Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_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 0.001886/0.001886, allocations: 81.5 kB / 19.44 MB, free: 344 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 0.002107/0.002107, allocations: 173.2 kB / 22.76 MB, free: 1.664 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 1.708/1.708, allocations: 177.1 MB / 203.1 MB, free: 5.613 MB / 186.7 MB
"
[Timeout remaining time 178]
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 3.334/3.334, allocations: 274.5 MB / 0.5215 GB, free: 14.17 MB / 458.7 MB
"
[Timeout remaining time 176]
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.PK_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin")
translateModel(Pharmacolibrary.Examples.PK_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.144e-06/2.144e-06, allocations: 0 / 0.6472 GB, free: 39.12 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 4.322e-05/4.537e-05, allocations: 5.266 kB / 0.6472 GB, free: 39.12 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Gentamicin): time 0.00372/0.003765, allocations: 2.085 MB / 0.6493 GB, free: 37.75 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001053/0.004818, allocations: 0.5537 MB / 0.6498 GB, free: 37.38 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.671e-05/0.004915, allocations: 1.594 kB / 0.6498 GB, free: 37.38 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001509/0.005066, allocations: 20.48 kB / 0.6498 GB, free: 37.37 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001773/0.005243, allocations: 51.66 kB / 0.6499 GB, free: 37.35 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002123/0.005455, allocations: 48.02 kB / 0.6499 GB, free: 37.32 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0003159/0.005771, allocations: 206.3 kB / 0.6501 GB, free: 37.26 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001496/0.005921, allocations: 26.94 kB / 0.6501 GB, free: 37.24 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001681/0.006089, allocations: 103.8 kB / 0.6502 GB, free: 37.2 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001403/0.006229, allocations: 63.62 kB / 0.6503 GB, free: 37.17 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 4.046e-05/0.00627, allocations: 15.06 kB / 0.6503 GB, free: 37.17 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 4.12e-05/0.006311, allocations: 16.94 kB / 0.6503 GB, free: 37.17 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 4.698e-05/0.006358, allocations: 34.94 kB / 0.6504 GB, free: 37.15 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001031/0.006461, allocations: 58.16 kB / 0.6504 GB, free: 37.12 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002704/0.006731, allocations: 168.2 kB / 0.6506 GB, free: 37.05 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 5.039e-06/0.006736, allocations: 1.938 kB / 0.6506 GB, free: 37.05 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 2.094e-06/0.006738, allocations: 0 / 0.6506 GB, free: 37.05 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 6.713e-06/0.006745, allocations: 0 / 0.6506 GB, free: 37.05 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: 26
 * Number of variables: 26
Notification: Performance of Generate backend data structure: time 0.0008701/0.007615, allocations: 0.5287 MB / 0.6511 GB, free: 36.56 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 4.801e-05/0.007663, allocations: 10.56 kB / 0.6511 GB, free: 36.56 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.464e-05/0.007748, allocations: 33.52 kB / 0.6511 GB, free: 36.54 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003034/0.008051, allocations: 177.6 kB / 0.6513 GB, free: 36.38 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.887e-05/0.00807, allocations: 10.56 kB / 0.6513 GB, free: 36.38 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.284e-05/0.008113, allocations: 18.05 kB / 0.6513 GB, free: 36.37 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002865/0.008399, allocations: 155.6 kB / 0.6515 GB, free: 36.27 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.862e-05/0.008418, allocations: 3.094 kB / 0.6515 GB, free: 36.27 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.896e-05/0.008437, allocations: 6.219 kB / 0.6515 GB, free: 36.27 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.314e-06/0.008444, allocations: 2 kB / 0.6515 GB, free: 36.27 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002708/0.008715, allocations: 116.4 kB / 0.6516 GB, free: 36.22 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006779/0.009393, allocations: 431.5 kB / 0.652 GB, free: 35.87 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003179/0.009711, allocations: 169.7 kB / 0.6522 GB, free: 35.77 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001393/0.00985, allocations: 84.42 kB / 0.6523 GB, free: 35.71 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.984e-05/0.00987, allocations: 3.406 kB / 0.6523 GB, free: 35.71 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003276/0.0102, allocations: 229.5 kB / 0.6525 GB, free: 35.54 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 1.513e-06/0.0102, allocations: 0 / 0.6525 GB, free: 35.54 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0014/0.0116, allocations: 0.6749 MB / 0.6531 GB, free: 35.08 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.323e-05/0.01167, allocations: 136.2 kB / 0.6533 GB, free: 34.92 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001764/0.01185, allocations: 231.3 kB / 0.6535 GB, free: 34.73 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.116e-05/0.01187, allocations: 31.17 kB / 0.6535 GB, free: 34.7 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 8.673e-05/0.01196, allocations: 162.8 kB / 0.6537 GB, free: 34.54 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 5.973e-05/0.01202, allocations: 81.62 kB / 0.6538 GB, free: 34.48 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.495e-05/0.01211, allocations: 56.94 kB / 0.6538 GB, free: 34.44 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 