Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_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 0.001083/0.001083, allocations: 80.75 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 0.001129/0.001129, 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 0.9232/0.9232, 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 1.582/1.582, 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.Pharmacogenomics.Patient_PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin")
translateModel(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.162e-06/1.162e-06, allocations: 0 / 0.5954 GB, free: 2.645 MB / 0.5105 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.587e-05/1.703e-05, allocations: 9.547 kB / 0.5954 GB, free: 2.637 MB / 0.5105 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin): time 0.002898/0.002915, allocations: 2.522 MB / 0.5979 GB, free: 132 kB / 0.5105 GB
Notification: Performance of NFInst.instExpressions: time 0.001258/0.004173, allocations: 0.9523 MB / 0.5988 GB, free: 15.18 MB / 0.5261 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.006e-05/0.004263, allocations: 4 kB / 0.5988 GB, free: 15.18 MB / 0.5261 GB
Notification: Performance of NFTyping.typeComponents: time 0.0003455/0.004609, allocations: 127.2 kB / 0.5989 GB, free: 15.06 MB / 0.5261 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001317/0.004741, allocations: 80.05 kB / 0.599 GB, free: 15 MB / 0.5261 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003393/0.00508, allocations: 146.2 kB / 0.5992 GB, free: 14.86 MB / 0.5261 GB
Notification: Performance of NFFlatten.flatten: time 0.000261/0.005341, allocations: 294.5 kB / 0.5994 GB, free: 14.62 MB / 0.5261 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001084/0.005449, allocations: 51.38 kB / 0.5995 GB, free: 14.57 MB / 0.5261 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001503/0.0056, allocations: 151.6 kB / 0.5996 GB, free: 14.42 MB / 0.5261 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001287/0.005728, allocations: 99.69 kB / 0.5997 GB, free: 14.32 MB / 0.5261 GB
Notification: Performance of NFPackage.collectConstants: time 2.652e-05/0.005755, allocations: 20 kB / 0.5998 GB, free: 14.3 MB / 0.5261 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001867/0.005941, allocations: 167.3 kB / 0.5999 GB, free: 14.14 MB / 0.5261 GB
Notification: Performance of NFScalarize.scalarize: time 6.354e-05/0.006005, allocations: 59.75 kB / 0.6 GB, free: 14.08 MB / 0.5261 GB
Notification: Performance of NFVerifyModel.verify: time 7.468e-05/0.00608, allocations: 87.77 kB / 0.6001 GB, free: 13.99 MB / 0.5261 GB
Notification: Performance of NFConvertDAE.convert: time 0.000315/0.006395, allocations: 346.7 kB / 0.6004 GB, free: 13.65 MB / 0.5261 GB
Notification: Performance of FrontEnd - DAE generated: time 1.603e-06/0.006396, allocations: 0 / 0.6004 GB, free: 13.65 MB / 0.5261 GB
Notification: Performance of FrontEnd: time 7.72e-07/0.006397, allocations: 0 / 0.6004 GB, free: 13.65 MB / 0.5261 GB
Notification: Performance of Transformations before backend: time 3.777e-06/0.006401, allocations: 0 / 0.6004 GB, free: 13.65 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: 40
 * Number of variables: 40
Notification: Performance of Generate backend data structure: time 0.0005841/0.006985, allocations: 0.5845 MB / 0.601 GB, free: 13.02 MB / 0.5261 GB
Notification: Performance of prepare preOptimizeDAE: time 2.873e-05/0.007014, allocations: 12.02 kB / 0.601 GB, free: 13.01 MB / 0.5261 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001852/0.007199, allocations: 96.78 kB / 0.6011 GB, free: 12.91 MB / 0.5261 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001653/0.007364, allocations: 196.7 kB / 0.6012 GB, free: 12.7 MB / 0.5261 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.806e-05/0.007382, allocations: 12.38 kB / 0.6013 GB, free: 12.69 MB / 0.5261 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.954e-05/0.007412, allocations: 20.36 kB / 0.6013 GB, free: 12.67 MB / 0.5261 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002114/0.007623, allocations: 236.8 kB / 0.6015 GB, free: 12.41 MB / 0.5261 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.244e-05/0.007636, allocations: 3.953 kB / 0.6015 GB, free: 12.41 MB / 0.5261 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.357e-05/0.007649, allocations: 11.94 kB / 0.6015 GB, free: 12.39 MB / 0.5261 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.25e-06/0.007654, allocations: 4 kB / 0.6015 GB, free: 12.39 MB / 0.5261 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001159/0.00777, allocations: 152.9 kB / 0.6017 GB, free: 12.23 MB / 0.5261 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004059/0.008176, allocations: 323 kB / 0.602 GB, free: 11.89 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001607/0.008337, allocations: 227.1 kB / 0.6022 GB, free: 11.65 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 6.712e-05/0.008404, allocations: 122 kB / 0.6023 GB, free: 11.51 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 7.925e-06/0.008412, allocations: 4 kB / 0.6023 GB, free: 11.5 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001838/0.008596, allocations: 280.1 kB / 0.6026 GB, free: 11.19 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=26): time 1.633e-06/0.008597, allocations: 4 kB / 0.6026 GB, free: 11.18 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=27): time 0.0008018/0.009399, allocations: 0.9149 MB / 0.6035 GB, free: 10.14 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.433e-05/0.009464, allocations: 195.9 kB / 0.6037 GB, free: 9.91 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001321/0.009596, allocations: 237 kB / 0.6039 GB, free: 9.672 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 1.83e-05/0.009614, allocations: 33.7 kB / 0.6039 GB, free: 9.633 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 5.153e-05/0.009665, allocations: 125 kB / 0.604 GB, free: 9.5 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 0.0003025/0.009968, allocations: 95.22 kB / 0.6041 GB, free: 9.406 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.477e-05/0.01002, allocations: 53.92 kB / 0.6042 GB, free: 9.348 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 7.627e-05/0.0101, allocations: 350.7 kB / 0.6045 GB, free: 8.996 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 