Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.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 0.001125/0.001125, allocations: 80.81 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 0.001298/0.001298, allocations: 173 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 1.017/1.017, allocations: 177.1 MB / 203.8 MB, free: 5.48 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 1.654/1.654, allocations: 273.5 MB / 0.5213 GB, free: 14.75 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.DevModels.SingleDoseDiffusion,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion")
translateModel(Pharmacolibrary.DevModels.SingleDoseDiffusion,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 9.81e-07/9.81e-07, allocations: 1.422 kB / 0.5954 GB, free: 2.836 MB / 0.5105 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.045e-05/1.143e-05, allocations: 2.312 kB / 0.5954 GB, free: 2.832 MB / 0.5105 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.SingleDoseDiffusion): time 0.002726/0.002737, allocations: 2.906 MB / 0.5982 GB, free: 15.95 MB / 0.5261 GB
Notification: Performance of NFInst.instExpressions: time 0.0009113/0.003649, allocations: 0.7448 MB / 0.599 GB, free: 15.21 MB / 0.5261 GB
Notification: Performance of NFInst.updateImplicitVariability: time 7.476e-05/0.003723, allocations: 7.938 kB / 0.599 GB, free: 15.2 MB / 0.5261 GB
Notification: Performance of NFTyping.typeComponents: time 6.154e-05/0.003785, allocations: 39.64 kB / 0.599 GB, free: 15.16 MB / 0.5261 GB
Notification: Performance of NFTyping.typeBindings: time 0.00021/0.003995, allocations: 113.3 kB / 0.5991 GB, free: 15.09 MB / 0.5261 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001998/0.004195, allocations: 95.75 kB / 0.5992 GB, free: 15 MB / 0.5261 GB
Notification: Performance of NFFlatten.flatten: time 0.0002832/0.004478, allocations: 410.7 kB / 0.5996 GB, free: 14.62 MB / 0.5261 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002363/0.004714, allocations: 218.8 kB / 0.5998 GB, free: 14.41 MB / 0.5261 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002193/0.004934, allocations: 247.5 kB / 0.6 GB, free: 14.16 MB / 0.5261 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001822/0.005116, allocations: 155.6 kB / 0.6002 GB, free: 14.01 MB / 0.5261 GB
Notification: Performance of NFPackage.collectConstants: time 3.984e-05/0.005156, allocations: 32 kB / 0.6002 GB, free: 13.98 MB / 0.5261 GB
Notification: Performance of NFFlatten.collectFunctions: time 3.407e-05/0.00519, allocations: 36 kB / 0.6002 GB, free: 13.95 MB / 0.5261 GB
Notification: Performance of NFScalarize.scalarize: time 4.999e-05/0.00524, allocations: 75.73 kB / 0.6003 GB, free: 13.87 MB / 0.5261 GB
Notification: Performance of NFVerifyModel.verify: time 9.371e-05/0.005333, allocations: 131.7 kB / 0.6004 GB, free: 13.74 MB / 0.5261 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002232/0.005557, allocations: 263.1 kB / 0.6007 GB, free: 13.48 MB / 0.5261 GB
Notification: Performance of FrontEnd - DAE generated: time 2.865e-06/0.005559, allocations: 4 kB / 0.6007 GB, free: 13.48 MB / 0.5261 GB
Notification: Performance of FrontEnd: time 7.32e-07/0.00556, allocations: 0 / 0.6007 GB, free: 13.48 MB / 0.5261 GB
Notification: Performance of Transformations before backend: time 4.027e-06/0.005564, allocations: 4 kB / 0.6007 GB, free: 13.48 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: 65
 * Number of variables: 65
Notification: Performance of Generate backend data structure: time 0.0006117/0.006176, allocations: 0.5398 MB / 0.6012 GB, free: 12.9 MB / 0.5261 GB
Notification: Performance of prepare preOptimizeDAE: time 3.099e-05/0.006207, allocations: 12.03 kB / 0.6012 GB, free: 12.89 MB / 0.5261 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.032e-05/0.006267, allocations: 40.91 kB / 0.6013 GB, free: 12.85 MB / 0.5261 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001682/0.006435, allocations: 161.4 kB / 0.6014 GB, free: 12.67 MB / 0.5261 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.006e-05/0.006455, allocations: 21.03 kB / 0.6015 GB, free: 12.65 MB / 0.5261 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.991e-05/0.006495, allocations: 40.28 kB / 0.6015 GB, free: 12.61 MB / 0.5261 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002785/0.006774, allocations: 339 kB / 0.6018 GB, free: 12.25 MB / 0.5261 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.555e-05/0.006789, allocations: 7.891 kB / 0.6018 GB, free: 12.24 MB / 0.5261 