Experiment.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 0.00116/0.00116, allocations: 91.55 kB / 20.19 MB, free: 4.348 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 0.001245/0.001245, allocations: 169 kB / 23.5 MB, free: 1.047 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 0.9984/0.9984, allocations: 177.1 MB / 203.8 MB, free: 5.223 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 1.615/1.615, allocations: 273.5 MB / 0.5213 GB, free: 14.84 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.PKPG_Gentamicin_Experiment,tolerance=1e-06,outputFormat="empty",numberOfIntervals=1728,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PKPG_Gentamicin_Experiment")
translateModel(Pharmacolibrary.Examples.Pharmacogenomics.PKPG_Gentamicin_Experiment,tolerance=1e-06,outputFormat="empty",numberOfIntervals=1728,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PKPG_Gentamicin_Experiment") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.543e-06/1.543e-06, allocations: 0 / 0.647 GB, free: 38.68 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.978e-05/2.132e-05, allocations: 4.156 kB / 0.647 GB, free: 38.67 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.PKPG_Gentamicin_Experiment): time 0.00654/0.006562, allocations: 5.282 MB / 0.6521 GB, free: 35.32 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001514/0.008076, allocations: 1.629 MB / 0.6537 GB, free: 34.22 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001794/0.008255, allocations: 15.44 kB / 0.6538 GB, free: 34.22 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0004491/0.008704, allocations: 241.1 kB / 0.654 GB, free: 34.1 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0003209/0.009025, allocations: 355 kB / 0.6543 GB, free: 33.86 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.000454/0.009479, allocations: 392.9 kB / 0.6547 GB, free: 33.63 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0007391/0.01022, allocations: 1.29 MB / 0.656 GB, free: 32.92 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002268/0.01045, allocations: 195.1 kB / 0.6561 GB, free: 32.8 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0005281/0.01097, allocations: 0.6416 MB / 0.6568 GB, free: 32.5 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.000429/0.0114, allocations: 414.4 kB / 0.6572 GB, free: 32.34 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 0.000118/0.01152, allocations: 114.2 kB / 0.6573 GB, free: 32.34 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0002439/0.01176, allocations: 263.2 kB / 0.6575 GB, free: 32.29 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 0.0001512/0.01192, allocations: 285.3 kB / 0.6578 GB, free: 32.11 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0002494/0.01216, allocations: 377 kB / 0.6582 GB, free: 31.93 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0007236/0.01289, allocations: 1.066 MB / 0.6592 GB, free: 31.37 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 3.467e-06/0.01289, allocations: 0 / 0.6592 GB, free: 31.37 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.212e-06/0.01289, allocations: 0 / 0.6592 GB, free: 31.37 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 1.043e-05/0.0129, allocations: 2.531 kB / 0.6592 GB, free: 31.37 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: 160
 * Number of variables: 160
Notification: Performance of Generate backend data structure: time 0.001365/0.01427, allocations: 1.914 MB / 0.6611 GB, free: 29.82 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.857e-05/0.01431, allocations: 9.719 kB / 0.6611 GB, free: 29.82 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0005804/0.01489, allocations: 471.5 kB / 0.6615 GB, free: 29.63 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0005317/0.01542, allocations: 0.5653 MB / 0.6621 GB, free: 29.22 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.844e-05/0.01546, allocations: 51.62 kB / 0.6621 GB, free: 29.2 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 9.09e-05/0.01555, allocations: 83.02 kB / 0.6622 GB, free: 29.18 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0008068/0.01636, allocations: 0.9826 MB / 0.6632 GB, free: 28.54 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 2.264e-05/0.01638, allocations: 6.719 kB / 0.6632 GB, free: 28.53 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.197e-05/0.01642, allocations: 31.97 kB / 0.6632 GB, free: 28.51 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.369e-05/0.01643, allocations: 14 kB / 0.6632 GB, free: 28.51 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000521/0.01695, allocations: 0.6861 MB / 0.6639 GB, free: 28.06 