Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.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 0.001663/0.001663, 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 0.002149/0.002149, allocations: 173 kB / 23.49 MB, free: 1.059 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 0.9244/0.9244, allocations: 177.1 MB / 203.8 MB, free: 5.641 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 1.586/1.586, allocations: 273.5 MB / 0.5213 GB, free: 14.84 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_Digoxin,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin")
translateModel(Pharmacolibrary.Examples.PK_1C_Digoxin,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.894e-06/1.894e-06, allocations: 0 / 0.6462 GB, free: 39.18 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.774e-05/2.964e-05, allocations: 2.312 kB / 0.6462 GB, free: 39.17 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Digoxin): time 0.003316/0.003346, allocations: 2.069 MB / 0.6482 GB, free: 37.83 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001029/0.004375, allocations: 0.5499 MB / 0.6488 GB, free: 37.47 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.197e-05/0.004467, allocations: 2.312 kB / 0.6488 GB, free: 37.47 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001218/0.004589, allocations: 15.56 kB / 0.6488 GB, free: 37.46 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001714/0.00476, allocations: 59.58 kB / 0.6488 GB, free: 37.43 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.000212/0.004972, allocations: 43.45 kB / 0.6489 GB, free: 37.41 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002988/0.005271, allocations: 190.5 kB / 0.6491 GB, free: 37.36 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001412/0.005413, allocations: 31.36 kB / 0.6491 GB, free: 37.33 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001841/0.005597, allocations: 102.3 kB / 0.6492 GB, free: 37.29 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001553/0.005752, allocations: 62.78 kB / 0.6492 GB, free: 37.27 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 4.201e-05/0.005794, allocations: 15.09 kB / 0.6493 GB, free: 37.27 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 3.475e-05/0.005829, allocations: 15.69 kB / 0.6493 GB, free: 37.27 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 3.881e-05/0.005867, allocations: 28.75 kB / 0.6493 GB, free: 37.25 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 9.501e-05/0.005962, allocations: 59.73 kB / 0.6494 GB, free: 37.22 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002279/0.00619, allocations: 121.9 kB / 0.6495 GB, free: 37.16 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 4.509e-06/0.006195, allocations: 1.094 kB / 0.6495 GB, free: 37.16 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 9.81e-07/0.006196, allocations: 0 / 0.6495 GB, free: 37.16 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 6.041e-06/0.006202, allocations: 0 / 0.6495 GB, free: 37.16 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 0.0006883/0.00689, allocations: 0.5172 MB / 0.65 GB, free: 36.67 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 4.381e-05/0.006934, allocations: 9.312 kB / 0.65 GB, free: 36.67 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.434e-05/0.007018, allocations: 33.52 kB / 0.65 GB, free: 36.66 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002782/0.007297, allocations: 169 kB / 0.6502 GB, free: 36.5 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.929e-05/0.007316, allocations: 10.25 kB / 0.6502 GB, free: 36.49 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.955e-05/0.007355, allocations: 9.375 kB / 0.6502 GB, free: 36.49 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002669/0.007622, allocations: 149.5 kB / 0.6503 GB, free: 36.39 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.706e-05/0.007639, allocations: 9.422 kB / 0.6503 GB, free: 36.39 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.911e-05/0.007658, allocations: 6.156 kB / 0.6504 GB, free: 36.38 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.508e-06/0.007668, allocations: 3.75 kB / 0.6504 GB, free: 36.38 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001565/0.007824, allocations: 75.69 kB / 0.6504 GB, free: 36.35 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006294/0.008454, allocations: 400.2 kB / 0.6508 GB, free: 36.02 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002403/0.008694, allocations: 129.1 kB / 0.6509 GB, free: 35.93 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 9.906e-05/0.008793, allocations: 64.31 kB / 0.651 GB, free: 35.88 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.569e-05/0.008809, allocations: 5.125 kB / 0.651 GB, free: 35.88 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002617/0.009071, allocations: 197.9 kB / 0.6512 GB, free: 35.72 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 2.525e-06/0.009073, allocations: 0 / 0.6512 GB, free: 35.72 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.001178/0.01025, allocations: 0.5743 MB / 0.6517 GB, free: 35.3 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.179e-05/0.01032, allocations: 142.3 kB / 0.6519 GB, free: 35.14 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001479/0.01047, allocations: 202.2 kB / 0.6521 GB, free: 34.96 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.636e-05/0.0105, allocations: 32.95 kB / 0.6521 GB, free: 34.93 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 