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.893e-05/0.006808, allocations: 12 kB / 0.6018 GB, free: 12.23 MB / 0.5261 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.454e-06/0.006816, allocations: 4 kB / 0.6018 GB, free: 12.22 MB / 0.5261 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001451/0.006961, allocations: 135 kB / 0.602 GB, free: 12.09 MB / 0.5261 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007115/0.007672, allocations: 0.5894 MB / 0.6025 GB, free: 11.48 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002153/0.007888, allocations: 156.2 kB / 0.6027 GB, free: 11.32 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 7.544e-05/0.007963, allocations: 66.78 kB / 0.6028 GB, free: 11.24 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.552e-05/0.007979, allocations: 4 kB / 0.6028 GB, free: 11.24 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001697/0.008148, allocations: 225.5 kB / 0.603 GB, free: 10.99 MB / 0.5261 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.000102/0.00825, allocations: 31.88 kB / 0.603 GB, free: 10.96 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=30): time 1.282e-06/0.008252, allocations: 4 kB / 0.603 GB, free: 10.95 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=31): time 0.0006868/0.008938, allocations: 0.6023 MB / 0.6036 GB, free: 10.29 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.362e-05/0.008992, allocations: 136.5 kB / 0.6037 GB, free: 10.13 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.964e-05/0.009092, allocations: 187.3 kB / 0.6039 GB, free: 9.93 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 2.11e-05/0.009113, allocations: 29.7 kB / 0.6039 GB, free: 9.895 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 5.973e-05/0.009172, allocations: 152.6 kB / 0.6041 GB, free: 9.742 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 5.645e-05/0.009229, allocations: 111 kB / 0.6042 GB, free: 9.633 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.146e-05/0.0093, allocations: 81.95 kB / 0.6043 GB, free: 9.543 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 7.907e-05/0.009379, allocations: 334.8 kB / 0.6046 GB, free: 9.207 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.723e-05/0.009457, allocations: 113.7 kB / 0.6047 GB, free: 9.082 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001103/0.009567, allocations: 211.5 kB / 0.6049 GB, free: 8.82 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002432/0.00981, allocations: 384.6 kB / 0.6053 GB, free: 8.383 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.565e-06/0.009813, allocations: 4 kB / 0.6053 GB, free: 8.379 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=49) (initialization): time 0.0002417/0.01005, allocations: 328.7 kB / 0.6056 GB, free: 8.027 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 3.348e-05/0.01009, allocations: 71.33 kB / 0.6056 GB, free: 7.945 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.58e-06/0.01009, allocations: 4 kB / 0.6056 GB, free: 7.941 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.244e-05/0.01011, allocations: 4 kB / 0.6057 GB, free: 7.938 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001797/0.01029, allocations: 83.89 kB / 0.6057 GB, free: 7.855 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 4.728e-06/0.01029, allocations: 4 kB / 0.6057 GB, free: 7.852 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.205e-05/0.01038, allocations: 19.98 kB / 0.6058 GB, free: 7.832 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.734e-05/0.0104, allocations: 20.23 kB / 0.6058 GB, free: 7.812 MB / 0.5261 GB
Warning: Assuming fixed start value for the following 8 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
         artery.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         tissueCompartment.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         RBC.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         RBC.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         RBC.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         RBC.rising:DISCRETE(fixed = true protected = true )  type: Boolean
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 12
 * Number of states: 0 ()
 * Number of discrete variables: 13 ($PRE.RBC.Cmin,RBC.Cmin,$PRE.RBC.Cmax,RBC.Cmax,$PRE.RBC.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,RBC.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition2,$whenCondition1,$whenCondition3)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (47):