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001648/0.0186, allocations: 2.008 MB / 0.6658 GB, free: 26.76 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0006408/0.01924, allocations: 0.8477 MB / 0.6667 GB, free: 26.12 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003325/0.01958, allocations: 0.5926 MB / 0.6673 GB, free: 25.63 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.797e-05/0.0196, allocations: 17.56 kB / 0.6673 GB, free: 25.63 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0006588/0.02026, allocations: 1.111 MB / 0.6684 GB, free: 24.77 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=104): time 2.335e-06/0.02027, allocations: 1.406 kB / 0.6684 GB, free: 24.77 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=108): time 0.003293/0.02356, allocations: 4.806 MB / 0.6731 GB, free: 21.16 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001131/0.02367, allocations: 0.6893 MB / 0.6737 GB, free: 20.35 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0006782/0.02435, allocations: 0.8471 MB / 0.6746 GB, free: 19.96 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 5.316e-05/0.0244, allocations: 57.86 kB / 0.6746 GB, free: 19.91 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0002568/0.02466, allocations: 0.503 MB / 0.6751 GB, free: 19.5 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 0.0001906/0.02485, allocations: 354.1 kB / 0.6754 GB, free: 19.23 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002188/0.02507, allocations: 207.2 kB / 0.6756 GB, free: 19.13 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 8.417e-05/0.02515, allocations: 0.5192 MB / 0.6761 GB, free: 18.63 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000456/0.02561, allocations: 0.725 MB / 0.6768 GB, free: 18.03 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005255/0.02613, allocations: 1.109 MB / 0.6779 GB, free: 16.92 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001196/0.02733, allocations: 2.285 MB / 0.6802 GB, free: 14.86 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.189e-06/0.02734, allocations: 4.875 kB / 0.6802 GB, free: 14.86 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=152) (initialization): time 0.001695/0.02903, allocations: 2.152 MB / 0.6823 GB, free: 13.4 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 0.0001055/0.02914, allocations: 468.3 kB / 0.6827 GB, free: 12.88 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.028e-05/0.02915, allocations: 7.781 kB / 0.6827 GB, free: 12.88 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.195e-05/0.02917, allocations: 11.56 kB / 0.6827 GB, free: 12.88 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0004774/0.02965, allocations: 212.9 kB / 0.6829 GB, free: 12.86 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.021e-05/0.02967, allocations: 18.08 kB / 0.683 GB, free: 12.86 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003227/0.02999, allocations: 62.69 kB / 0.683 GB, free: 12.84 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001989/0.03019, allocations: 223.1 kB / 0.6832 GB, free: 12.82 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 24 variables:
         patient4.dose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         patient4.dose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         patient4.central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         patient3.dose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         patient3.dose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         patient3.central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         patient2.dose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         patient2.dose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         patient2.central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         patient1.dose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         patient1.dose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         patient1.central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         patient1.central.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient1.central.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient2.central.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient2.central.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient3.central.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient3.central.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient4.central.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient4.central.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient1.central.rising:DISCRETE(fixed = true protected = true )  type: Boolean
