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 0.001356/0.001356, allocations: 84.23 kB / 19.42 MB, free: 476 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 0.0009437/0.0009437, allocations: 173 kB / 22.72 MB, free: 1.805 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 1.006/1.006, allocations: 177.1 MB / 203.1 MB, free: 5.629 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 1.724/1.724, allocations: 273.5 MB / 0.5205 GB, free: 14.7 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 1.302e-06/1.302e-06, allocations: 0 / 0.6462 GB, free: 38.68 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.329e-05/1.459e-05, allocations: 3.5 kB / 0.6462 GB, free: 38.68 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Gentamicin): time 0.001918/0.001932, allocations: 2.117 MB / 0.6483 GB, free: 37.3 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0006543/0.002587, allocations: 0.5507 MB / 0.6488 GB, free: 36.94 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 6.709e-05/0.002654, allocations: 2.219 kB / 0.6488 GB, free: 36.94 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 9.855e-05/0.002752, allocations: 25.81 kB / 0.6489 GB, free: 36.93 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001233/0.002876, allocations: 54.3 kB / 0.6489 GB, free: 36.9 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001575/0.003033, allocations: 49.59 kB / 0.649 GB, free: 36.88 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002037/0.003237, allocations: 202.2 kB / 0.6492 GB, free: 36.82 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001109/0.003348, allocations: 32.34 kB / 0.6492 GB, free: 36.8 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001219/0.00347, allocations: 105.8 kB / 0.6493 GB, free: 36.76 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 9.785e-05/0.003568, allocations: 60 kB / 0.6493 GB, free: 36.74 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.801e-05/0.003596, allocations: 14.09 kB / 0.6494 GB, free: 36.74 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.239e-05/0.003618, allocations: 14.62 kB / 0.6494 GB, free: 36.74 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 2.934e-05/0.003647, allocations: 36.48 kB / 0.6494 GB, free: 36.72 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 5.741e-05/0.003705, allocations: 51.5 kB / 0.6495 GB, free: 36.7 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001488/0.003854, allocations: 119.4 kB / 0.6496 GB, free: 36.64 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.144e-06/0.003856, allocations: 3.938 kB / 0.6496 GB, free: 36.64 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 6.01e-07/0.003856, allocations: 0 / 0.6496 GB, free: 36.64 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.449e-06/0.003861, allocations: 1.062 kB / 0.6496 GB, free: 36.64 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 0.0004907/0.004352, allocations: 0.5319 MB / 0.6501 GB, free: 36.14 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.237e-05/0.004384, allocations: 9.719 kB / 0.6501 GB, free: 36.14 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.364e-05/0.004438, allocations: 23.88 kB / 0.6501 GB, free: 36.13 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001419/0.004579, allocations: 164.7 kB / 0.6503 GB, free: 35.97 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.912e-05/0.004599, allocations: 9.688 kB / 0.6503 GB, free: 35.96 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.271e-05/0.004631, allocations: 23.81 kB / 0.6503 GB, free: 35.96 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001741/0.004805, allocations: 141.2 kB / 0.6504 GB, free: 35.86 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.216e-05/0.004817, allocations: 4 kB / 0.6505 GB, free: 35.86 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.485e-05/0.004832, allocations: 3.625 kB / 0.6505 GB, free: 35.86 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.867e-06/0.004841, allocations: 1.469 kB / 0.6505 GB, free: 35.86 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 9.704e-05/0.004938, allocations: 81.2 kB / 0.6505 GB, free: 35.82 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0003935/0.005332, allocations: 405.5 kB / 0.6509 GB, free: 35.48 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001326/0.005464, allocations: 116.3 kB / 0.651 GB, free: 35.41 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 5.239e-05/0.005517, allocations: 73.27 kB / 0.6511 GB, free: 35.35 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 8.897e-06/0.005526, allocations: 2.281 kB / 0.6511 GB, free: 35.35 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001494/0.005675, allocations: 199.2 kB / 0.6513 GB, free: 35.19 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 2.455e-06/0.005677, allocations: 4.781 kB / 0.6513 GB, free: 35.19 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0006497/0.006327, allocations: 0.5731 MB / 0.6519 GB, free: 34.77 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.914e-05/0.006356, allocations: 134.3 kB / 0.652 GB, free: 34.61 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.552e-05/0.006442, allocations: 211.5 kB / 0.6522 GB, free: 34.43 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.242e-05/0.006454, allocations: 33.33 kB / 0.6522 GB, free: 34.4 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 4.007e-05/0.006494, allocations: 160.4 kB / 0.6524 GB, free: 34.25 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 3.157e-05/0.006526, allocations: 71.09 