7.747e-05/0.01057, allocations: 155.9 kB / 0.6523 GB, free: 34.78 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 6.248e-05/0.01064, allocations: 67.91 kB / 0.6523 GB, free: 34.73 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.524e-05/0.01073, allocations: 52.02 kB / 0.6524 GB, free: 34.69 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 0.0001287/0.01086, allocations: 0.4975 MB / 0.6529 GB, free: 34.19 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001521/0.01101, allocations: 106.3 kB / 0.653 GB, free: 34.1 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001696/0.01118, allocations: 190.2 kB / 0.6531 GB, free: 33.91 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003827/0.01157, allocations: 326.2 kB / 0.6535 GB, free: 33.62 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.889e-06/0.01157, allocations: 3.312 kB / 0.6535 GB, free: 33.62 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0004703/0.01204, allocations: 318.7 kB / 0.6538 GB, free: 33.4 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.287e-05/0.01208, allocations: 60.62 kB / 0.6538 GB, free: 33.34 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.937e-06/0.01209, allocations: 1.844 kB / 0.6538 GB, free: 33.34 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.244e-05/0.01211, allocations: 5.984 kB / 0.6538 GB, free: 33.34 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001752/0.01229, allocations: 47.02 kB / 0.6539 GB, free: 33.34 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.113e-05/0.0123, allocations: 11.95 kB / 0.6539 GB, free: 33.33 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.062e-05/0.01239, allocations: 11.34 kB / 0.6539 GB, free: 33.33 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.78e-05/0.01241, allocations: 13.06 kB / 0.6539 GB, free: 33.32 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 0.0001956/0.01261, allocations: 226.1 kB / 0.6541 GB, free: 33.11 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.268e-05/0.01264, allocations: 26.56 kB / 0.6541 GB, free: 33.1 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.364e-05/0.01267, allocations: 19.12 kB / 0.6542 GB, free: 33.09 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.338e-06/0.01268, allocations: 3.5 kB / 0.6542 GB, free: 33.09 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.51e-06/0.01268, allocations: 2.312 kB / 0.6542 GB, free: 33.09 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.531e-06/0.01269, allocations: 3.938 kB / 0.6542 GB, free: 33.09 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004055/0.01309, allocations: 0.5204 MB / 0.6547 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.944e-06/0.01309, allocations: 2.031 kB / 0.6547 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000122/0.01322, allocations: 30.81 kB / 0.6547 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 4.138e-06/0.01322, allocations: 0.9062 kB / 0.6547 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.624e-05/0.01324, allocations: 10.91 kB / 0.6547 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.996e-06/0.01324, allocations: 2.344 kB / 0.6547 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.515e-06/0.01324, allocations: 7.125 kB / 0.6547 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003059/0.01355, allocations: 459.6 kB / 0.6552 GB, free: 32.32 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.876e-05/0.01357, allocations: 15.5 kB / 0.6552 GB, free: 32.31 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.582e-05/0.01359, allocations: 8.406 kB / 0.6552 GB, free: 32.31 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.26e-05/0.01367, allocations: 9.344 kB / 0.6552 GB, free: 32.31 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.919e-05/0.01372, allocations: 16.88 kB / 0.6552 GB, free: 32.3 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.297e-05/0.01374, allocations: 9.75 kB / 0.6552 GB, free: 32.3 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 4.733e-05/0.01378, allocations: 150.3 kB / 0.6554 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 6e-08/0.01378, allocations: 1.031 kB / 0.6554 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002074/0.01399, allocations: 47.88 kB / 0.6554 GB, free: 32.17 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 9.236e-05/0.01408, allocations: 109.5 kB / 0.6555 GB, free: 32.08 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002456/0.01433, allocations: 323 kB / 0.6558 GB, free: 31.82 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 2.023e-06/0.01433, allocations: 0 / 0.6558 GB, free: 31.82 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 8.816e-05/0.01442, allocations: 153.3 kB / 0.656 GB, free: 31.71 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003679/0.01479, allocations: 49.81 kB / 0.656 GB, free: 31.69 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00471/0.0195, allocations: 0.602 MB / 0.6566 GB, free: 31.29 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 8.222e-05/0.01958, allocations: 115.4 kB / 0.6567 GB, free: 31.2 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.422e-05/0.01964, allocations: 24.06 kB / 0.6567 GB, free: 31.19 MB / 0.5262 GB
Notification: Performance of SimCode: time 1.093e-06/0.01965, allocations: 3.938 kB / 0.6567 GB, free: 31.19 MB / 0.5262 GB
Notification: Performance of Templates: time 0.006966/0.02661, allocations: 2.283 MB / 0.659 GB, free: 31.02 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 6.2704539289698005]