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 0.0008892/0.0008892, allocations: 100.4 kB / 19.7 MB, free: 440 kB / 13.93 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 0.000918/0.000918, allocations: 215.3 kB / 23 MB, free: 2.945 MB / 13.93 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 0.969/0.969, allocations: 230.6 MB / 256.8 MB, free: 9.602 MB / 202.7 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 1.77/1.77, allocations: 334.3 MB / 0.6323 GB, free: 7.984 MB / 442.7 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: Pharmacolibrary requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed.
Notification: Performance of FrontEnd - loaded program: time 0.001865/0.001865, allocations: 63.91 kB / 0.867 GB, free: 8.199 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1771/0.179, allocations: 112.8 MB / 0.9772 GB, free: 7.117 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Digoxin): time 0.002378/0.1813, allocations: 1.977 MB / 0.9791 GB, free: 5.129 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.000675/0.182, allocations: 0.5221 MB / 0.9796 GB, free: 4.605 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 6.33e-05/0.1821, allocations: 4 kB / 0.9796 GB, free: 4.602 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 9.804e-05/0.1822, allocations: 15.8 kB / 0.9797 GB, free: 4.586 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001247/0.1823, allocations: 55.61 kB / 0.9797 GB, free: 4.531 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001456/0.1824, allocations: 43.95 kB / 0.9797 GB, free: 4.488 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0001823/0.1826, allocations: 183.2 kB / 0.9799 GB, free: 4.309 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.000119/0.1827, allocations: 25.91 kB / 0.9799 GB, free: 4.273 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 8.143e-05/0.1828, allocations: 71.72 kB / 0.98 GB, free: 4.203 MB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 9.391e-05/0.1829, allocations: 71.67 kB / 0.9801 GB, free: 4.133 MB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 2.366e-05/0.1829, allocations: 16 kB / 0.9801 GB, free: 4.117 MB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.072e-05/0.183, allocations: 16 kB / 0.9801 GB, free: 4.102 MB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 3.167e-05/0.183, allocations: 27.92 kB / 0.9801 GB, free: 4.074 MB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 6.294e-05/0.1831, allocations: 71.64 kB / 0.9802 GB, free: 4.004 MB / 0.6824 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001611/0.1832, allocations: 163.4 kB / 0.9804 GB, free: 3.844 MB / 0.6824 GB
Notification: Performance of FrontEnd - DAE generated: time 3.146e-06/0.1832, allocations: 0 / 0.9804 GB, free: 3.844 MB / 0.6824 GB
Notification: Performance of FrontEnd: time 1.513e-06/0.1832, allocations: 0 / 0.9804 GB, free: 3.844 MB / 0.6824 GB
Notification: Performance of Transformations before backend: time 5.711e-06/0.1832, allocations: 0 / 0.9804 GB, free: 3.844 MB / 0.6824 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 0.0006055/0.1838, allocations: 436.8 kB / 0.9808 GB, free: 3.375 MB / 0.6824 GB
Notification: Performance of prepare preOptimizeDAE: time 3.227e-05/0.1839, allocations: 14.11 kB / 0.9808 GB, free: 3.363 MB / 0.6824 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.073e-05/0.1839, allocations: 12.89 kB / 0.9808 GB, free: 3.352 MB / 0.6824 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002328/0.1841, allocations: 186.2 kB / 0.981 GB, free: 3.145 MB / 0.6824 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 9.918e-06/0.1841, allocations: 4.375 kB / 0.981 GB, free: 3.141 MB / 0.6824 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.163e-05/0.1842, allocations: 20.08 kB / 0.981 GB, free: 3.121 MB / 0.6824 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002057/0.1844, allocations: 155.3 kB / 0.9812 GB, free: 2.957 MB / 0.6824 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.174e-05/0.1844, allocations: 3.938 kB / 0.9812 GB, free: 2.953 MB / 0.6824 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.357e-05/0.1844, allocations: 8 kB / 0.9812 GB, free: 2.945 MB / 0.6824 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.911e-06/0.1844, allocations: 3.984 kB / 0.9812 GB, free: 2.941 MB / 0.6824 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001806/0.1846, allocations: 133.5 kB / 0.9813 GB, free: 2.805 MB / 0.6824 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004583/0.1851, allocations: 360.1 kB / 0.9816 GB, free: 2.422 MB / 0.6824 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002307/0.1853, allocations: 164.2 kB / 0.9818 GB, free: 2.246 MB / 0.6824 GB
Notification: Performance of preOpt resolveLoops (simulation): time 9.742e-05/0.1854, allocations: 90.67 kB / 0.9819 GB, free: 2.148 MB / 0.6824 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.35e-05/0.1854, allocations: 3.938 kB / 0.9819 GB, free: 2.145 MB / 0.6824 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002158/0.1856, allocations: 222.9 kB / 0.9821 GB, free: 1.898 MB / 0.6824 GB
Notification: Performance of pre-optimization done (n=20): time 1.323e-06/0.1856, allocations: 4 kB / 0.9821 GB, free: 1.895 MB / 0.6824 GB
Notification: Performance of matching and sorting (n=21): time 0.0008964/0.1865, allocations: 0.6728 MB / 0.9828 GB, free: 1.16 MB / 0.6824 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.993e-05/0.1866, allocations: 136.5 kB / 0.9829 GB, free: 0.9961 MB / 0.6824 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001015/0.1867, allocations: 156.2 kB / 0.983 GB, free: 0.8359 MB / 0.6824 GB
Notification: Performance of collectPreVariables (initialization): time 1.715e-05/0.1867, allocations: 37.7 kB / 0.9831 GB, free: 0.793 MB / 0.6824 GB
