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 0.0009839/0.0009839, allocations: 80.94 kB / 19.94 MB, free: 4.543 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 0.001059/0.001059, allocations: 177.4 kB / 23.36 MB, free: 1.129 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 0.9637/0.9637, allocations: 177.1 MB / 203.8 MB, free: 5.477 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 2.275/2.275, allocations: 273.5 MB / 0.5213 GB, free: 14.6 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 5.71e-07/5.71e-07, allocations: 0 / 0.5954 GB, free: 2.637 MB / 0.5105 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.146e-05/1.203e-05, allocations: 5.125 kB / 0.5955 GB, free: 2.633 MB / 0.5105 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Gentamicin): time 0.002612/0.002624, allocations: 2.166 MB / 0.5976 GB, free: 488 kB / 0.5105 GB
Notification: Performance of NFInst.instExpressions: time 0.0006719/0.003296, allocations: 0.5569 MB / 0.5981 GB, free: 15.92 MB / 0.5261 GB
Notification: Performance of NFInst.updateImplicitVariability: time 4.704e-05/0.003343, allocations: 4 kB / 0.5981 GB, free: 15.92 MB / 0.5261 GB
Notification: Performance of NFTyping.typeComponents: time 5.899e-05/0.003402, allocations: 17.11 kB / 0.5981 GB, free: 15.9 MB / 0.5261 GB
Notification: Performance of NFTyping.typeBindings: time 9.206e-05/0.003494, allocations: 49.31 kB / 0.5982 GB, free: 15.87 MB / 0.5261 GB
Notification: Performance of NFTyping.typeClassSections: time 9.984e-05/0.003594, allocations: 47.88 kB / 0.5982 GB, free: 15.82 MB / 0.5261 GB
Notification: Performance of NFFlatten.flatten: time 0.0001649/0.003759, allocations: 211.6 kB / 0.5984 GB, free: 15.67 MB / 0.5261 GB
Notification: Performance of NFFlatten.resolveConnections: time 7.678e-05/0.003836, allocations: 30.62 kB / 0.5985 GB, free: 15.64 MB / 0.5261 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001124/0.003948, allocations: 104.1 kB / 0.5986 GB, free: 15.55 MB / 0.5261 GB
Notification: Performance of NFSimplifyModel.simplify: time 8.759e-05/0.004036, allocations: 60.8 kB / 0.5986 GB, free: 15.49 MB / 0.5261 GB
Notification: Performance of NFPackage.collectConstants: time 2.034e-05/0.004056, allocations: 12 kB / 0.5986 GB, free: 15.48 MB / 0.5261 GB
Notification: Performance of NFFlatten.collectFunctions: time 1.72e-05/0.004073, allocations: 16 kB / 0.5986 GB, free: 15.46 MB / 0.5261 GB
Notification: Performance of NFScalarize.scalarize: time 2.63e-05/0.0041, allocations: 31.89 kB / 0.5987 GB, free: 15.43 MB / 0.5261 GB
Notification: Performance of NFVerifyModel.verify: time 5.244e-05/0.004152, allocations: 59.84 kB / 0.5987 GB, free: 15.37 MB / 0.5261 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001251/0.004277, allocations: 123.5 kB / 0.5988 GB, free: 15.25 MB / 0.5261 GB
Notification: Performance of FrontEnd - DAE generated: time 1.082e-06/0.004278, allocations: 0 / 0.5988 GB, free: 15.25 MB / 0.5261 GB
Notification: Performance of FrontEnd: time 4.1e-07/0.004279, allocations: 4 kB / 0.5988 GB, free: 15.25 MB / 0.5261 GB
Notification: Performance of Transformations before backend: time 2.565e-06/0.004281, allocations: 0 / 0.5988 GB, free: 15.25 MB / 0.5261 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 0.0003626/0.004644, allocations: 407.6 kB / 0.5992 GB, free: 14.82 MB / 0.5261 GB
Notification: Performance of prepare preOptimizeDAE: time 2.251e-05/0.004666, allocations: 12.03 kB / 0.5992 GB, free: 14.8 MB / 0.5261 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 3.04e-05/0.004697, allocations: 24.91 kB / 0.5993 GB, free: 14.78 MB / 0.5261 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000114/0.004811, allocations: 138.1 kB / 0.5994 GB, free: 14.62 MB / 0.5261 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.243e-05/0.004823, allocations: 12.38 kB / 0.5994 GB, free: 14.61 MB / 0.5261 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 1.792e-05/0.004841, allocations: 12.38 kB / 0.5994 GB, free: 14.6 MB / 0.5261 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001288/0.00497, allocations: 141.5 kB / 0.5996 GB, free: 14.45 MB / 0.5261 GB
Notification: Performance of preOpt findStateOrder (simulation): time 7.495e-06/0.004978, allocations: 4 kB / 0.5996 GB, free: 14.44 MB / 0.5261 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.775e-06/0.004985, allocations: 4 kB / 0.5996 GB, free: 14.44 MB / 0.5261 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.807e-06/0.004989, allocations: 0 / 0.5996 GB, free: 14.44 MB / 0.5261 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001002/0.005089, allocations: 70.31 kB / 0.5996 GB, free: 14.36 MB / 0.5261 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0003523/0.005442, allocations: 259.9 kB / 0.5999 GB, free: 14.09 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001241/0.005566, allocations: 96.23 kB / 0.6 GB, free: 13.98 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 4.181e-05/0.005608, allocations: 62.48 kB / 0.6 GB, free: 13.91 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 6.212e-06/0.005614, allocations: 4 kB / 0.6 GB, free: 13.91 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001315/0.005745, allocations: 190.8 kB / 0.6002 GB, free: 13.7 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=20): time 1.213e-06/0.005746, allocations: 0 / 0.6002 GB, free: 13.7 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=21): time 0.0005419/0.006288, allocations: 0.4962 MB / 0.6007 GB, free: 13.14 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.029e-05/0.006339, allocations: 140.5 kB / 0.6008 GB, free: 12.97 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.732e-05/0.006426, allocations: 159.1 kB / 0.601 GB, free: 12.8 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 2.321e-05/0.006449, allocations: 29.7 kB / 0.601 GB, free: 12.77 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 