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 0.000991/0.000991, allocations: 80.81 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 0.0009757/0.0009757, allocations: 173 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 0.9962/0.9962, allocations: 177.1 MB / 203.8 MB, free: 5.484 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 0.08466/0.08466, allocations: 17.47 MB / 277.7 MB, free: 11.44 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 1.643e-06/1.643e-06, allocations: 0 / 300.8 MB, free: 1.742 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.177e-05/1.342e-05, allocations: 2.312 kB / 300.8 MB, free: 1.738 MB / 266.7 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 0.02867/0.02869, allocations: 36.4 MB / 337.2 MB, free: 15.95 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01571/0.0444, allocations: 19.41 MB / 356.6 MB, free: 12.47 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0005259/0.04493, allocations: 23.81 kB / 356.6 MB, free: 12.45 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0007196/0.04565, allocations: 400.8 kB / 357 MB, free: 12.05 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.002618/0.04827, allocations: 1.694 MB / 358.7 MB, free: 10.35 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004037/0.0523, allocations: 2.593 MB / 361.3 MB, free: 7.738 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001561/0.05386, allocations: 2.047 MB / 363.3 MB, free: 5.684 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0007861/0.05465, allocations: 0.9632 MB / 364.3 MB, free: 4.688 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009522/0.0556, allocations: 1.373 MB / 365.7 MB, free: 3.312 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0008736/0.05648, allocations: 0.9316 MB / 366.6 MB, free: 2.379 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.000165/0.05664, allocations: 176 kB / 366.8 MB, free: 2.207 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.002705/0.05935, allocations: 2.152 MB / 368.9 MB, free: 52 kB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002492/0.05959, allocations: 434.6 kB / 369.3 MB, free: 15.62 MB / 346.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0004161/0.06001, allocations: 0.6393 MB / 370 MB, free: 14.98 MB / 346.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.003054/0.06306, allocations: 3.899 MB / 373.9 MB, free: 11.07 MB / 346.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.407e-06/0.06307, allocations: 0 / 373.9 MB, free: 11.07 MB / 346.7 MB
Notification: Performance of FrontEnd: time 1.182e-06/0.06307, allocations: 3.938 kB / 373.9 MB, free: 11.07 MB / 346.7 MB
Notification: Performance of Transformations before backend: time 1.111e-05/0.06308, allocations: 0 / 373.9 MB, free: 11.07 MB / 346.7 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 0.00211/0.06519, allocations: 2.125 MB / 376 MB, free: 8.906 MB / 346.7 MB
Notification: Performance of prepare preOptimizeDAE: time 2.921e-05/0.06522, allocations: 8.031 kB / 376 MB, free: 8.898 MB / 346.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0009352/0.06615, allocations: 0.5143 MB / 376.5 MB, free: 8.383 MB / 346.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0007064/0.06686, allocations: 0.5942 MB / 377.1 MB, free: 7.762 MB / 346.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001093/0.06697, allocations: 210 kB / 377.3 MB, free: 7.531 MB / 346.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001498/0.06712, allocations: 144.3 kB / 377.5 MB, free: 7.391 MB / 346.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001176/0.0683, allocations: 1.252 MB / 378.7 MB, free: 6.094 MB / 346.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.39e-05/0.06832, allocations: 192 / 378.7 MB, free: 6.094 MB / 346.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 8.878e-05/0.06841, allocations: 56.12 kB / 378.8 MB, free: 6.039 MB / 346.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.33e-05/0.06843, allocations: 32 kB / 378.8 MB, free: 6.008 MB / 346.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001185/0.06962, allocations: 1.078 MB / 379.9 MB, free: 4.914 MB / 346.7 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 0.003958/0.07357, allocations: 3.262 MB / 383.1 MB, free: 1.594 MB / 346.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002809/0.07638, allocations: 2.85 MB / 386 MB, free: 14.71 MB / 362.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003602/0.07674, allocations: 368.5 kB / 386.4 MB, free: 14.36 MB / 362.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.003893/0.08064, allocations: 3.2 MB / 389.6 MB, free: 11.13 MB / 362.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.581e-05/0.08066, allocations: 47.56 kB / 389.6 MB, free: 11.08 MB / 362.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0002723/0.08093, allocations: 131.2 kB / 389.7 MB, free: 10.95 MB / 362.7 MB
Notification: Performance of pre-optimization done (n=97): time 1.964e-06/0.08094, allocations: 0 / 389.7 MB, free: 10.95 MB / 362.7 MB
Notification: Performance of matching and sorting (n=116): time 0.007092/0.08803, allocations: 3.086 MB / 392.8 MB, free: 7.824 MB / 362.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.308e-05/0.08806, allocations: 72.28 kB / 392.9 MB, free: 7.742 MB / 362.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003784/0.08844, allocations: 0.6515 MB / 393.5 MB, free: 7.078 MB / 362.7 MB
Notification: Performance of collectPreVariables (initialization): time 5.153e-05/0.08849, allocations: 49.7 kB / 393.6 MB, free: 7.023 MB / 362.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002294/0.08872, allocations: 0.5985 MB / 394.2 MB, free: 6.418 MB / 362.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002012/0.08892, allocations: 428.3 kB / 394.6 MB, free: 5.996 MB / 362.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002384/0.08916, allocations: 291.3 kB / 394.9 MB, free: 5.703 MB / 362.7 MB
