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 0.001173/0.001173, allocations: 93.06 kB / 19.65 MB, free: 276 kB / 13.93 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 0.001353/0.001353, allocations: 169 kB / 23.02 MB, free: 1.547 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 0.8916/0.8916, allocations: 177.1 MB / 203.4 MB, free: 5.586 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 1.581/1.581, allocations: 273.5 MB / 0.5209 GB, free: 14.79 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 1.502e-06/1.502e-06, allocations: 0 / 0.647 GB, free: 38.59 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.17e-05/1.32e-05, allocations: 5.266 kB / 0.647 GB, free: 38.59 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKPG_1C_Gentamicin): time 0.002047/0.00206, allocations: 2.502 MB / 0.6494 GB, free: 36.98 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0009376/0.002997, allocations: 0.9324 MB / 0.6503 GB, free: 36.39 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 7.358e-05/0.003071, allocations: 7.406 kB / 0.6503 GB, free: 36.39 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0003214/0.003392, allocations: 112.3 kB / 0.6504 GB, free: 36.34 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.000102/0.003494, allocations: 87.59 kB / 0.6505 GB, free: 36.31 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002761/0.003771, allocations: 142.2 kB / 0.6507 GB, free: 36.24 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.000229/0.004, allocations: 290.7 kB / 0.6509 GB, free: 36.12 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001082/0.004108, allocations: 39.55 kB / 0.651 GB, free: 36.09 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001368/0.004245, allocations: 155.5 kB / 0.6511 GB, free: 36.02 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001283/0.004373, allocations: 86.62 kB / 0.6512 GB, free: 36 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 3.028e-05/0.004403, allocations: 18.62 kB / 0.6512 GB, free: 36 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001591/0.004562, allocations: 176.3 kB / 0.6514 GB, free: 35.93 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 6.191e-05/0.004624, allocations: 56.67 kB / 0.6514 GB, free: 35.91 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 8.092e-05/0.004705, allocations: 83.62 kB / 0.6515 GB, free: 35.87 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0003378/0.005043, allocations: 321.9 kB / 0.6518 GB, free: 35.73 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 3.426e-06/0.005046, allocations: 6.312 kB / 0.6518 GB, free: 35.73 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 5.82e-07/0.005047, allocations: 1.406 kB / 0.6518 GB, free: 35.73 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.999e-06/0.005052, allocations: 0 / 0.6518 GB, free: 35.73 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 0.0006068/0.005659, allocations: 0.7019 MB / 0.6525 GB, free: 35.09 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 4.38e-05/0.005702, allocations: 9.375 kB / 0.6525 GB, free: 35.09 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002317/0.005934, allocations: 108.5 kB / 0.6526 GB, free: 35.05 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002025/0.006137, allocations: 220.9 kB / 0.6528 GB, free: 34.86 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.15e-05/0.006158, allocations: 13.69 kB / 0.6529 GB, free: 34.86 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.422e-05/0.006192, allocations: 19.16 kB / 0.6529 GB, free: 34.85 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.000274/0.006466, allocations: 258.6 kB / 0.6531 GB, free: 34.67 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.582e-05/0.006482, allocations: 3.219 kB / 0.6531 GB, free: 34.67 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.807e-05/0.0065, allocations: 6.375 kB / 0.6531 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.538e-06/0.00651, allocations: 3.375 kB / 0.6531 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000166/0.006676, allocations: 174.2 kB / 0.6533 GB, free: 34.55 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005523/0.007228, allocations: 0.5091 MB / 0.6538 GB, free: 34.18 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002156/0.007444, allocations: 217.6 kB / 0.654 GB, free: 34.02 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001016/0.007545, allocations: 145.1 kB / 0.6541 GB, free: 33.9 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.095e-05/0.007556, allocations: 8.625 kB / 0.6541 GB, free: 33.9 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001879/0.007744, allocations: 290.3 kB / 0.6544 GB, free: 33.66 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 1.733e-06/0.007746, allocations: 1.25 kB / 0.6544 GB, free: 33.66 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.001062/0.008807, allocations: 1.1 MB / 0.6555 GB, free: 32.83 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.706e-05/0.008865, allocations: 193.5 kB / 0.6557 GB, free: 32.61 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002543/0.009119, allocations: 317.6 kB / 0.656 GB, free: 32.39 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.771e-05/0.009137, allocations: 34.58 kB / 0.656 GB, free: 32.36 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 9.004e-05/0.009227, allocations: 207.7 kB / 0.6562 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 4.68e-05/0.009273, allocations: 93.25 kB / 0.6563 GB, free: 32.1 