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 0.001214/0.001214, allocations: 73.97 kB / 20.65 MB, free: 3.848 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 0.001404/0.001404, allocations: 169 kB / 24.06 MB, free: 456 kB / 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 1.032/1.032, allocations: 177.1 MB / 204.5 MB, free: 5.484 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 1.547/1.547, allocations: 273.5 MB / 0.522 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.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 1.402e-06/1.402e-06, allocations: 0 / 0.6482 GB, free: 38.5 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.884e-05/2.025e-05, allocations: 2.312 kB / 0.6482 GB, free: 38.5 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKPG_1C_Gentamicin): time 0.002389/0.002409, allocations: 2.478 MB / 0.6506 GB, free: 36.9 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0009729/0.003382, allocations: 0.9209 MB / 0.6515 GB, free: 36.31 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 7.567e-05/0.003458, allocations: 1.625 kB / 0.6515 GB, free: 36.31 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.00031/0.003768, allocations: 117.2 kB / 0.6516 GB, free: 36.26 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001012/0.003869, allocations: 86.48 kB / 0.6517 GB, free: 36.23 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002641/0.004133, allocations: 138.2 kB / 0.6518 GB, free: 36.16 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002396/0.004373, allocations: 293.6 kB / 0.6521 GB, free: 36.04 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001109/0.004484, allocations: 42.12 kB / 0.6521 GB, free: 36.01 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001372/0.004621, allocations: 152.6 kB / 0.6523 GB, free: 35.95 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.000126/0.004747, allocations: 87.14 kB / 0.6524 GB, free: 35.92 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.799e-05/0.004775, allocations: 19.56 kB / 0.6524 GB, free: 35.92 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001553/0.00493, allocations: 167.7 kB / 0.6525 GB, free: 35.86 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 5.803e-05/0.004988, allocations: 57.84 kB / 0.6526 GB, free: 35.83 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 6.768e-05/0.005056, allocations: 82.53 kB / 0.6527 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002851/0.005341, allocations: 335.8 kB / 0.653 GB, free: 35.65 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.275e-06/0.005343, allocations: 0 / 0.653 GB, free: 35.65 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 9.51e-07/0.005344, allocations: 1.469 kB / 0.653 GB, free: 35.65 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.429e-06/0.005348, allocations: 0 / 0.653 GB, free: 35.65 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 0.0005384/0.005887, allocations: 0.7048 MB / 0.6537 GB, free: 35.01 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.163e-05/0.005918, allocations: 9.344 kB / 0.6537 GB, free: 35.01 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001958/0.006114, allocations: 110.2 kB / 0.6538 GB, free: 34.97 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001588/0.006273, allocations: 210.5 kB / 0.654 GB, free: 34.78 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.724e-05/0.00629, allocations: 15.56 kB / 0.654 GB, free: 34.77 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.583e-05/0.006316, allocations: 17.59 kB / 0.654 GB, free: 34.77 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002024/0.006519, allocations: 234.6 kB / 0.6543 GB, free: 34.6 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.008e-05/0.006529, allocations: 5.312 kB / 0.6543 GB, free: 34.6 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.329e-05/0.006542, allocations: 9.938 kB / 0.6543 GB, free: 34.59 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.891e-06/0.006548, allocations: 3.938 kB / 0.6543 GB, free: 34.59 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000107/0.006655, allocations: 150.2 kB / 0.6544 GB, free: 34.49 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004493/0.007104, allocations: 474.8 kB / 0.6549 GB, free: 34.15 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001766/0.007281, allocations: 190 kB / 0.6551 GB, free: 34 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 7.294e-05/0.007354, allocations: 130.1 kB / 0.6552 GB, free: 33.89 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 8.757e-06/0.007362, allocations: 11.44 kB / 0.6552 GB, free: 33.89 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001676/0.00753, allocations: 269.9 kB / 0.6554 GB, free: 33.66 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 1.562e-06/0.007532, allocations: 1.469 kB / 0.6554 GB, free: 33.66 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.0008481/0.00838, allocations: 0.9816 MB / 0.6564 GB, free: 32.89 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.489e-05/0.008425, allocations: 195.7 kB / 0.6566 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002031/0.008628, allocations: 313.5 kB / 0.6569 GB, free: 32.45 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.793e-05/0.008646, allocations: 33.64 kB / 0.6569 GB, free: 32.41 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 8.372e-05/0.008729, allocations: 207.7 kB / 0.6571 GB, free: 32.23 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 4.778e-05/0.008777, allocations: 91.28 kB / 0.6572 