Notification: Performance of setup shared object (initialization): time 8.726e-05/0.08925, allocations: 353.8 kB / 395.2 MB, free: 5.352 MB / 362.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002339/0.08948, allocations: 194.7 kB / 395.4 MB, free: 5.16 MB / 362.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004353/0.08992, allocations: 0.7067 MB / 396.1 MB, free: 4.234 MB / 362.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0008142/0.09073, allocations: 1.084 MB / 397.2 MB, free: 2.918 MB / 362.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.36e-06/0.09074, allocations: 4 kB / 397.2 MB, free: 2.914 MB / 362.7 MB
Notification: Performance of matching and sorting (n=197) (initialization): time 0.00199/0.09273, allocations: 1.18 MB / 398.4 MB, free: 1.715 MB / 362.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.977e-05/0.09275, allocations: 14.19 kB / 398.4 MB, free: 1.703 MB / 362.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.315e-05/0.09276, allocations: 16 kB / 398.4 MB, free: 1.688 MB / 362.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001488/0.09425, allocations: 454 kB / 398.9 MB, free: 1.234 MB / 362.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007061/0.09495, allocations: 419.3 kB / 399.3 MB, free: 0.8242 MB / 362.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002407/0.09736, allocations: 3.004 MB / 402.3 MB, free: 13.65 MB / 378.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000399/0.09776, allocations: 56.03 kB / 402.3 MB, free: 13.59 MB / 378.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.963e-05/0.09784, allocations: 71.97 kB / 402.4 MB, free: 13.52 MB / 378.7 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 0.0002199/0.09806, allocations: 212.2 kB / 402.6 MB, free: 13.3 MB / 378.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001254/0.09819, allocations: 99.86 kB / 402.7 MB, free: 13.21 MB / 378.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.002241/0.1004, allocations: 1.106 MB / 403.8 MB, free: 12.08 MB / 378.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 9.869e-06/0.1004, allocations: 12 kB / 403.8 MB, free: 12.07 MB / 378.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.637e-06/0.1004, allocations: 4 kB / 403.8 MB, free: 12.07 MB / 378.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.174e-05/0.1005, allocations: 7.969 kB / 403.8 MB, free: 12.06 MB / 378.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001059/0.1015, allocations: 0.8247 MB / 404.7 MB, free: 11.19 MB / 378.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.81e-06/0.1015, allocations: 0 / 404.7 MB, free: 11.19 MB / 378.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0007252/0.1022, allocations: 263.6 kB / 404.9 MB, free: 10.93 MB / 378.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001897/0.1041, allocations: 426.1 kB / 405.3 MB, free: 10.51 MB / 378.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.795e-05/0.1042, allocations: 35.98 kB / 405.4 MB, free: 10.47 MB / 378.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002609/0.1068, allocations: 2.921 MB / 408.3 MB, free: 7.379 MB / 378.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.547e-06/0.1068, allocations: 11.94 kB / 408.3 MB, free: 7.367 MB / 378.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.002721/0.1096, allocations: 1.297 MB / 409.6 MB, free: 6.035 MB / 378.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002739/0.1098, allocations: 135.2 kB / 409.7 MB, free: 5.902 MB / 378.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001105/0.1099, allocations: 24 kB / 409.8 MB, free: 5.879 MB / 378.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003638/0.1103, allocations: 24 kB / 409.8 MB, free: 5.855 MB / 378.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002148/0.1105, allocations: 112.8 kB / 409.9 MB, free: 5.746 MB / 378.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.668e-05/0.1106, allocations: 35.98 kB / 409.9 MB, free: 5.711 MB / 378.7 MB
Notification: Performance of sorting global known variables: time 0.0002627/0.1109, allocations: 288.5 kB / 410.2 MB, free: 5.426 MB / 378.7 MB
Notification: Performance of sort global known variables: time 9e-08/0.1109, allocations: 0 / 410.2 MB, free: 5.426 MB / 378.7 MB
Notification: Performance of remove unused functions: time 0.001751/0.1126, allocations: 0.8337 MB / 411 MB, free: 4.59 MB / 378.7 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 0.001383/0.114, allocations: 1.024 MB / 412.1 MB, free: 3.555 MB / 378.7 MB
Notification: Performance of simCode: created initialization part: time 0.001355/0.1153, allocations: 1.048 MB / 413.1 MB, free: 2.477 MB / 378.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.29e-05/0.1154, allocations: 15 kB / 413.1 MB, free: 2.465 MB / 378.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0007174/0.1161, allocations: 0.6475 MB / 413.8 MB, free: 1.785 MB / 378.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0007764/0.1169, allocations: 259.6 kB / 414 MB, free: 1.531 MB / 378.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00336/0.1202, allocations: 2.161 MB / 416.2 MB, free: 15.31 MB / 394.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001927/0.1204, allocations: 230.5 kB / 416.4 MB, free: 15.06 MB / 394.7 MB
Notification: Performance of simCode: alias equations: time 0.000759/0.1212, allocations: 284.5 kB / 416.7 MB, free: 14.78 MB / 394.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0006955/0.1219, allocations: 373.1 kB / 417.1 MB, free: 14.41 MB / 394.7 MB
Notification: Performance of SimCode: time 7.32e-07/0.1219, allocations: 0 / 417.1 MB, free: 14.41 MB / 394.7 MB
Notification: Performance of Templates: time 0.148/0.2699, allocations: 32.85 MB / 449.9 MB, free: 109.3 MB / 410.7 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 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.EnzymeKinetics.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 3.6293128640390933]