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.88e-05/0.009362, allocations: 61.84 kB / 0.6564 GB, free: 32.06 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 9.403e-05/0.009456, allocations: 0.5233 MB / 0.6569 GB, free: 31.55 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001349/0.009591, allocations: 182.6 kB / 0.6571 GB, free: 31.4 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001557/0.009747, allocations: 275.4 kB / 0.6573 GB, free: 31.13 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003533/0.0101, allocations: 0.559 MB / 0.6579 GB, free: 30.62 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.546e-06/0.0101, allocations: 1.312 kB / 0.6579 GB, free: 30.62 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0004274/0.01053, allocations: 0.5448 MB / 0.6584 GB, free: 30.25 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.307e-05/0.01057, allocations: 120.1 kB / 0.6585 GB, free: 30.12 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.883e-06/0.01058, allocations: 5.312 kB / 0.6585 GB, free: 30.11 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.629e-05/0.0106, allocations: 2.938 kB / 0.6585 GB, free: 30.11 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00015/0.01075, allocations: 53.06 kB / 0.6586 GB, free: 30.11 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.925e-06/0.01076, allocations: 2.844 kB / 0.6586 GB, free: 30.11 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.186e-05/0.01084, allocations: 17.66 kB / 0.6586 GB, free: 30.11 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.276e-05/0.01089, allocations: 52.2 kB / 0.6586 GB, free: 30.1 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 0.0001566/0.01105, allocations: 285.5 kB / 0.6589 GB, free: 29.83 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.922e-05/0.01114, allocations: 85.86 kB / 0.659 GB, free: 29.8 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.535e-05/0.01117, allocations: 31.97 kB / 0.659 GB, free: 29.78 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.176e-06/0.01117, allocations: 2.938 kB / 0.659 GB, free: 29.78 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.236e-06/0.01118, allocations: 0 / 0.659 GB, free: 29.78 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.127e-06/0.01118, allocations: 1.375 kB / 0.659 GB, free: 29.78 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005214/0.0117, allocations: 0.7968 MB / 0.6598 GB, free: 29.18 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.843e-06/0.0117, allocations: 1.375 kB / 0.6598 GB, free: 29.18 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000119/0.01182, allocations: 34.36 kB / 0.6598 GB, free: 29.18 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.495e-06/0.01183, allocations: 1.375 kB / 0.6598 GB, free: 29.18 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.098e-05/0.01185, allocations: 20.64 kB / 0.6599 GB, free: 29.17 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.424e-06/0.01185, allocations: 1.438 kB / 0.6599 GB, free: 29.17 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.473e-06/0.01185, allocations: 0 / 0.6599 GB, free: 29.17 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005354/0.01239, allocations: 0.789 MB / 0.6606 GB, free: 28.59 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.313e-05/0.01241, allocations: 27.25 kB / 0.6607 GB, free: 28.57 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.889e-05/0.01244, allocations: 9.562 kB / 0.6607 GB, free: 28.57 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.389e-05/0.01252, allocations: 14.8 kB / 0.6607 GB, free: 28.57 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.014e-05/0.01258, allocations: 25.3 kB / 0.6607 GB, free: 28.56 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.322e-05/0.01263, allocations: 50.44 kB / 0.6608 GB, free: 28.55 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 9.843e-05/0.01272, allocations: 208 kB / 0.6609 GB, free: 28.41 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 7e-08/0.01272, allocations: 3.938 kB / 0.661 GB, free: 28.41 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002379/0.01296, allocations: 76.56 kB / 0.661 GB, free: 28.4 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 0.0001854/0.01315, allocations: 160.8 kB / 0.6612 GB, free: 28.3 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0003647/0.01351, allocations: 0.592 MB / 0.6618 GB, free: 27.77 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 2.194e-06/0.01351, allocations: 1.375 kB / 0.6618 GB, free: 27.77 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001511/0.01367, allocations: 352.5 kB / 0.6621 GB, free: 27.46 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003052/0.01397, allocations: 80.27 kB / 0.6622 GB, free: 27.44 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001554/0.01552, allocations: 0.839 MB / 0.663 GB, free: 26.88 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 7.633e-05/0.0156, allocations: 100.4 kB / 0.6631 GB, free: 26.8 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 8.425e-05/0.01569, allocations: 22.66 kB / 0.6631 GB, free: 26.79 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.748e-05/0.01574, allocations: 21.16 kB / 0.6631 GB, free: 26.79 MB / 0.5262 GB
Notification: Performance of SimCode: time 7.92e-07/0.01574, allocations: 0 / 0.6631 GB, free: 26.79 MB / 0.5262 GB
Notification: Performance of Templates: time 0.007531/0.02327, allocations: 5.06 MB / 0.6681 GB, free: 26.31 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: 4.81628887122497]