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 0.001017/0.001017, allocations: 92.2 kB / 20.19 MB, free: 4.363 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 0.0009646/0.0009646, 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 0.9863/0.9863, allocations: 177.1 MB / 203.8 MB, free: 5.633 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 1.556/1.556, allocations: 273.5 MB / 0.5213 GB, free: 14.82 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 1.393e-06/1.393e-06, allocations: 0 / 0.647 GB, free: 38.75 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.588e-05/2.727e-05, allocations: 5.266 kB / 0.647 GB, free: 38.75 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Gentamicin): time 0.002281/0.002308, allocations: 2.11 MB / 0.649 GB, free: 37.38 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0006978/0.003006, allocations: 0.5562 MB / 0.6496 GB, free: 37.01 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 7.244e-05/0.003078, allocations: 2.25 kB / 0.6496 GB, free: 37.01 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001043/0.003183, allocations: 18.56 kB / 0.6496 GB, free: 37 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001201/0.003303, allocations: 53.09 kB / 0.6497 GB, free: 36.98 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001476/0.00345, allocations: 46.73 kB / 0.6497 GB, free: 36.95 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002065/0.003657, allocations: 204 kB / 0.6499 GB, free: 36.89 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001189/0.003776, allocations: 28.03 kB / 0.6499 GB, free: 36.87 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001171/0.003893, allocations: 111.2 kB / 0.65 GB, free: 36.82 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001038/0.003997, allocations: 58.3 kB / 0.6501 GB, free: 36.81 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.866e-05/0.004025, allocations: 18.97 kB / 0.6501 GB, free: 36.81 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.009e-05/0.004046, allocations: 13.62 kB / 0.6501 GB, free: 36.81 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 3.024e-05/0.004076, allocations: 30.8 kB / 0.6501 GB, free: 36.79 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 6.125e-05/0.004137, allocations: 59.36 kB / 0.6502 GB, free: 36.76 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001606/0.004298, allocations: 126.3 kB / 0.6503 GB, free: 36.7 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.665e-06/0.0043, allocations: 0 / 0.6503 GB, free: 36.7 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.092e-06/0.004301, allocations: 1.125 kB / 0.6503 GB, free: 36.7 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 5.13e-06/0.004306, allocations: 0 / 0.6503 GB, free: 36.7 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 0.0005295/0.004836, allocations: 0.5234 MB / 0.6508 GB, free: 36.21 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.513e-05/0.004871, allocations: 10.03 kB / 0.6508 GB, free: 36.21 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.248e-05/0.004934, allocations: 34.05 kB / 0.6509 GB, free: 36.19 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001973/0.005131, allocations: 180.8 kB / 0.651 GB, free: 36.03 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.361e-05/0.005144, allocations: 10.16 kB / 0.6511 GB, free: 36.02 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.87e-05/0.005173, allocations: 15.06 kB / 0.6511 GB, free: 36.02 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001734/0.005347, allocations: 149.5 kB / 0.6512 GB, free: 35.92 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.222e-05/0.005359, allocations: 5.594 kB / 0.6512 GB, free: 35.92 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.331e-05/0.005372, allocations: 7.125 kB / 0.6512 GB, free: 35.91 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.135e-06/0.00538, allocations: 2.344 kB / 0.6512 GB, free: 35.91 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 9.774e-05/0.005478, allocations: 80.44 kB / 0.6513 GB, free: 35.88 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004284/0.005906, allocations: 398 kB / 0.6517 GB, free: 35.55 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001474/0.006054, allocations: 116.2 kB / 0.6518 GB, free: 35.47 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 5.252e-05/0.006106, allocations: 65.97 kB / 0.6519 GB, free: 35.42 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 9.999e-06/0.006116, allocations: 8.469 kB / 0.6519 GB, free: 35.42 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001628/0.006279, allocations: 199.2 kB / 0.6521 GB, free: 35.25 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 2.013e-06/0.006281, allocations: 1.312 kB / 0.6521 GB, free: 35.25 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0007191/0.007, allocations: 0.575 MB / 0.6526 GB, free: 34.83 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.947e-05/0.00704, allocations: 137.5 kB / 0.6527 GB, free: 34.68 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.772e-05/0.007137, allocations: 208.7 kB / 0.6529 GB, free: 34.5 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.397e-05/0.007151, allocations: 36.64 kB / 0.653 GB, free: 34.46 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 4.723e-05/0.007199, allocations: 163.6 kB / 0.6531 GB, free: 34.31 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 3.29e-05/0.007231, allocations: 66.25 kB / 0.6532 GB, free: 34.25 