0.0001207/0.01223, allocations: 0.5182 MB / 0.6543 GB, free: 33.93 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001938/0.01243, allocations: 139.1 kB / 0.6544 GB, free: 33.83 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002773/0.0127, allocations: 235.2 kB / 0.6547 GB, free: 33.61 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005435/0.01325, allocations: 415 kB / 0.6551 GB, free: 33.28 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.435e-06/0.01325, allocations: 1.656 kB / 0.6551 GB, free: 33.28 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0005068/0.01376, allocations: 366.6 kB / 0.6554 GB, free: 33.05 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.969e-05/0.01381, allocations: 66.78 kB / 0.6555 GB, free: 32.98 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.215e-06/0.01381, allocations: 0 / 0.6555 GB, free: 32.98 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.38e-05/0.01384, allocations: 10.91 kB / 0.6555 GB, free: 32.98 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002308/0.01407, allocations: 51.19 kB / 0.6555 GB, free: 32.98 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.189e-05/0.01408, allocations: 2.156 kB / 0.6555 GB, free: 32.98 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001465/0.01423, allocations: 12.56 kB / 0.6556 GB, free: 32.97 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.117e-05/0.01426, allocations: 12.28 kB / 0.6556 GB, free: 32.97 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: 13 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,central.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (30):
 * Single equations (assignments): 28
 * Array equations: 0
 * Algorithm blocks: 2
 * 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 0.0002597/0.01452, allocations: 233 kB / 0.6558 GB, free: 32.76 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 5.291e-05/0.01457, allocations: 26.97 kB / 0.6558 GB, free: 32.75 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.548e-05/0.01463, allocations: 19.8 kB / 0.6558 GB, free: 32.73 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.194e-06/0.01463, allocations: 6.188 kB / 0.6558 GB, free: 32.73 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.775e-06/0.01464, allocations: 0.5625 kB / 0.6558 GB, free: 32.73 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.36e-06/0.01465, allocations: 4.531 kB / 0.6558 GB, free: 32.73 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008408/0.01549, allocations: 0.5845 MB / 0.6564 GB, free: 32.28 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.056e-06/0.01549, allocations: 0.5625 kB / 0.6564 GB, free: 32.28 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001956/0.01569, allocations: 31.23 kB / 0.6564 GB, free: 32.28 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 4.459e-06/0.01569, allocations: 1.094 kB / 0.6564 GB, free: 32.28 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.635e-05/0.01572, allocations: 9.562 kB / 0.6565 GB, free: 32.27 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.15e-06/0.01572, allocations: 5.031 kB / 0.6565 GB, free: 32.27 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.214e-06/0.01572, allocations: 0 / 0.6565 GB, free: 32.27 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0007814/0.0165, allocations: 0.5318 MB / 0.657 GB, free: 31.9 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.669e-05/0.01653, allocations: 13.78 kB / 0.657 GB, free: 31.89 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.783e-05/0.01657, allocations: 8.469 kB / 0.657 GB, free: 31.89 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001279/0.0167, allocations: 11.94 kB / 0.657 GB, free: 31.89 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.645e-05/0.01678, allocations: 16.92 kB / 0.657 GB, free: 31.88 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.558e-05/0.0168, allocations: 4.219 kB / 0.657 GB, free: 31.88 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001022/0.0169, allocations: 169.4 kB / 0.6572 GB, free: 31.75 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 6e-08/0.0169, allocations: 0 / 0.6572 GB, free: 31.75 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0003031/0.0172, allocations: 48.88 kB / 0.6572 GB, free: 31.75 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: 8 ($whenCondition1,$whenCondition2,$whenCondition3,singleDose.pulse.T_start,singleDose.pulse.count,central.Cmax,central.Cmin,central.rising)
 * Number of discrete states: 6 (singleDose.pulse.count,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (18):
 * Single equations (assignments): 15
 * Array equations: 0
 * Algorithm blocks: 1
 * 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 0.0001313/0.01734, allocations: 116.6 kB / 0.6574 GB, free: 31.65 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0005223/0.01786, allocations: 381.4 kB / 0.6577 GB, free: 31.37 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 4.899e-06/0.01786, allocations: 9.312 kB / 0.6577 GB, free: 31.36 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002192/0.01808, allocations: 174.5 kB / 0.6579 GB, free: 31.24 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004285/0.01851, allocations: 54.25 kB / 0.6579 GB, free: 31.23 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001103/0.01961, allocations: 0.5552 MB / 0.6585 GB, free: 30.87 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001042/0.01972, allocations: 112.1 kB / 0.6586 GB, free: 30.79 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 9.19e-05/0.01981, allocations: 18.8 kB / 0.6586 GB, free: 30.79 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.003e-05/0.01987, allocations: 18.31 kB / 0.6586 GB, free: 30.78 MB / 0.5262 GB
Notification: Performance of SimCode: time 1.092e-06/0.01987, allocations: 3.938 kB / 0.6586 GB, free: 30.77 MB / 0.5262 GB
Notification: Performance of Templates: time 0.006966/0.02684, allocations: 2.629 MB / 0.6612 GB, free: 30.55 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 9.564863031031564]