kB / 0.6524 GB, free: 34.19 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 4.888e-05/0.006575, allocations: 56 kB / 0.6525 GB, free: 34.15 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 4.706e-05/0.006622, allocations: 0.5009 MB / 0.653 GB, free: 33.65 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.207e-05/0.006694, allocations: 105.4 kB / 0.6531 GB, free: 33.56 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 9.252e-05/0.006786, allocations: 195 kB / 0.6533 GB, free: 33.36 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001856/0.006972, allocations: 322.1 kB / 0.6536 GB, free: 33.07 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.214e-06/0.006974, allocations: 1.969 kB / 0.6536 GB, free: 33.07 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002307/0.007205, allocations: 307.1 kB / 0.6539 GB, free: 32.87 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.505e-05/0.00723, allocations: 68.31 kB / 0.6539 GB, free: 32.8 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.438e-06/0.007234, allocations: 0 / 0.6539 GB, free: 32.8 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.646e-05/0.007251, allocations: 9.094 kB / 0.6539 GB, free: 32.8 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001376/0.007388, allocations: 48.34 kB / 0.654 GB, free: 32.79 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.454e-06/0.007396, allocations: 3.594 kB / 0.654 GB, free: 32.79 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.118e-05/0.007467, allocations: 17.03 kB / 0.654 GB, free: 32.79 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.328e-05/0.00748, allocations: 15.59 kB / 0.654 GB, free: 32.78 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 0.0001186/0.007599, allocations: 221.3 kB / 0.6542 GB, free: 32.57 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.425e-05/0.007623, allocations: 27.16 kB / 0.6543 GB, free: 32.56 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.008e-05/0.007653, allocations: 19.12 kB / 0.6543 GB, free: 32.55 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.655e-06/0.007656, allocations: 6.375 kB / 0.6543 GB, free: 32.55 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.887e-06/0.00766, allocations: 3.938 kB / 0.6543 GB, free: 32.54 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.577e-06/0.007663, allocations: 3.656 kB / 0.6543 GB, free: 32.54 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003304/0.007994, allocations: 0.5153 MB / 0.6548 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.503e-06/0.007995, allocations: 0 / 0.6548 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001079/0.008103, allocations: 37.02 kB / 0.6548 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.064e-06/0.008105, allocations: 0 / 0.6548 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.369e-05/0.008119, allocations: 6.375 kB / 0.6548 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.292e-06/0.00812, allocations: 1.625 kB / 0.6548 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.993e-06/0.008122, allocations: 5.391 kB / 0.6548 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003192/0.008442, allocations: 463.3 kB / 0.6553 GB, free: 31.78 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.449e-05/0.008456, allocations: 7.641 kB / 0.6553 GB, free: 31.78 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.276e-05/0.008479, allocations: 11.69 kB / 0.6553 GB, free: 31.77 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.797e-05/0.008547, allocations: 5.812 kB / 0.6553 GB, free: 31.77 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.901e-05/0.008596, allocations: 21.56 kB / 0.6553 GB, free: 31.77 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.062e-05/0.008606, allocations: 7.938 kB / 0.6553 GB, free: 31.77 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 4.327e-05/0.00865, allocations: 152.6 kB / 0.6555 GB, free: 31.64 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 7e-08/0.00865, allocations: 3.25 kB / 0.6555 GB, free: 31.64 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0001926/0.008842, allocations: 52.64 kB / 0.6555 GB, free: 31.64 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 5.977e-05/0.008902, allocations: 110.2 kB / 0.6556 GB, free: 31.54 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002209/0.009123, allocations: 327 kB / 0.656 GB, free: 31.29 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.162e-06/0.009124, allocations: 3.062 kB / 0.656 GB, free: 31.29 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 8.186e-05/0.009206, allocations: 150.4 kB / 0.6561 GB, free: 31.17 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002599/0.009466, allocations: 53.48 kB / 0.6562 GB, free: 31.15 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001293/0.01076, allocations: 0.5822 MB / 0.6567 GB, free: 30.79 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.518e-05/0.0108, allocations: 86.14 kB / 0.6568 GB, free: 30.7 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 5.797e-05/0.01086, allocations: 18.58 kB / 0.6568 GB, free: 30.7 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.424e-05/0.01091, allocations: 19.06 kB / 0.6568 GB, free: 30.69 MB / 0.5262 GB
Notification: Performance of SimCode: time 6.52e-07/0.01091, allocations: 0.5625 kB / 0.6568 GB, free: 30.69 MB / 0.5262 GB
Notification: Performance of Templates: time 0.004347/0.01525, allocations: 2.619 MB / 0.6594 GB, free: 30.47 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: 5.071232385002077]