 * Single equations (assignments): 45
 * 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 0.0001383/0.01054, allocations: 193.3 kB / 0.606 GB, free: 7.605 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.08e-05/0.01057, allocations: 35.84 kB / 0.606 GB, free: 7.574 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002008/0.01077, allocations: 231 kB / 0.6062 GB, free: 7.332 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.585e-06/0.01077, allocations: 4 kB / 0.6062 GB, free: 7.328 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.312e-06/0.01077, allocations: 3.938 kB / 0.6062 GB, free: 7.324 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.108e-06/0.01078, allocations: 0 / 0.6062 GB, free: 7.324 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003658/0.01114, allocations: 444.4 kB / 0.6066 GB, free: 6.855 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 9.31e-07/0.01114, allocations: 0 / 0.6066 GB, free: 6.855 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000143/0.01129, allocations: 47.91 kB / 0.6067 GB, free: 6.809 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.827e-06/0.01129, allocations: 8 kB / 0.6067 GB, free: 6.801 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.451e-05/0.01131, allocations: 7.984 kB / 0.6067 GB, free: 6.793 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.605e-06/0.01131, allocations: 4 kB / 0.6067 GB, free: 6.789 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.82e-07/0.01131, allocations: 0 / 0.6067 GB, free: 6.789 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002791/0.01159, allocations: 401.3 kB / 0.6071 GB, free: 6.367 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.94e-05/0.01161, allocations: 15.86 kB / 0.6071 GB, free: 6.352 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.704e-05/0.01163, allocations: 8 kB / 0.6071 GB, free: 6.344 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.587e-05/0.01172, allocations: 15.98 kB / 0.6071 GB, free: 6.328 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.813e-05/0.01177, allocations: 31.89 kB / 0.6072 GB, free: 6.297 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.021e-05/0.01178, allocations: 4 kB / 0.6072 GB, free: 6.293 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 4.506e-05/0.01182, allocations: 52.8 kB / 0.6072 GB, free: 6.238 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 4e-08/0.01182, allocations: 0 / 0.6072 GB, free: 6.238 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.0001986/0.01202, allocations: 79.98 kB / 0.6073 GB, free: 6.16 MB / 0.5261 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 8 (singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,artery.M,artery.AUC,tissueCompartment.M,tissueCompartment.AUC,RBC.C,RBC.AUC)
 * Number of discrete variables: 8 ($whenCondition3,$whenCondition1,$whenCondition2,singleDose.pulse.T_start,singleDose.pulse.count,RBC.Cmax,RBC.Cmin,RBC.rising)
 * Number of discrete states: 6 (singleDose.pulse.count,RBC.Cmin,$whenCondition2,RBC.Cmax,$whenCondition1,RBC.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (28):
 * Single equations (assignments): 25
 * 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 8.447e-05/0.01211, allocations: 90.48 kB / 0.6074 GB, free: 6.066 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.0002546/0.01236, allocations: 363.9 kB / 0.6077 GB, free: 5.668 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 4.338e-06/0.01237, allocations: 7.938 kB / 0.6077 GB, free: 5.66 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001088/0.01247, allocations: 165.8 kB / 0.6079 GB, free: 5.477 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002308/0.01271, allocations: 82.95 kB / 0.608 GB, free: 5.398 MB / 0.5261 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001218/0.01392, allocations: 0.7126 MB / 0.6087 GB, free: 4.652 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.928e-05/0.01397, allocations: 92.25 kB / 0.6088 GB, free: 4.543 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 8.271e-05/0.01406, allocations: 37.89 kB / 0.6088 GB, free: 4.508 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001577/0.01421, allocations: 131.3 kB / 0.6089 GB, free: 4.379 MB / 0.5261 GB
Notification: Performance of SimCode: time 5.51e-07/0.01421, allocations: 4 kB / 0.6089 GB, free: 4.375 MB / 0.5261 GB
Notification: Performance of Templates: time 0.005586/0.0198, allocations: 4.317 MB / 0.6131 GB, free: 288 kB / 0.5261 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.145304713863879]