Notification: Performance of collectInitialEqns (initialization): time 4.899e-05/0.1867, allocations: 100.5 kB / 0.9832 GB, free: 0.6914 MB / 0.6824 GB
Notification: Performance of collectInitialBindings (initialization): time 4.057e-05/0.1868, allocations: 79.34 kB / 0.9832 GB, free: 0.6133 MB / 0.6824 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.156e-05/0.1868, allocations: 49.7 kB / 0.9833 GB, free: 0.5586 MB / 0.6824 GB
Notification: Performance of setup shared object (initialization): time 7.304e-05/0.1869, allocations: 326.8 kB / 0.9836 GB, free: 236 kB / 0.6824 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001314/0.187, allocations: 136.6 kB / 0.9837 GB, free: 84 kB / 0.6824 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001656/0.1872, allocations: 214.8 kB / 0.9839 GB, free: 15.83 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005154/0.1877, allocations: 0.4984 MB / 0.9844 GB, free: 15.27 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.814e-06/0.1877, allocations: 0 / 0.9844 GB, free: 15.27 MB / 0.698 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0003502/0.1881, allocations: 376 kB / 0.9848 GB, free: 14.88 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 3.439e-05/0.1881, allocations: 64.8 kB / 0.9849 GB, free: 14.8 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.965e-06/0.1881, allocations: 11.92 kB / 0.9849 GB, free: 14.79 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.293e-05/0.1881, allocations: 0 / 0.9849 GB, free: 14.79 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001274/0.1882, allocations: 51.91 kB / 0.9849 GB, free: 14.74 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.753e-06/0.1882, allocations: 8.125 kB / 0.9849 GB, free: 14.73 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.259e-05/0.1883, allocations: 19.98 kB / 0.9849 GB, free: 14.71 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.224e-05/0.1883, allocations: 8 kB / 0.9849 GB, free: 14.7 MB / 0.698 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 0.0001514/0.1885, allocations: 192.3 kB / 0.9851 GB, free: 14.5 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 1.671e-05/0.1885, allocations: 15.91 kB / 0.9851 GB, free: 14.49 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.187e-05/0.1885, allocations: 25.16 kB / 0.9852 GB, free: 14.46 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.503e-06/0.1885, allocations: 0 / 0.9852 GB, free: 14.46 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.499e-06/0.1885, allocations: 0 / 0.9852 GB, free: 14.46 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.456e-06/0.1885, allocations: 0 / 0.9852 GB, free: 14.46 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005946/0.1891, allocations: 0.5095 MB / 0.9857 GB, free: 13.9 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.694e-06/0.1891, allocations: 0 / 0.9857 GB, free: 13.9 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001114/0.1893, allocations: 35.97 kB / 0.9857 GB, free: 13.87 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.195e-06/0.1893, allocations: 0 / 0.9857 GB, free: 13.87 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.339e-05/0.1893, allocations: 11.98 kB / 0.9857 GB, free: 13.86 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.025e-06/0.1893, allocations: 7.938 kB / 0.9857 GB, free: 13.85 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.883e-06/0.1893, allocations: 7.938 kB / 0.9857 GB, free: 13.84 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004218/0.1897, allocations: 476.8 kB / 0.9862 GB, free: 13.34 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.711e-05/0.1897, allocations: 11.91 kB / 0.9862 GB, free: 13.33 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.333e-05/0.1897, allocations: 8.062 kB / 0.9862 GB, free: 13.32 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.615e-05/0.1898, allocations: 19.98 kB / 0.9862 GB, free: 13.3 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.835e-05/0.1899, allocations: 19.97 kB / 0.9862 GB, free: 13.28 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.006e-05/0.1899, allocations: 7.984 kB / 0.9862 GB, free: 13.27 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 5.473e-05/0.1899, allocations: 113.8 kB / 0.9864 GB, free: 13.16 MB / 0.698 GB
Notification: Performance of sort global known variables: time 6e-08/0.1899, allocations: 0 / 0.9864 GB, free: 13.16 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0001896/0.1901, allocations: 44 kB / 0.9864 GB, free: 13.12 MB / 0.698 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 7.264e-05/0.1902, allocations: 109.7 kB / 0.9865 GB, free: 13.01 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.0003414/0.1905, allocations: 371.7 kB / 0.9869 GB, free: 12.6 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 1.132e-06/0.1905, allocations: 0 / 0.9869 GB, free: 12.6 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.000135/0.1907, allocations: 169 kB / 0.987 GB, free: 12.42 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002418/0.1909, allocations: 36.34 kB / 0.9871 GB, free: 12.38 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0007985/0.1917, allocations: 0.6917 MB / 0.9877 GB, free: 11.65 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 6.606e-05/0.1918, allocations: 103.5 kB / 0.9878 GB, free: 11.52 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.354e-05/0.1918, allocations: 27.44 kB / 0.9879 GB, free: 11.5 MB / 0.698 GB
Notification: Performance of SimCode: time 3.2e-07/0.1918, allocations: 0 / 0.9879 GB, free: 11.5 MB / 0.698 GB
Notification: Performance of Templates: time 0.002764/0.1946, allocations: 2.263 MB / 0.9901 GB, free: 9.246 MB / 0.698 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 > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 7.365102255018428]