Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_master_Chemical.Obsolete.Examples.EnzymeKinetics.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 0.0009643/0.0009643, allocations: 93.06 kB / 19.65 MB, free: 276 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 0.001006/0.001006, allocations: 169 kB / 23.02 MB, free: 1.547 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 1.031/1.031, allocations: 177.1 MB / 203.4 MB, free: 5.648 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo): time 0.1047/0.1047, allocations: 17.46 MB / 277.4 MB, free: 11.57 MB / 266.7 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/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(Chemical.Obsolete.Examples.EnzymeKinetics,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.EnzymeKinetics")
translateModel(Chemical.Obsolete.Examples.EnzymeKinetics,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.EnzymeKinetics") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.485e-06/2.485e-06, allocations: 4 kB / 353.5 MB, free: 9.863 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.319e-05/2.568e-05, allocations: 2.312 kB / 353.5 MB, free: 9.859 MB / 282.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/Obsolete.mo:14335:7-14335:66:writable] Warning: An inner declaration for outer component system could not be found and was automatically generated.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/Obsolete.mo:14335:7-14335:66:writable] Notification: The diagnostics message for the missing inner is: 
Your model is using an outer \"system\" component but
an inner \"system\" component is not defined.
For simulation drag Modelica.Fluid.System into your model
to specify system properties.
Notification: Performance of NFInst.instantiate(Chemical.Obsolete.Examples.EnzymeKinetics): time 0.02882/0.02885, allocations: 30.6 MB / 384.1 MB, free: 11.38 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01612/0.04497, allocations: 19.69 MB / 403.8 MB, free: 7.625 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0007981/0.04576, allocations: 19.81 kB / 403.8 MB, free: 7.605 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0008783/0.04664, allocations: 384.9 kB / 404.2 MB, free: 7.227 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.003418/0.05006, allocations: 1.729 MB / 406 MB, free: 5.484 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004857/0.05492, allocations: 2.613 MB / 408.6 MB, free: 2.855 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.002097/0.05701, allocations: 2.043 MB / 410.6 MB, free: 0.8047 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.1216/0.1786, allocations: 0.9491 MB / 411.6 MB, free: 36.01 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.002031/0.1807, allocations: 1.381 MB / 412.9 MB, free: 36.01 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001691/0.1824, allocations: 0.9438 MB / 413.9 MB, free: 36.01 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0005331/0.1829, allocations: 177.8 kB / 414.1 MB, free: 36.01 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.005424/0.1883, allocations: 2.072 MB / 416.1 MB, free: 36.01 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0004925/0.1888, allocations: 442.4 kB / 416.6 MB, free: 36.01 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.001215/0.19, allocations: 0.6339 MB / 417.2 MB, free: 36.01 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.007441/0.1975, allocations: 3.902 MB / 421.1 MB, free: 35.65 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 5.791e-06/0.1975, allocations: 0 / 421.1 MB, free: 35.65 MB / 330.7 MB
Notification: Performance of FrontEnd: time 2.174e-06/0.1975, allocations: 0 / 421.1 MB, free: 35.65 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 5.033e-05/0.1975, allocations: 0 / 421.1 MB, free: 35.65 MB / 330.7 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 337
 * Number of variables: 337
Notification: Performance of Generate backend data structure: time 0.002932/0.2004, allocations: 2.261 MB / 423.4 MB, free: 34.55 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.773e-05/0.2005, allocations: 10.03 kB / 423.4 MB, free: 34.55 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.00103/0.2015, allocations: 0.5467 MB / 423.9 MB, free: 34.36 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0008579/0.2024, allocations: 0.7672 MB / 424.7 MB, free: 34.1 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001077/0.2025, allocations: 211.6 kB / 424.9 MB, free: 33.97 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000159/0.2026, allocations: 139.1 kB / 425 MB, free: 33.96 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001437/0.2041, allocations: 1.369 MB / 426.4 MB, free: 33.8 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.213e-05/0.2041, allocations: 3.656 kB / 426.4 MB, free: 33.8 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 9.158e-05/0.2042, allocations: 50.44 kB / 426.4 MB, free: 33.8 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.136e-05/0.2042, allocations: 37.84 kB / 426.5 MB, free: 33.8 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001608/0.2058, allocations: 1.434 MB / 427.9 MB, free: 33.77 MB / 330.7 MB
Warning: The model contains alias variables with redundant start and/or conflicting nominal values. It is recommended to resolve the conflicts, because otherwise the system could be hard to solve. To print the conflicting alias sets and the chosen candidates please use -d=aliasConflicts.
