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 0.0009903/0.0009903, allocations: 77.95 kB / 20.66 MB, free: 3.832 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 0.001465/0.001465, allocations: 165 kB / 24.05 MB, free: 452 kB / 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 1.006/1.006, allocations: 177.1 MB / 204.5 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 0.08652/0.08652, allocations: 17.46 MB / 278.5 MB, free: 11.39 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 1.532e-06/1.532e-06, allocations: 0 / 354.8 MB, free: 9.562 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.973e-05/3.126e-05, allocations: 9.484 kB / 354.8 MB, free: 9.555 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 0.02998/0.03001, allocations: 30.52 MB / 385.3 MB, free: 11.17 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01601/0.04603, allocations: 19.12 MB / 404.4 MB, free: 7.98 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.00107/0.0471, allocations: 23.81 kB / 404.5 MB, free: 7.957 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0008664/0.04796, allocations: 396.9 kB / 404.8 MB, free: 7.566 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.003782/0.05174, allocations: 1.722 MB / 406.6 MB, free: 5.832 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005568/0.05731, allocations: 2.617 MB / 409.2 MB, free: 3.199 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.002448/0.05976, allocations: 2.039 MB / 411.2 MB, free: 1.152 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001159/0.06092, allocations: 0.9554 MB / 412.2 MB, free: 176 kB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.1398/0.2007, allocations: 1.384 MB / 413.6 MB, free: 36.58 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.002369/0.203, allocations: 0.9406 MB / 414.5 MB, free: 36.58 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0005678/0.2036, allocations: 173.4 kB / 414.7 MB, free: 36.58 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.006846/0.2105, allocations: 2.069 MB / 416.7 MB, free: 36.58 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0006812/0.2111, allocations: 443.9 kB / 417.2 MB, free: 36.58 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.001276/0.2124, allocations: 0.634 MB / 417.8 MB, free: 36.58 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.007299/0.2197, allocations: 3.901 MB / 421.7 MB, free: 36.23 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 5.911e-06/0.2197, allocations: 3.906 kB / 421.7 MB, free: 36.23 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.583e-06/0.2197, allocations: 0 / 421.7 MB, free: 36.23 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 5.904e-05/0.2198, allocations: 0 / 421.7 MB, free: 36.23 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 0.003365/0.2231, allocations: 2.263 MB / 424 MB, free: 35.12 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.634e-05/0.2232, allocations: 9.594 kB / 424 MB, free: 35.12 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001202/0.2244, allocations: 0.5507 MB / 424.5 MB, free: 34.94 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001597/0.226, allocations: 0.7616 MB / 425.3 MB, free: 34.67 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001579/0.2261, allocations: 210.2 kB / 425.5 MB, free: 34.54 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002627/0.2264, allocations: 146.4 kB / 425.6 MB, free: 34.54 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002124/0.2285, allocations: 1.234 MB / 426.9 MB, free: 34.38 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.356e-05/0.2286, allocations: 192 / 426.9 MB, free: 34.38 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001561/0.2287, allocations: 55.53 kB / 426.9 MB, free: 34.38 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.241e-05/0.2287, allocations: 36.78 kB / 427 MB, free: 34.37 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002133/0.2309, allocations: 1.223 MB / 428.2 MB, free: 34.33 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 0.008036/0.2389, allocations: 4.082 MB / 432.3 MB, free: 32.98 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.005039/0.244, allocations: 2.938 MB / 435.2 MB, free: 32.5 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0008684/0.2448, allocations: 420.6 kB / 435.6 MB, free: 32.45 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006779/0.2516, allocations: 3.579 MB / 439.2 MB, free: 29.48 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.851e-05/0.2516, allocations: 42.39 kB / 439.2 MB, free: 29.43 MB / 330.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0003899/0.252, allocations: 141.3 kB / 439.4 MB, free: 29.3 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=97): time 3.416e-06/0.252, allocations: 4 kB / 439.4 MB, free: 29.3 MB / 330.7 MB
Notification: Performance of matching and sorting (n=116): time 0.007337/0.2594, allocations: 3.088 MB / 442.5 MB, free: 26.25 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.534e-05/0.2594, allocations: 68.34 kB / 442.5 MB, free: 26.17 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004581/0.2598, allocations: 0.7322 MB / 443.3 MB, free: 25.54 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 5.96e-05/0.2599, allocations: 45.7 kB / 443.3 MB, free: 25.49 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002098/0.2601, allocations: 0.7203 MB / 444 MB, free: 24.8 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001801/0.2603, allocations: 428.9 kB / 444.5 MB, free: 24.41 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002313/0.2605, allocations: 306.3 kB / 444.8 MB, free: 24.14 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 8.176e-05/0.2606, allocations: 0.5302 MB / 445.3 MB, free: 23.62 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002443/0.2609, allocations: 219.8 kB / 445.5 MB, free: 23.41 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004329/0.2613, allocations: 0.9491 MB / 446.4 MB, free: 22.19 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0008769/0.2622, allocations: 1.313 MB / 447.8 MB, free: 20.69 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.052e-06/0.2622, allocations: 6.656 kB / 447.8 MB, free: 20.69 MB / 330.7 MB