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.413e-05/0.007286, allocations: 56.69 kB / 0.6533 GB, free: 34.21 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 5.596e-05/0.007342, allocations: 0.5004 MB / 0.6537 GB, free: 33.71 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.559e-05/0.007417, allocations: 102.1 kB / 0.6538 GB, free: 33.62 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 9.44e-05/0.007512, allocations: 199.8 kB / 0.654 GB, free: 33.42 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001961/0.007708, allocations: 317.4 kB / 0.6543 GB, free: 33.14 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.483e-06/0.007709, allocations: 0 / 0.6543 GB, free: 33.14 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002482/0.007957, allocations: 316.2 kB / 0.6546 GB, free: 32.93 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.91e-05/0.007986, allocations: 64.95 kB / 0.6547 GB, free: 32.86 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.661e-06/0.007992, allocations: 6.125 kB / 0.6547 GB, free: 32.86 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.659e-05/0.008009, allocations: 8.844 kB / 0.6547 GB, free: 32.86 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001454/0.008154, allocations: 49.58 kB / 0.6548 GB, free: 32.85 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.993e-06/0.008161, allocations: 1.875 kB / 0.6548 GB, free: 32.85 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.899e-05/0.00824, allocations: 12.72 kB / 0.6548 GB, free: 32.85 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.203e-05/0.008252, allocations: 10.84 kB / 0.6548 GB, free: 32.85 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 0.0001487/0.008401, allocations: 228.6 kB / 0.655 GB, free: 32.64 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.648e-05/0.008427, allocations: 21.12 kB / 0.655 GB, free: 32.63 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.495e-05/0.008462, allocations: 26.89 kB / 0.655 GB, free: 32.61 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.266e-06/0.008465, allocations: 7.25 kB / 0.6551 GB, free: 32.61 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.579e-06/0.00847, allocations: 1.312 kB / 0.6551 GB, free: 32.61 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.788e-06/0.008474, allocations: 0 / 0.6551 GB, free: 32.61 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003648/0.008839, allocations: 0.5241 MB / 0.6556 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.994e-06/0.008841, allocations: 0 / 0.6556 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001186/0.008959, allocations: 33.31 kB / 0.6556 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.625e-06/0.008962, allocations: 0 / 0.6556 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.352e-05/0.008975, allocations: 6.094 kB / 0.6556 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.094e-06/0.008977, allocations: 5.938 kB / 0.6556 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.51e-07/0.008978, allocations: 3.969 kB / 0.6556 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000311/0.009289, allocations: 463.3 kB / 0.6561 GB, free: 31.84 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.979e-05/0.009309, allocations: 11.84 kB / 0.6561 GB, free: 31.83 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.904e-05/0.009338, allocations: 11.55 kB / 0.6561 GB, free: 31.83 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.262e-05/0.009411, allocations: 5.719 kB / 0.6561 GB, free: 31.83 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.967e-05/0.00947, allocations: 19.78 kB / 0.6561 GB, free: 31.82 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.301e-05/0.009483, allocations: 8.938 kB / 0.6561 GB, free: 31.82 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 5.914e-05/0.009543, allocations: 150.9 kB / 0.6563 GB, free: 31.7 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 6.1e-08/0.009543, allocations: 0 / 0.6563 GB, free: 31.7 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002042/0.009747, allocations: 52.95 kB / 0.6563 GB, free: 31.69 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 8.005e-05/0.009827, allocations: 109 kB / 0.6564 GB, free: 31.6 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002323/0.01006, allocations: 323.5 kB / 0.6567 GB, free: 31.34 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.573e-06/0.01006, allocations: 6.25 kB / 0.6567 GB, free: 31.34 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 8.351e-05/0.01014, allocations: 148.8 kB / 0.6569 GB, free: 31.22 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002845/0.01043, allocations: 55.09 kB / 0.6569 GB, free: 31.21 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001324/0.01175, allocations: 0.584 MB / 0.6575 GB, free: 30.84 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.03e-05/0.0118, allocations: 81.98 kB / 0.6576 GB, free: 30.76 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 6.397e-05/0.01187, allocations: 21.64 kB / 0.6576 GB, free: 30.75 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.972e-05/0.01192, allocations: 19.16 kB / 0.6576 GB, free: 30.75 MB / 0.5262 GB
Notification: Performance of SimCode: time 7.61e-07/0.01192, allocations: 0.5625 kB / 0.6576 GB, free: 30.75 MB / 0.5262 GB
Notification: Performance of Templates: time 0.004765/0.01668, allocations: 2.625 MB / 0.6602 GB, free: 30.53 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: 4.800519678974524]