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 0.001287/0.001287, allocations: 80.88 kB / 19.94 MB, free: 4.547 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 0.001439/0.001439, allocations: 181 kB / 23.36 MB, free: 1.133 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 1.052/1.052, allocations: 177.1 MB / 203.8 MB, free: 5.496 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 1.613/1.613, allocations: 273.5 MB / 0.5213 GB, free: 14.69 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 1.663e-06/1.663e-06, allocations: 0 / 0.5954 GB, free: 2.789 MB / 0.5105 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.481e-05/2.647e-05, allocations: 10.38 kB / 0.5954 GB, free: 2.781 MB / 0.5105 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Digoxin): time 0.002543/0.00257, allocations: 2.067 MB / 0.5974 GB, free: 0.7188 MB / 0.5105 GB
Notification: Performance of NFInst.instExpressions: time 0.0008525/0.003422, allocations: 0.5546 MB / 0.598 GB, free: 172 kB / 0.5105 GB
Notification: Performance of NFInst.updateImplicitVariability: time 6.496e-05/0.003487, allocations: 0 / 0.598 GB, free: 172 kB / 0.5105 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001372/0.003624, allocations: 19.8 kB / 0.598 GB, free: 152 kB / 0.5105 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002119/0.003836, allocations: 51.45 kB / 0.598 GB, free: 116 kB / 0.5105 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001692/0.004005, allocations: 43.88 kB / 0.5981 GB, free: 72 kB / 0.5105 GB
Notification: Performance of NFFlatten.flatten: time 0.0002215/0.004227, allocations: 194.7 kB / 0.5983 GB, free: 15.93 MB / 0.5261 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001046/0.004331, allocations: 26.55 kB / 0.5983 GB, free: 15.9 MB / 0.5261 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001425/0.004474, allocations: 108.7 kB / 0.5984 GB, free: 15.8 MB / 0.5261 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001069/0.004581, allocations: 57.06 kB / 0.5984 GB, free: 15.75 MB / 0.5261 GB
Notification: Performance of NFPackage.collectConstants: time 3.136e-05/0.004612, allocations: 16 kB / 0.5985 GB, free: 15.73 MB / 0.5261 GB
Notification: Performance of NFFlatten.collectFunctions: time 1.863e-05/0.004631, allocations: 13.42 kB / 0.5985 GB, free: 15.72 MB / 0.5261 GB
Notification: Performance of NFScalarize.scalarize: time 3.951e-05/0.00467, allocations: 30.97 kB / 0.5985 GB, free: 15.7 MB / 0.5261 GB
Notification: Performance of NFVerifyModel.verify: time 5.935e-05/0.00473, allocations: 59.89 kB / 0.5986 GB, free: 15.64 MB / 0.5261 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001571/0.004887, allocations: 119.6 kB / 0.5987 GB, free: 15.52 MB / 0.5261 GB
Notification: Performance of FrontEnd - DAE generated: time 3.115e-06/0.00489, allocations: 0 / 0.5987 GB, free: 15.52 MB / 0.5261 GB
Notification: Performance of FrontEnd: time 1.062e-06/0.004891, allocations: 0 / 0.5987 GB, free: 15.52 MB / 0.5261 GB
Notification: Performance of Transformations before backend: time 4.228e-06/0.004895, allocations: 0 / 0.5987 GB, free: 15.52 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 0.0004872/0.005382, allocations: 403.7 kB / 0.5991 GB, free: 15.09 MB / 0.5261 GB
Notification: Performance of prepare preOptimizeDAE: time 3.256e-05/0.005415, allocations: 12.03 kB / 0.5991 GB, free: 15.08 MB / 0.5261 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.136e-05/0.005456, allocations: 16.92 kB / 0.5991 GB, free: 15.06 MB / 0.5261 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000142/0.005598, allocations: 141.6 kB / 0.5992 GB, free: 14.9 MB / 0.5261 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.655e-05/0.005615, allocations: 8.375 kB / 0.5992 GB, free: 14.89 MB / 0.5261 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.603e-05/0.005641, allocations: 12.38 kB / 0.5992 GB, free: 14.88 MB / 0.5261 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001616/0.005803, allocations: 134.8 kB / 0.5994 GB, free: 14.73 MB / 0.5261 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.218e-05/0.005815, allocations: 11.86 kB / 0.5994 GB, free: 14.72 MB / 0.5261 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.026e-05/0.005825, allocations: 4 kB / 0.5994 GB, free: 14.72 MB / 0.5261 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.093e-06/0.005832, allocations: 15.45 kB / 0.5994 GB, free: 14.71 MB / 0.5261 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 7.575e-05/0.005908, allocations: 61.67 kB / 0.5995 GB, free: 14.64 MB / 0.5261 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0003535/0.006261, allocations: 259.9 kB / 0.5997 GB, free: 14.37 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001172/0.006379, allocations: 103.7 kB / 0.5998 GB, free: 14.26 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 4.412e-05/0.006423, allocations: 58.55 kB / 0.5999 GB, free: 14.19 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 8.786e-06/0.006431, allocations: 0 / 0.5999 GB, free: 14.19 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001766/0.006608, allocations: 189 kB / 0.6 GB, free: 13.98 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=20): time 1.734e-06/0.00661, allocations: 7.938 kB / 0.6 GB, free: 13.97 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=21): time 0.0006307/0.007241, allocations: 0.5056 MB / 0.6005 GB, free: 13.41 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.023e-05/0.007291, allocations: 132.5 kB / 0.6007 GB, free: 13.25 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.3e-05/0.007374, allocations: 152.7 kB / 0.6008 GB, free: 13.09 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 1.532e-05/0.007389, allocations: 29.7 kB / 0.6008 GB, free: 13.05 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 4.045e-05/0.00743, allocations: 