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 0.001022/0.001022, allocations: 92.2 kB / 20.19 MB, free: 4.359 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 0.0009897/0.0009897, allocations: 169 kB / 23.49 MB, free: 1.062 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 0.9548/0.9548, allocations: 177.1 MB / 203.8 MB, free: 5.613 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 1.62/1.62, allocations: 273.5 MB / 0.5213 GB, free: 14.86 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.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 1.894e-06/1.894e-06, allocations: 0 / 0.6462 GB, free: 39.09 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.587e-05/2.776e-05, allocations: 3.5 kB / 0.6462 GB, free: 39.09 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Gentamicin): time 0.002394/0.002421, allocations: 2.116 MB / 0.6483 GB, free: 37.71 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0007559/0.003177, allocations: 0.5487 MB / 0.6488 GB, free: 37.35 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 7.3e-05/0.00325, allocations: 1.688 kB / 0.6488 GB, free: 37.35 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001207/0.003371, allocations: 26.02 kB / 0.6488 GB, free: 37.34 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001396/0.003511, allocations: 60.12 kB / 0.6489 GB, free: 37.31 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001657/0.003676, allocations: 41.61 kB / 0.6489 GB, free: 37.29 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002663/0.003943, allocations: 197.4 kB / 0.6491 GB, free: 37.23 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001545/0.004097, allocations: 33.97 kB / 0.6491 GB, free: 37.21 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001506/0.004248, allocations: 106 kB / 0.6492 GB, free: 37.16 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001434/0.004391, allocations: 70.36 kB / 0.6493 GB, free: 37.14 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 4.172e-05/0.004433, allocations: 15.81 kB / 0.6493 GB, free: 37.14 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.974e-05/0.004463, allocations: 15.28 kB / 0.6493 GB, free: 37.14 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 4.978e-05/0.004512, allocations: 28.78 kB / 0.6494 GB, free: 37.12 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001003/0.004613, allocations: 58.81 kB / 0.6494 GB, free: 37.09 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002533/0.004866, allocations: 126.1 kB / 0.6495 GB, free: 37.03 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 4.088e-06/0.00487, allocations: 0.9062 kB / 0.6495 GB, free: 37.03 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.744e-06/0.004872, allocations: 0 / 0.6495 GB, free: 37.03 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 8.166e-06/0.00488, allocations: 1.25 kB / 0.6496 GB, free: 37.03 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 0.0007803/0.00566, allocations: 0.5259 MB / 0.6501 GB, free: 36.54 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 5.443e-05/0.005715, allocations: 9.812 kB / 0.6501 GB, free: 36.54 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.846e-05/0.005803, allocations: 27 kB / 0.6501 GB, free: 36.52 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002648/0.006068, allocations: 179.6 kB / 0.6503 GB, free: 36.36 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.503e-05/0.006083, allocations: 6 kB / 0.6503 GB, free: 36.36 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.495e-05/0.006118, allocations: 13.28 kB / 0.6503 GB, free: 36.36 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002278/0.006346, allocations: 146.8 kB / 0.6504 GB, free: 36.26 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.645e-05/0.006362, allocations: 3.281 kB / 0.6504 GB, free: 36.26 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.694e-05/0.006379, allocations: 5.906 kB / 0.6504 GB, free: 36.25 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.175e-05/0.006391, allocations: 4.656 kB / 0.6504 GB, free: 36.25 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001212/0.006512, allocations: 83.23 kB / 0.6505 GB, free: 36.21 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005489/0.007061, allocations: 398 kB / 0.6509 GB, free: 35.89 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001865/0.007248, allocations: 125.5 kB / 0.651 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 6.784e-05/0.007315, allocations: 63.97 kB / 0.6511 GB, free: 35.75 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.287e-05/0.007328, allocations: 4.25 kB / 0.6511 GB, free: 35.75 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002126/0.007541, allocations: 202.8 kB / 0.6513 GB, free: 35.59 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 2.895e-06/0.007544, allocations: 5.219 kB / 0.6513 GB, free: 35.58 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0009262/0.00847, allocations: 0.5734 MB / 0.6518 GB, free: 35.16 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.797e-05/0.008528, allocations: 141.8 kB / 0.652 GB, free: 35 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001158/0.008644, allocations: 207.9 kB / 0.6522 GB, free: 34.83 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.678e-05/0.00866, allocations: 31.2 kB / 0.6522 GB, free: 34.79 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 6.168e-05/0.008722, allocations: 160.4 kB / 0.6524 GB, free: 34.64 