Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.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 0.001074/0.001074, 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 0.001474/0.001474, allocations: 177 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 1.009/1.009, allocations: 177.1 MB / 203.8 MB, free: 5.473 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 1.676/1.676, allocations: 273.5 MB / 0.5213 GB, free: 14.59 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_LithiumCarbonate,tolerance=1e-09,outputFormat="empty",numberOfIntervals=864000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate")
translateModel(Pharmacolibrary.Examples.PK_1C_LithiumCarbonate,tolerance=1e-09,outputFormat="empty",numberOfIntervals=864000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.373e-06/1.373e-06, allocations: 0 / 0.5954 GB, free: 2.633 MB / 0.5105 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.468e-05/1.605e-05, allocations: 10.58 kB / 0.5954 GB, free: 2.625 MB / 0.5105 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_LithiumCarbonate): time 0.002282/0.002298, allocations: 2.174 MB / 0.5976 GB, free: 468 kB / 0.5105 GB
Notification: Performance of NFInst.instExpressions: time 0.000774/0.003072, allocations: 0.5582 MB / 0.5981 GB, free: 15.9 MB / 0.5261 GB
Notification: Performance of NFInst.updateImplicitVariability: time 6.799e-05/0.00314, allocations: 0 / 0.5981 GB, free: 15.9 MB / 0.5261 GB
Notification: Performance of NFTyping.typeComponents: time 9.56e-05/0.003235, allocations: 15.8 kB / 0.5981 GB, free: 15.89 MB / 0.5261 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001983/0.003434, allocations: 62.61 kB / 0.5982 GB, free: 15.84 MB / 0.5261 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001822/0.003616, allocations: 43.94 kB / 0.5982 GB, free: 15.8 MB / 0.5261 GB
Notification: Performance of NFFlatten.flatten: time 0.0002062/0.003822, allocations: 204.9 kB / 0.5984 GB, free: 15.66 MB / 0.5261 GB
Notification: Performance of NFFlatten.resolveConnections: time 9.121e-05/0.003913, allocations: 38.55 kB / 0.5985 GB, free: 15.62 MB / 0.5261 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001196/0.004033, allocations: 106.7 kB / 0.5986 GB, free: 15.52 MB / 0.5261 GB
Notification: Performance of NFSimplifyModel.simplify: time 9.606e-05/0.004129, allocations: 59.86 kB / 0.5986 GB, free: 15.46 MB / 0.5261 GB
Notification: Performance of NFPackage.collectConstants: time 2.246e-05/0.004152, allocations: 12 kB / 0.5986 GB, free: 15.45 MB / 0.5261 GB
Notification: Performance of NFFlatten.collectFunctions: time 1.854e-05/0.00417, allocations: 16 kB / 0.5986 GB, free: 15.43 MB / 0.5261 GB
Notification: Performance of NFScalarize.scalarize: time 3.013e-05/0.0042, allocations: 27.86 kB / 0.5987 GB, free: 15.41 MB / 0.5261 GB
Notification: Performance of NFVerifyModel.verify: time 5.246e-05/0.004253, allocations: 63.83 kB / 0.5987 GB, free: 15.34 MB / 0.5261 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001407/0.004393, allocations: 123.6 kB / 0.5989 GB, free: 15.22 MB / 0.5261 GB
Notification: Performance of FrontEnd - DAE generated: time 1.743e-06/0.004395, allocations: 0 / 0.5989 GB, free: 15.22 MB / 0.5261 GB
Notification: Performance of FrontEnd: time 7.91e-07/0.004396, allocations: 0 / 0.5989 GB, free: 15.22 MB / 0.5261 GB
Notification: Performance of Transformations before backend: time 3.567e-06/0.0044, allocations: 0 / 0.5989 GB, free: 15.22 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 0.0004265/0.004826, allocations: 411.6 kB / 0.5992 GB, free: 14.79 MB / 0.5261 GB
Notification: Performance of prepare preOptimizeDAE: time 2.832e-05/0.004854, allocations: 8.031 kB / 0.5993 GB, free: 14.78 MB / 0.5261 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 3.654e-05/0.004891, allocations: 24.86 kB / 0.5993 GB, free: 14.76 MB / 0.5261 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001289/0.00502, allocations: 147.7 kB / 0.5994 GB, free: 14.59 MB / 0.5261 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.675e-05/0.005036, allocations: 12.38 kB / 0.5994 GB, free: 14.58 MB / 0.5261 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.1e-05/0.005057, allocations: 16.38 kB / 0.5994 GB, free: 14.56 MB / 0.5261 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001446/0.005202, allocations: 