Notification: Performance of matching and sorting (n=197) (initialization): time 0.002399/0.2646, allocations: 1.473 MB / 449.2 MB, free: 19.32 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.097e-05/0.2646, allocations: 12 kB / 449.2 MB, free: 19.31 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.409e-05/0.2646, allocations: 16 kB / 449.3 MB, free: 19.3 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001608/0.2662, allocations: 471.3 kB / 449.7 MB, free: 18.86 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006289/0.2668, allocations: 376.5 kB / 450.1 MB, free: 18.51 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002498/0.2693, allocations: 4.325 MB / 454.4 MB, free: 14.02 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0006631/0.27, allocations: 48 kB / 454.5 MB, free: 13.98 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 8.395e-05/0.2701, allocations: 75.97 kB / 454.5 MB, free: 13.9 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 0.0003341/0.2704, allocations: 259.6 kB / 454.8 MB, free: 13.66 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001872/0.2706, allocations: 147.2 kB / 454.9 MB, free: 13.52 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0023/0.2729, allocations: 1.301 MB / 456.2 MB, free: 12.26 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 8.336e-06/0.2729, allocations: 12 kB / 456.2 MB, free: 12.25 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.36e-06/0.2729, allocations: 4 kB / 456.3 MB, free: 12.25 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.086e-05/0.2729, allocations: 7.969 kB / 456.3 MB, free: 12.24 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001022/0.274, allocations: 0.9281 MB / 457.2 MB, free: 11.41 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 9.167e-06/0.274, allocations: 6.562 kB / 457.2 MB, free: 11.4 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004524/0.2744, allocations: 228.7 kB / 457.4 MB, free: 11.19 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001575/0.276, allocations: 452.1 kB / 457.9 MB, free: 10.77 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 8.004e-05/0.2761, allocations: 43.97 kB / 457.9 MB, free: 10.73 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002251/0.2783, allocations: 4.212 MB / 462.1 MB, free: 6.34 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.026e-06/0.2783, allocations: 4 kB / 462.1 MB, free: 6.336 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.002431/0.2808, allocations: 1.559 MB / 463.7 MB, free: 4.762 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0003278/0.2811, allocations: 203.2 kB / 463.9 MB, free: 4.562 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 8.621e-05/0.2812, allocations: 20 kB / 463.9 MB, free: 4.543 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002885/0.2815, allocations: 27.94 kB / 463.9 MB, free: 4.516 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001661/0.2816, allocations: 127.5 kB / 464 MB, free: 4.395 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.47e-05/0.2817, allocations: 45.33 kB / 464.1 MB, free: 4.355 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.0001911/0.2819, allocations: 404.6 kB / 464.5 MB, free: 4 MB / 330.7 MB
Notification: Performance of sort global known variables: time 8e-08/0.2819, allocations: 0 / 464.5 MB, free: 4 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.002043/0.2839, allocations: 0.8376 MB / 465.3 MB, free: 3.16 MB / 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 0.001319/0.2852, allocations: 1.028 MB / 466.4 MB, free: 2.289 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.001172/0.2864, allocations: 1.232 MB / 467.6 MB, free: 1.094 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.635e-06/0.2864, allocations: 2.688 kB / 467.6 MB, free: 1.094 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0005564/0.287, allocations: 0.797 MB / 468.4 MB, free: 300 kB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0007025/0.2877, allocations: 270.8 kB / 468.6 MB, free: 60 kB / 330.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003244/0.2909, allocations: 2.184 MB / 470.8 MB, free: 13.89 MB / 346.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001724/0.2911, allocations: 234.4 kB / 471.1 MB, free: 13.64 MB / 346.7 MB
Notification: Performance of simCode: alias equations: time 0.0006542/0.2917, allocations: 280.2 kB / 471.3 MB, free: 13.45 MB / 346.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0005598/0.2923, allocations: 418 kB / 471.7 MB, free: 13.04 MB / 346.7 MB
Notification: Performance of SimCode: time 9.32e-07/0.2923, allocations: 0 / 471.7 MB, free: 13.04 MB / 346.7 MB
Notification: Performance of Templates: time 0.03501/0.3273, allocations: 33.32 MB / 0.4932 GB, free: 12.89 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: 3.877382737118751]