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 4.159e-05/0.008764, allocations: 70.23 kB / 0.6524 GB, free: 34.59 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.119e-05/0.008825, allocations: 51.17 kB / 0.6525 GB, free: 34.55 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 7.66e-05/0.008901, allocations: 0.4983 MB / 0.653 GB, free: 34.05 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 9.116e-05/0.008993, allocations: 109.8 kB / 0.6531 GB, free: 33.96 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001209/0.009114, allocations: 190.5 kB / 0.6532 GB, free: 33.76 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002517/0.009365, allocations: 327.6 kB / 0.6536 GB, free: 33.48 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.543e-06/0.009367, allocations: 0 / 0.6536 GB, free: 33.48 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0003105/0.009677, allocations: 313.3 kB / 0.6539 GB, free: 33.26 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.887e-05/0.009726, allocations: 59.53 kB / 0.6539 GB, free: 33.2 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.556e-06/0.009735, allocations: 6.578 kB / 0.6539 GB, free: 33.2 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.683e-05/0.009761, allocations: 11.16 kB / 0.6539 GB, free: 33.2 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001838/0.009945, allocations: 53.58 kB / 0.654 GB, free: 33.19 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.101e-05/0.009956, allocations: 3 kB / 0.654 GB, free: 33.19 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.188e-05/0.01004, allocations: 12.06 kB / 0.654 GB, free: 33.18 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.914e-05/0.01006, allocations: 7.969 kB / 0.654 GB, free: 33.18 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: 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 0.0002054/0.01026, allocations: 225.4 kB / 0.6542 GB, free: 32.98 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.411e-05/0.0103, allocations: 25.03 kB / 0.6542 GB, free: 32.96 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.559e-05/0.01034, allocations: 19.8 kB / 0.6543 GB, free: 32.95 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.763e-06/0.01035, allocations: 11.14 kB / 0.6543 GB, free: 32.95 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.541e-06/0.01035, allocations: 0 / 0.6543 GB, free: 32.95 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.492e-06/0.01036, allocations: 3.656 kB / 0.6543 GB, free: 32.95 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004732/0.01083, allocations: 0.5274 MB / 0.6548 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.266e-06/0.01084, allocations: 0 / 0.6548 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000139/0.01098, allocations: 30.58 kB / 0.6548 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 6.332e-06/0.01098, allocations: 4.891 kB / 0.6548 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.727e-05/0.011, allocations: 2 kB / 0.6548 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.825e-06/0.011, allocations: 2.375 kB / 0.6548 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.914e-06/0.011, allocations: 0 / 0.6548 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003706/0.01138, allocations: 470.1 kB / 0.6553 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.011e-05/0.0114, allocations: 15 kB / 0.6553 GB, free: 32.17 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.048e-05/0.01143, allocations: 11.22 kB / 0.6553 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.766e-05/0.0115, allocations: 13.36 kB / 0.6553 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.779e-05/0.01158, allocations: 16.97 kB / 0.6553 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.419e-05/0.0116, allocations: 8.891 kB / 0.6553 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 5.997e-05/0.01166, allocations: 155.9 kB / 0.6555 GB, free: 32.03 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 8e-08/0.01166, allocations: 0 / 0.6555 GB, free: 32.03 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0001995/0.01186, allocations: 43.78 kB / 0.6555 GB, free: 32.03 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 0.0001044/0.01196, allocations: 103.4 kB / 0.6556 GB, free: 31.94 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002978/0.01226, allocations: 324.9 kB / 0.6559 GB, free: 31.68 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 2.034e-06/0.01226, allocations: 3.906 kB / 0.6559 GB, free: 31.68 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001062/0.01237, allocations: 154.6 kB / 0.6561 GB, free: 31.56 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003108/0.01268, allocations: 42.41 kB / 0.6561 GB, free: 31.55 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00153/0.01421, allocations: 0.618 MB / 0.6567 GB, free: 31.14 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001227/0.01433, allocations: 112.3 kB / 0.6568 GB, free: 31.06 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 7.731e-05/0.01441, allocations: 27.34 kB / 0.6569 GB, free: 31.05 MB / 0.5262 GB
Notification: Performance of SimCode: time 1.773e-06/0.01441, allocations: 0 / 0.6569 GB, free: 31.05 MB / 0.5262 GB
Notification: Performance of Templates: time 0.00439/0.0188, allocations: 2.392 MB / 0.6592 GB, free: 30.87 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 > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 6.434170854976401]