132.6 kB / 0.5996 GB, free: 14.42 MB / 0.5261 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.072e-05/0.005213, allocations: 11.88 kB / 0.5996 GB, free: 14.41 MB / 0.5261 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 9.959e-06/0.005223, allocations: 4 kB / 0.5996 GB, free: 14.4 MB / 0.5261 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 4.488e-06/0.005227, allocations: 7.938 kB / 0.5996 GB, free: 14.39 MB / 0.5261 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 7.361e-05/0.005301, allocations: 72.94 kB / 0.5997 GB, free: 14.32 MB / 0.5261 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0003281/0.005629, allocations: 255.9 kB / 0.5999 GB, free: 14.05 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001022/0.005731, allocations: 104.2 kB / 0.6 GB, free: 13.94 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 3.829e-05/0.005769, allocations: 58.55 kB / 0.6001 GB, free: 13.87 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 8.496e-06/0.005778, allocations: 4 kB / 0.6001 GB, free: 13.87 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001442/0.005922, allocations: 196.3 kB / 0.6003 GB, free: 13.64 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=20): time 1.153e-06/0.005923, allocations: 0 / 0.6003 GB, free: 13.64 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=21): time 0.0005378/0.006461, allocations: 0.4919 MB / 0.6007 GB, free: 13.09 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.637e-05/0.006507, allocations: 136.5 kB / 0.6009 GB, free: 12.93 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.077e-05/0.006588, allocations: 149.1 kB / 0.601 GB, free: 12.77 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 1.584e-05/0.006604, allocations: 37.7 kB / 0.601 GB, free: 12.73 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 3.944e-05/0.006643, allocations: 104.5 kB / 0.6011 GB, free: 12.62 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 3.618e-05/0.00668, allocations: 75.36 kB / 0.6012 GB, free: 12.55 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 4.948e-05/0.006729, allocations: 53.66 kB / 0.6013 GB, free: 12.49 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 7.067e-05/0.0068, allocations: 326.8 kB / 0.6016 GB, free: 12.16 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 5.832e-05/0.006858, allocations: 96.7 kB / 0.6017 GB, free: 12.05 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 8.069e-05/0.006939, allocations: 164.4 kB / 0.6018 GB, free: 11.85 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001634/0.007102, allocations: 292.2 kB / 0.6021 GB, free: 11.51 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.113e-06/0.007103, allocations: 0 / 0.6021 GB, free: 11.51 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0001675/0.007271, allocations: 248.2 kB / 0.6023 GB, free: 11.24 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 3.053e-05/0.007301, allocations: 63.39 kB / 0.6024 GB, free: 11.16 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.398e-06/0.007306, allocations: 0 / 0.6024 GB, free: 11.16 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 9.488e-06/0.007315, allocations: 4.188 kB / 0.6024 GB, free: 11.16 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001654/0.007481, allocations: 67.84 kB / 0.6025 GB, free: 11.09 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 5.45e-06/0.007486, allocations: 4 kB / 0.6025 GB, free: 11.09 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001104/0.007596, allocations: 15.98 kB / 0.6025 GB, free: 11.07 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.532e-05/0.007612, allocations: 4 kB / 0.6025 GB, free: 11.07 MB / 0.5261 GB
Warning: Assuming fixed start value for the following 6 variables:
         central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         periodicDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         periodicDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" 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,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,$PRE.central.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,central.rising,$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 0.0001421/0.007754, allocations: 180.5 kB / 0.6027 GB, free: 10.88 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.414e-05/0.007778, allocations: 19.98 kB / 0.6027 GB, free: 10.86 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 2.678e-05/0.007805, allocations: 17.28 kB / 0.6027 GB, free: 10.84 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.426e-06/0.007808, allocations: 7.469 kB / 0.6027 GB, free: 10.84 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.034e-06/0.00781, allocations: 0 / 0.6027 GB, free: 10.84 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.196e-06/0.007813, allocations: 0 / 0.6027 GB, free: 10.84 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0002657/0.008079, allocations: 364.9 kB / 0.6031 GB, free: 10.44 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.353e-06/0.00808, allocations: 4 kB / 0.6031 GB, free: 10.44 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001299/0.00821, allocations: 47.91 kB / 0.6031 GB, free: 10.39 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.074e-06/0.008212, allocations: 0 / 0.6031 GB, free: 10.39 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.051e-05/0.008223, allocations: 4 kB / 0.6031 GB, free: 10.39 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.866e-06/0.008226, allocations: 7.984 kB / 0.6031 GB, free: 10.38 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.02e-07/0.008227, allocations: 0 / 0.6031 GB, free: 10.38 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002131/0.00844, allocations: 338.6 kB / 0.6034 GB, free: 10.02 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.984e-05/0.00846, allocations: 11.91 kB / 0.6035 GB, free: 10 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.102e-05/0.008481, allocations: 8 kB / 0.6035 GB, free: 9.996 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.834e-05/0.008549, allocations: 15.98 kB / 0.6035 GB, free: 9.98 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.33e-05/0.008592, allocations: 19.97 kB / 0.6035 GB, free: 9.961 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 9.468e-06/0.008602, allocations: 7.984 kB / 0.6035 GB, free: 9.953 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 2.674e-05/0.008629, allocations: 32.89 kB / 0.6035 GB, free: 9.922 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 4e-08/0.008629, allocations: 0 / 0.6035 GB, free: 9.922 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.0001558/0.008784, allocations: 55.94 kB / 0.6036 GB, free: 9.867 MB / 0.5261 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (central.C,central.AUC,elim.MExc,periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass)
 * Number of discrete variables: 8 ($whenCondition1,$whenCondition2,$whenCondition3,central.Cmax,central.Cmin,central.rising,periodicDose.pulse.T_start,periodicDose.pulse.count)
 * Number of discrete states: 6 (periodicDose.pulse.count,central.Cmin,$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 6.604e-05/0.00885, allocations: 92.41 kB / 0.6037 GB, free: 9.766 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.000187/0.009037, allocations: 300.8 kB / 0.604 GB, free: 9.426 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 2.585e-06/0.00904, allocations: 4.062 kB / 0.604 GB, free: 9.422 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 7.983e-05/0.00912, allocations: 144.3 kB / 0.6041 GB, free: 9.262 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0001901/0.00931, allocations: 51.16 kB / 0.6042 GB, free: 9.215 MB / 0.5261 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00132/0.01063, allocations: 0.5204 MB / 0.6047 GB, free: 8.668 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.028e-05/0.01067, allocations: 79.92 kB / 0.6047 GB, free: 8.57 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 5.532e-05/0.01073, allocations: 17.64 kB / 0.6048 GB, free: 8.555 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001144/0.01084, allocations: 107.3 kB / 0.6049 GB, free: 8.449 MB / 0.5261 GB
Notification: Performance of SimCode: time 7.82e-07/0.01084, allocations: 0 / 0.6049 GB, free: 8.449 MB / 0.5261 GB
Notification: Performance of Templates: time 0.004081/0.01492, allocations: 2.946 MB / 0.6077 GB, free: 5.66 MB / 0.5261 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate -abortSlowSimulation -alarm=240 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.830939766950905]