104.5 kB / 0.6009 GB, free: 12.95 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 3.662e-05/0.007466, allocations: 71.41 kB / 0.601 GB, free: 12.88 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.225e-05/0.007518, allocations: 41.69 kB / 0.601 GB, free: 12.83 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 7.785e-05/0.007596, allocations: 334.8 kB / 0.6014 GB, free: 12.49 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 6.166e-05/0.007658, allocations: 100.7 kB / 0.6015 GB, free: 12.38 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 7.97e-05/0.007738, allocations: 156.4 kB / 0.6016 GB, free: 12.18 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001695/0.007907, allocations: 288.7 kB / 0.6019 GB, free: 11.85 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.154e-06/0.007909, allocations: 0 / 0.6019 GB, free: 11.85 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.000176/0.008085, allocations: 262.2 kB / 0.6021 GB, free: 11.57 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 3.776e-05/0.008123, allocations: 63.41 kB / 0.6022 GB, free: 11.49 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.051e-06/0.008129, allocations: 0 / 0.6022 GB, free: 11.49 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.106e-05/0.00814, allocations: 4 kB / 0.6022 GB, free: 11.49 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001207/0.008261, allocations: 47.91 kB / 0.6022 GB, free: 11.44 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 4.178e-06/0.008265, allocations: 4 kB / 0.6022 GB, free: 11.44 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.058e-05/0.008336, allocations: 15.98 kB / 0.6023 GB, free: 11.42 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.169e-05/0.008347, allocations: 12.19 kB / 0.6023 GB, free: 11.41 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 0.0001511/0.008498, allocations: 181 kB / 0.6024 GB, free: 11.21 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.092e-05/0.008519, allocations: 19.92 kB / 0.6025 GB, free: 11.2 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.062e-05/0.00855, allocations: 25.27 kB / 0.6025 GB, free: 11.17 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.158e-06/0.008554, allocations: 7.609 kB / 0.6025 GB, free: 11.16 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.294e-06/0.008556, allocations: 0 / 0.6025 GB, free: 11.16 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.079e-06/0.008561, allocations: 3.25 kB / 0.6025 GB, free: 11.16 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0002819/0.008843, allocations: 354.3 kB / 0.6028 GB, free: 10.78 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.623e-06/0.008845, allocations: 0 / 0.6028 GB, free: 10.78 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001014/0.008946, allocations: 27.98 kB / 0.6029 GB, free: 10.75 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 4.719e-06/0.008951, allocations: 7.938 kB / 0.6029 GB, free: 10.74 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.047e-05/0.008962, allocations: 4 kB / 0.6029 GB, free: 10.74 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.774e-06/0.008963, allocations: 0 / 0.6029 GB, free: 10.74 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.915e-06/0.008966, allocations: 8 kB / 0.6029 GB, free: 10.73 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002185/0.009185, allocations: 339.8 kB / 0.6032 GB, free: 10.37 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.442e-05/0.009199, allocations: 11.91 kB / 0.6032 GB, free: 10.36 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.029e-05/0.009219, allocations: 8 kB / 0.6032 GB, free: 10.35 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.791e-05/0.009287, allocations: 15.98 kB / 0.6032 GB, free: 10.33 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.147e-05/0.009329, allocations: 15.97 kB / 0.6033 GB, free: 10.32 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.734e-06/0.009336, allocations: 4 kB / 0.6033 GB, free: 10.31 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 2.827e-05/0.009365, allocations: 31.41 kB / 0.6033 GB, free: 10.28 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 5e-08/0.009365, allocations: 0 / 0.6033 GB, free: 10.28 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.0001632/0.009528, allocations: 48 kB / 0.6033 GB, free: 10.23 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 9.375e-05/0.009622, allocations: 92.41 kB / 0.6034 GB, free: 10.13 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.0002118/0.009834, allocations: 308.4 kB / 0.6037 GB, free: 9.785 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 3.577e-06/0.009837, allocations: 0 / 0.6037 GB, free: 9.785 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 7.984e-05/0.009917, allocations: 140.4 kB / 0.6039 GB, free: 9.629 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002011/0.01012, allocations: 48.03 kB / 0.6039 GB, free: 9.586 MB / 0.5261 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001071/0.01119, allocations: 0.4971 MB / 0.6044 GB, free: 9.062 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.5e-05/0.01123, allocations: 75.98 kB / 0.6045 GB, free: 8.969 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 5.405e-05/0.01129, allocations: 17.48 kB / 0.6045 GB, free: 8.953 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001119/0.0114, allocations: 103.3 kB / 0.6046 GB, free: 8.852 MB / 0.5261 GB
Notification: Performance of SimCode: time 6.12e-07/0.0114, allocations: 7.875 kB / 0.6046 GB, free: 8.844 MB / 0.5261 GB
Notification: Performance of Templates: time 0.004264/0.01566, allocations: 2.596 MB / 0.6071 GB, free: 6.387 MB / 0.5261 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 -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.7527269017882645]