4.377e-05/0.006493, allocations: 104.6 kB / 0.6011 GB, free: 12.66 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 3.923e-05/0.006532, allocations: 71.41 kB / 0.6012 GB, free: 12.59 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.008e-05/0.006582, allocations: 53.67 kB / 0.6012 GB, free: 12.54 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 9.159e-05/0.006674, allocations: 330.8 kB / 0.6016 GB, free: 12.2 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 5.977e-05/0.006734, allocations: 100.6 kB / 0.6017 GB, free: 12.09 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 9.209e-05/0.006826, allocations: 168.4 kB / 0.6018 GB, free: 11.88 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002374/0.007063, allocations: 286.4 kB / 0.6021 GB, free: 11.55 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.273e-06/0.007064, allocations: 0 / 0.6021 GB, free: 11.55 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0001786/0.007243, allocations: 251.5 kB / 0.6023 GB, free: 11.28 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 3.124e-05/0.007274, allocations: 59.41 kB / 0.6024 GB, free: 11.21 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.735e-06/0.007277, allocations: 0 / 0.6024 GB, free: 11.21 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 8.045e-06/0.007285, allocations: 4 kB / 0.6024 GB, free: 11.21 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001543/0.007439, allocations: 64.08 kB / 0.6024 GB, free: 11.14 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 3.176e-06/0.007443, allocations: 8 kB / 0.6025 GB, free: 11.14 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 6.931e-05/0.007512, allocations: 19.92 kB / 0.6025 GB, free: 11.12 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 9.218e-06/0.007521, allocations: 4 kB / 0.6025 GB, free: 11.11 MB / 0.5261 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 0.0004428/0.007964, allocations: 180.5 kB / 0.6026 GB, free: 10.92 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.175e-05/0.007986, allocations: 19.98 kB / 0.6027 GB, free: 10.9 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 2.399e-05/0.00801, allocations: 21.27 kB / 0.6027 GB, free: 10.88 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.405e-06/0.008012, allocations: 7.938 kB / 0.6027 GB, free: 10.87 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.312e-06/0.008013, allocations: 0 / 0.6027 GB, free: 10.87 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.057e-06/0.008017, allocations: 3.938 kB / 0.6027 GB, free: 10.87 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000258/0.008275, allocations: 353.4 kB / 0.603 GB, free: 10.48 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 9.72e-07/0.008276, allocations: 0 / 0.603 GB, free: 10.48 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001225/0.008399, allocations: 51.84 kB / 0.6031 GB, free: 10.43 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.454e-06/0.008401, allocations: 4 kB / 0.6031 GB, free: 10.43 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.056e-05/0.008412, allocations: 4 kB / 0.6031 GB, free: 10.43 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.245e-06/0.008414, allocations: 4 kB / 0.6031 GB, free: 10.42 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 6.52e-07/0.008415, allocations: 0 / 0.6031 GB, free: 10.42 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002098/0.008625, allocations: 333 kB / 0.6034 GB, free: 10.06 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.528e-05/0.00864, allocations: 19.89 kB / 0.6034 GB, free: 10.04 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 1.848e-05/0.008658, allocations: 4 kB / 0.6034 GB, free: 10.04 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.399e-05/0.008722, allocations: 8 kB / 0.6034 GB, free: 10.03 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.001e-05/0.008762, allocations: 22.95 kB / 0.6035 GB, free: 10.01 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 9.929e-06/0.008772, allocations: 15.98 kB / 0.6035 GB, free: 9.996 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 2.753e-05/0.0088, allocations: 35.06 kB / 0.6035 GB, free: 9.961 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 9.1e-08/0.0088, allocations: 0 / 0.6035 GB, free: 9.961 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.0001546/0.008955, allocations: 48 kB / 0.6036 GB, free: 9.914 MB / 0.5261 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 6.416e-05/0.009019, allocations: 96.34 kB / 0.6037 GB, free: 9.809 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.0001816/0.0092, allocations: 300.5 kB / 0.6039 GB, free: 9.469 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 2.004e-06/0.009202, allocations: 0 / 0.6039 GB, free: 9.469 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 8.104e-05/0.009283, allocations: 144.4 kB / 0.6041 GB, free: 9.309 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0001798/0.009463, allocations: 47.22 kB / 0.6041 GB, free: 9.266 MB / 0.5261 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0009941/0.01046, allocations: 0.511 MB / 0.6046 GB, free: 8.73 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 3.787e-05/0.0105, allocations: 75.98 kB / 0.6047 GB, free: 8.637 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 4.845e-05/0.01054, allocations: 13.64 kB / 0.6047 GB, free: 8.625 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001087/0.01065, allocations: 99.34 kB / 0.6048 GB, free: 8.527 MB / 0.5261 GB
Notification: Performance of SimCode: time 7.21e-07/0.01065, allocations: 0 / 0.6048 GB, free: 8.527 MB / 0.5261 GB
Notification: Performance of Templates: time 0.004051/0.0147, allocations: 2.842 MB / 0.6076 GB, free: 5.844 MB / 0.5261 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 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.4373784288764]