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.646e-05/0.008853, allocations: 65.67 kB / 0.6573 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 7.299e-05/0.008926, allocations: 0.5264 MB / 0.6578 GB, free: 31.6 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001025/0.009029, allocations: 175.9 kB / 0.658 GB, free: 31.45 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001315/0.00916, allocations: 261.5 kB / 0.6582 GB, free: 31.18 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002664/0.009427, allocations: 0.5161 MB / 0.6587 GB, free: 30.7 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.343e-06/0.009428, allocations: 0 / 0.6587 GB, free: 30.7 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0003267/0.009755, allocations: 0.5 MB / 0.6592 GB, free: 30.34 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 3.696e-05/0.009792, allocations: 120.3 kB / 0.6593 GB, free: 30.21 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.171e-06/0.009798, allocations: 6.594 kB / 0.6593 GB, free: 30.2 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.087e-05/0.009809, allocations: 6.812 kB / 0.6593 GB, free: 30.2 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001365/0.009945, allocations: 54.91 kB / 0.6594 GB, free: 30.2 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 4.909e-06/0.00995, allocations: 4.469 kB / 0.6594 GB, free: 30.2 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.497e-05/0.01004, allocations: 13.78 kB / 0.6594 GB, free: 30.19 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.89e-05/0.01008, allocations: 52.38 kB / 0.6594 GB, free: 30.18 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 0.0001584/0.01024, allocations: 297.7 kB / 0.6597 GB, free: 29.91 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.015e-05/0.01033, allocations: 88.52 kB / 0.6598 GB, free: 29.88 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.26e-05/0.01037, allocations: 27.66 kB / 0.6598 GB, free: 29.86 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.217e-06/0.01037, allocations: 5.344 kB / 0.6598 GB, free: 29.86 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.435e-06/0.01037, allocations: 2.375 kB / 0.6598 GB, free: 29.86 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.479e-06/0.01038, allocations: 0 / 0.6598 GB, free: 29.86 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004402/0.01082, allocations: 0.7058 MB / 0.6605 GB, free: 29.31 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.733e-06/0.01082, allocations: 2.062 kB / 0.6605 GB, free: 29.31 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001174/0.01093, allocations: 34.42 kB / 0.6606 GB, free: 29.3 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.545e-06/0.01094, allocations: 1.469 kB / 0.6606 GB, free: 29.3 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.484e-05/0.01095, allocations: 11.83 kB / 0.6606 GB, free: 29.3 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.364e-06/0.01095, allocations: 1.406 kB / 0.6606 GB, free: 29.3 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.92e-07/0.01096, allocations: 0.875 kB / 0.6606 GB, free: 29.3 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004275/0.01138, allocations: 0.7476 MB / 0.6613 GB, free: 28.74 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.909e-05/0.0114, allocations: 21.14 kB / 0.6613 GB, free: 28.73 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.823e-05/0.01143, allocations: 9.625 kB / 0.6613 GB, free: 28.72 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.241e-05/0.01151, allocations: 14.47 kB / 0.6614 GB, free: 28.72 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.462e-05/0.01156, allocations: 23.3 kB / 0.6614 GB, free: 28.71 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.053e-05/0.0116, allocations: 47.36 kB / 0.6614 GB, free: 28.71 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 7.456e-05/0.01167, allocations: 204.5 kB / 0.6616 GB, free: 28.57 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 8e-08/0.01167, allocations: 0 / 0.6616 GB, free: 28.57 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002404/0.01191, allocations: 76.38 kB / 0.6617 GB, free: 28.56 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 0.0001871/0.0121, allocations: 167.7 kB / 0.6619 GB, free: 28.45 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002725/0.01237, allocations: 0.5648 MB / 0.6624 GB, free: 27.94 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.603e-06/0.01237, allocations: 2.219 kB / 0.6624 GB, free: 27.94 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001252/0.0125, allocations: 336.4 kB / 0.6627 GB, free: 27.63 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002928/0.01279, allocations: 60.36 kB / 0.6628 GB, free: 27.62 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001259/0.01405, allocations: 0.8297 MB / 0.6636 GB, free: 27.06 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.363e-05/0.0141, allocations: 96.36 kB / 0.6637 GB, free: 26.98 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 5.835e-05/0.01416, allocations: 22.19 kB / 0.6637 GB, free: 26.98 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001502/0.01431, allocations: 147.1 kB / 0.6638 GB, free: 26.91 MB / 0.5262 GB
Notification: Performance of SimCode: time 8.82e-07/0.01431, allocations: 0 / 0.6638 GB, free: 26.91 MB / 0.5262 GB
Notification: Performance of Templates: time 0.00785/0.02216, allocations: 5.266 MB / 0.669 GB, free: 26.38 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: 5.0190159496851265]