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004549/0.2104, allocations: 4.22 MB / 432.1 MB, free: 31.86 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002944/0.2133, allocations: 3.038 MB / 435.2 MB, free: 31.31 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0005418/0.2139, allocations: 495.5 kB / 435.7 MB, free: 31.21 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.004333/0.2182, allocations: 3.597 MB / 439.3 MB, free: 28.21 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.377e-05/0.2182, allocations: 49.08 kB / 439.3 MB, free: 28.16 MB / 330.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0003218/0.2185, allocations: 134.4 kB / 439.4 MB, free: 28.03 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=97): time 2.715e-06/0.2185, allocations: 0 / 439.4 MB, free: 28.03 MB / 330.7 MB
Notification: Performance of matching and sorting (n=116): time 0.007968/0.2265, allocations: 3.524 MB / 443 MB, free: 24.53 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.847e-05/0.2265, allocations: 64.41 kB / 443 MB, free: 24.45 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004915/0.227, allocations: 0.7411 MB / 443.8 MB, free: 23.69 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 5.254e-05/0.2271, allocations: 45.7 kB / 443.8 MB, free: 23.64 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002095/0.2273, allocations: 0.7198 MB / 444.5 MB, free: 22.92 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001671/0.2275, allocations: 419.4 kB / 444.9 MB, free: 22.51 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000237/0.2277, allocations: 297.1 kB / 445.2 MB, free: 22.21 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 7.311e-05/0.2278, allocations: 0.5303 MB / 445.8 MB, free: 21.68 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003801/0.2281, allocations: 287.8 kB / 446 MB, free: 21.4 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005413/0.2287, allocations: 1.006 MB / 447 MB, free: 20.09 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001212/0.2299, allocations: 1.42 MB / 448.5 MB, free: 18.45 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.711e-06/0.2299, allocations: 4 kB / 448.5 MB, free: 18.45 MB / 330.7 MB
Notification: Performance of matching and sorting (n=197) (initialization): time 0.002667/0.2326, allocations: 1.611 MB / 450.1 MB, free: 16.95 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.171e-05/0.2326, allocations: 18.59 kB / 450.1 MB, free: 16.93 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.351e-05/0.2326, allocations: 16 kB / 450.1 MB, free: 16.91 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001741/0.2343, allocations: 468.6 kB / 450.6 MB, free: 16.47 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000695/0.235, allocations: 378.8 kB / 450.9 MB, free: 16.12 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002775/0.2378, allocations: 4.375 MB / 455.3 MB, free: 11.55 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0006626/0.2385, allocations: 50.66 kB / 455.4 MB, free: 11.51 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 8.653e-05/0.2386, allocations: 91.97 kB / 455.5 MB, free: 11.42 MB / 330.7 MB
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 75
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (190):
 * Single equations (assignments): 187
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 1
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Equation system details (not torn):
 * Constant Jacobian (size): 0 systems
 * Linear Jacobian (size,density): 1 system
   {(2,100.0%)}
 * Non-linear Jacobian (size): 0 systems
 * Without analytic Jacobian (size): 0 systems
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 1 system
   {(1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of prepare postOptimizeDAE: time 0.0003158/0.2389, allocations: 257.3 kB / 455.7 MB, free: 11.18 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001659/0.239, allocations: 147.3 kB / 455.9 MB, free: 11.04 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.002569/0.2416, allocations: 1.413 MB / 457.3 MB, free: 9.664 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.224e-06/0.2416, allocations: 10.67 kB / 457.3 MB, free: 9.656 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.468e-06/0.2416, allocations: 4 kB / 457.3 MB, free: 9.652 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.518e-06/0.2416, allocations: 7.969 kB / 457.3 MB, free: 9.645 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0009526/0.2426, allocations: 