         patient2.central.rising:DISCRETE(fixed = true protected = true )  type: Boolean
         patient3.central.rising:DISCRETE(fixed = true protected = true )  type: Boolean
         patient4.central.rising:DISCRETE(fixed = true protected = true )  type: Boolean
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 28
 * Number of states: 0 ()
 * Number of discrete variables: 60 ($PRE.patient1.central.Cmin,patient1.central.Cmin,$PRE.patient1.central.Cmax,patient1.central.Cmax,$PRE.patient2.central.Cmin,patient2.central.Cmin,$PRE.patient2.central.Cmax,patient2.central.Cmax,$PRE.patient3.central.Cmin,patient3.central.Cmin,$PRE.patient3.central.Cmax,patient3.central.Cmax,$PRE.patient4.central.Cmin,patient4.central.Cmin,$PRE.patient4.central.Cmax,patient4.central.Cmax,$PRE.patient1.central.rising,$PRE.patient1.dose.pulse.count,$PRE.patient1.dose.pulse.T_start,patient1.CYP2C19.status,patient1.SLC22A2.status,patient1.central.rising,patient1.dose.pulse.count,patient1.dose.pulse.T_start,$whenCondition12,$whenCondition11,$whenCondition10,$PRE.patient2.central.rising,$PRE.patient2.dose.pulse.count,$PRE.patient2.dose.pulse.T_start,patient2.CYP2C19.status,patient2.SLC22A2.status,patient2.central.rising,patient2.dose.pulse.count,patient2.dose.pulse.T_start,$whenCondition9,$whenCondition8,$whenCondition7,$PRE.patient3.central.rising,$PRE.patient3.dose.pulse.count,$PRE.patient3.dose.pulse.T_start,patient3.CYP2C19.status,patient3.SLC22A2.status,patient3.central.rising,patient3.dose.pulse.count,patient3.dose.pulse.T_start,$whenCondition6,$whenCondition5,$whenCondition4,$PRE.patient4.central.rising,$PRE.patient4.dose.pulse.count,$PRE.patient4.dose.pulse.T_start,patient4.CYP2C19.status,patient4.SLC22A2.status,patient4.central.rising,patient4.dose.pulse.count,patient4.dose.pulse.T_start,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (136):
 * Single equations (assignments): 120
 * Array equations: 0
 * Algorithm blocks: 16
 * 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 0.0003984/0.03059, allocations: 0.6915 MB / 0.6839 GB, free: 12.18 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0003586/0.03094, allocations: 390.5 kB / 0.6843 GB, free: 12.03 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 9.574e-05/0.03104, allocations: 106.3 kB / 0.6844 GB, free: 11.96 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.366e-06/0.03105, allocations: 5.234 kB / 0.6844 GB, free: 11.96 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.038e-06/0.03105, allocations: 2.641 kB / 0.6844 GB, free: 11.96 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 8.183e-05/0.03113, allocations: 108.1 kB / 0.6845 GB, free: 11.88 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001053/0.03124, allocations: 42.22 kB / 0.6845 GB, free: 11.86 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002274/0.03147, allocations: 55.64 kB / 0.6846 GB, free: 11.85 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001866/0.03165, allocations: 101.4 kB / 0.6847 GB, free: 11.82 MB / 0.5262 GB
Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.001461/0.03311, allocations: 2.149 MB / 0.6868 GB, free: 10.28 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.002217/0.03533, allocations: 3.229 MB / 0.6899 GB, free: 7.973 MB / 0.5262 GB
Notification: Performance of postOpt setEvaluationStage (simulation): time 0.0005762/0.03591, allocations: 0.7027 MB / 0.6906 GB, free: 7.477 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0005537/0.03646, allocations: 0.4986 MB / 0.6911 GB, free: 7.254 MB / 0.5262 GB
Notification: Performance of Backend: time 5.01e-07/0.03646, allocations: 7.938 kB / 0.6911 GB, free: 7.246 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.001756/0.03822, allocations: 1.973 MB / 0.693 GB, free: 5.469 MB / 0.5262 GB
Notification: Performance of SimCode: time 0.003074/0.04129, allocations: 3.649 MB / 0.6966 GB, free: 2.582 MB / 0.5262 GB
Notification: Performance of Templates: time 0.01897/0.06026, allocations: 18.07 MB / 0.7142 GB, free: 2.621 MB / 0.5418 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PKPG_Gentamicin_Experiment.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PKPG_Gentamicin_Experiment.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PKPG_Gentamicin_Experiment.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PKPG_Gentamicin_Experiment.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PKPG_Gentamicin_Experiment.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PKPG_Gentamicin_Experiment -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PKPG_Gentamicin_Experiment.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.071877887006849]