9.112e-05/0.01019, allocations: 175.2 kB / 0.6047 GB, free: 8.797 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001081/0.0103, allocations: 243.5 kB / 0.6049 GB, free: 8.508 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002435/0.01054, allocations: 0.4927 MB / 0.6054 GB, free: 7.93 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.833e-06/0.01054, allocations: 0 / 0.6054 GB, free: 7.93 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0002908/0.01083, allocations: 451 kB / 0.6058 GB, free: 7.434 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 4.736e-05/0.01088, allocations: 122.8 kB / 0.6059 GB, free: 7.289 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.3e-06/0.01089, allocations: 0 / 0.6059 GB, free: 7.289 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.357e-05/0.0109, allocations: 7.938 kB / 0.606 GB, free: 7.281 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001198/0.01102, allocations: 51.91 kB / 0.606 GB, free: 7.23 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 5.39e-06/0.01103, allocations: 7.938 kB / 0.606 GB, free: 7.223 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.762e-05/0.0111, allocations: 16.17 kB / 0.606 GB, free: 7.207 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.651e-05/0.01115, allocations: 55.94 kB / 0.6061 GB, free: 7.152 MB / 0.5261 GB
Warning: Assuming fixed start value for the following 6 variables:
         dose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         dose.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: 15 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.dose.pulse.count,$PRE.dose.pulse.T_start,CYP2C19.status,SLC22A2.status,central.rising,dose.pulse.count,dose.pulse.T_start,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (34):
 * Single equations (assignments): 30
 * Array equations: 0
 * Algorithm blocks: 4
 * 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 0.0001529/0.0113, allocations: 245.5 kB / 0.6063 GB, free: 6.887 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.202e-05/0.01138, allocations: 87.84 kB / 0.6064 GB, free: 6.801 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.521e-05/0.01142, allocations: 30.95 kB / 0.6064 GB, free: 6.77 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.414e-06/0.01142, allocations: 4 kB / 0.6064 GB, free: 6.766 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.275e-06/0.01142, allocations: 0 / 0.6064 GB, free: 6.766 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.479e-06/0.01143, allocations: 3.938 kB / 0.6064 GB, free: 6.762 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003852/0.01181, allocations: 0.5859 MB / 0.607 GB, free: 6.121 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.212e-06/0.01182, allocations: 0 / 0.607 GB, free: 6.121 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001068/0.01192, allocations: 43.91 kB / 0.607 GB, free: 6.078 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.314e-06/0.01192, allocations: 0 / 0.607 GB, free: 6.078 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.474e-05/0.01194, allocations: 11.94 kB / 0.6071 GB, free: 6.066 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.402e-06/0.01194, allocations: 0 / 0.6071 GB, free: 6.066 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.172e-06/0.01194, allocations: 4 kB / 0.6071 GB, free: 6.062 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003908/0.01233, allocations: 0.6732 MB / 0.6077 GB, free: 5.316 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.125e-05/0.01235, allocations: 19.81 kB / 0.6077 GB, free: 5.297 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.79e-05/0.01238, allocations: 12 kB / 0.6078 GB, free: 5.285 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.791e-05/0.01246, allocations: 15.98 kB / 0.6078 GB, free: 5.27 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.568e-05/0.01251, allocations: 19.95 kB / 0.6078 GB, free: 5.25 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.823e-05/0.01254, allocations: 47.88 kB / 0.6078 GB, free: 5.203 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 6.258e-05/0.01261, allocations: 82.77 kB / 0.6079 GB, free: 5.125 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 7e-08/0.01261, allocations: 0 / 0.6079 GB, free: 5.125 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.0002035/0.01281, allocations: 76 kB / 0.608 GB, free: 5.051 MB / 0.5261 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (dose.TotalCumulativeMass,dose.variableDose.TotalCumulativeMass,central.C,central.AUC,elim.MExc)
 * Number of discrete variables: 10 ($whenCondition1,$whenCondition2,$whenCondition3,dose.pulse.T_start,dose.pulse.count,central.Cmax,central.Cmin,central.rising,SLC22A2.status,CYP2C19.status)
 * Number of discrete states: 8 (dose.pulse.count,SLC22A2.status,CYP2C19.status,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (22):
 * Single equations (assignments): 17
 * Array equations: 0
 * Algorithm blocks: 3
 * 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 0.0001664/0.01298, allocations: 149.5 kB / 0.6081 GB, free: 4.906 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.0002987/0.01328, allocations: 0.5576 MB / 0.6087 GB, free: 4.254 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 3.988e-06/0.01328, allocations: 4 kB / 0.6087 GB, free: 4.25 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001521/0.01343, allocations: 332 kB / 0.609 GB, free: 3.867 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002295/0.01366, allocations: 70.58 kB / 0.6091 GB, free: 3.805 MB / 0.5261 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001206/0.01487, allocations: 0.7798 MB / 0.6098 GB, free: 2.98 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.35e-05/0.01492, allocations: 100.3 kB / 0.6099 GB, free: 2.863 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 5.391e-05/0.01497, allocations: 17.95 kB / 0.6099 GB, free: 2.844 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001377/0.01511, allocations: 119.3 kB / 0.61 GB, free: 2.727 MB / 0.5261 GB
Notification: Performance of SimCode: time 5.21e-07/0.01511, allocations: 0 / 0.61 GB, free: 2.727 MB / 0.5261 GB
Notification: Performance of Templates: time 0.3542/0.3693, allocations: 5.237 MB / 0.6152 GB, free: 52.88 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.716633733827621]