0.9218 MB / 458.2 MB, free: 8.707 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.151e-06/0.2426, allocations: 4 kB / 458.2 MB, free: 8.703 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00048/0.2431, allocations: 222.7 kB / 458.4 MB, free: 8.496 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001636/0.2447, allocations: 449.2 kB / 458.9 MB, free: 8.07 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 6.736e-05/0.2448, allocations: 43.97 kB / 458.9 MB, free: 8.027 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002319/0.2471, allocations: 4.277 MB / 463.2 MB, free: 3.547 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.953e-06/0.2471, allocations: 4 kB / 463.2 MB, free: 3.543 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.002887/0.25, allocations: 1.719 MB / 464.9 MB, free: 1.785 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0003226/0.2503, allocations: 211.1 kB / 465.1 MB, free: 1.578 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 7.876e-05/0.2504, allocations: 30.62 kB / 465.1 MB, free: 1.551 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003043/0.2507, allocations: 24 kB / 465.2 MB, free: 1.527 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001689/0.2509, allocations: 112.8 kB / 465.3 MB, free: 1.418 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.654e-05/0.2509, allocations: 47.97 kB / 465.3 MB, free: 1.371 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.0002975/0.2512, allocations: 434.9 kB / 465.8 MB, free: 0.9492 MB / 330.7 MB
Notification: Performance of sort global known variables: time 6e-08/0.2512, allocations: 0 / 465.8 MB, free: 0.9492 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.001894/0.2531, allocations: 0.8415 MB / 466.6 MB, free: 108 kB / 330.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 5
 * Number of states: 6 (solution.temperature,P.logn,S.logn,ES.logn,E.logn,liquidWater.logn)
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (120):
 * Single equations (assignments): 117
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 1
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Equation system details (not torn):
 * Constant Jacobian (size): 0 systems
 * Linear Jacobian (size,density): 1 system
   {(2,100.0%)}
 * Non-linear Jacobian (size): 0 systems
 * Without analytic Jacobian (size): 0 systems
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 1 system
   {(1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of Backend phase and start with SimCode phase: time 0.001504/0.2546, allocations: 0.9826 MB / 467.6 MB, free: 15.28 MB / 346.7 MB
Notification: Performance of simCode: created initialization part: time 0.001769/0.2564, allocations: 1.341 MB / 468.9 MB, free: 13.95 MB / 346.7 MB
Notification: Performance of simCode: created event and clocks part: time 3.266e-06/0.2564, allocations: 3.375 kB / 468.9 MB, free: 13.95 MB / 346.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0008606/0.2572, allocations: 0.8503 MB / 469.8 MB, free: 13.09 MB / 346.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000761/0.258, allocations: 271.1 kB / 470 MB, free: 12.85 MB / 346.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003462/0.2615, allocations: 2.211 MB / 472.2 MB, free: 10.64 MB / 346.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001711/0.2616, allocations: 249 kB / 472.5 MB, free: 10.38 MB / 346.7 MB
Notification: Performance of simCode: alias equations: time 0.0006506/0.2623, allocations: 282.6 kB / 472.8 MB, free: 10.18 MB / 346.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002974/0.2626, allocations: 183.2 kB / 472.9 MB, free: 10 MB / 346.7 MB
Notification: Performance of SimCode: time 1.913e-06/0.2626, allocations: 3.469 kB / 472.9 MB, free: 10 MB / 346.7 MB
Notification: Performance of Templates: time 0.03082/0.2934, allocations: 29.05 MB / 0.4902 GB, free: 14.12 MB / 378.7 MB
"
[Timeout remaining time 660]
make -j1 -f Chemical_master_Chemical.Obsolete.Examples.EnzymeKinetics.makefile [Timeout 660]
(rm -f Chemical_master_Chemical.Obsolete.Examples.EnzymeKinetics.pipe ; mkfifo Chemical_master_Chemical.Obsolete.Examples.EnzymeKinetics.pipe ; head -c 1048576 < Chemical_master_Chemical.Obsolete.Examples.EnzymeKinetics.pipe >> ../files/Chemical_master_Chemical.Obsolete.Examples.EnzymeKinetics.sim & ./Chemical_master_Chemical.Obsolete.Examples.EnzymeKinetics -abortSlowSimulation -alarm=240  -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.EnzymeKinetics.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 3.8843431500717998]