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 0.0009001/0.0009001, allocations: 81.17 kB / 19.87 MB, free: 4.621 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 0.0008879/0.0008879, allocations: 169 kB / 23.27 MB, free: 1.223 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 0.9394/0.9394, allocations: 177.2 MB / 203.7 MB, free: 5.52 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 0.08585/0.08585, allocations: 17.46 MB / 277.7 MB, free: 11.42 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 1.603e-06/1.603e-06, allocations: 0 / 354 MB, free: 9.586 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.173e-05/1.334e-05, allocations: 6.25 kB / 354 MB, free: 9.578 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 0.02647/0.02648, allocations: 30.55 MB / 384.5 MB, free: 11.16 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01545/0.04193, allocations: 19.13 MB / 403.7 MB, free: 7.961 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0008559/0.04279, allocations: 23.81 kB / 403.7 MB, free: 7.938 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0007753/0.04356, allocations: 388.8 kB / 404.1 MB, free: 7.555 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.002843/0.04641, allocations: 1.726 MB / 405.8 MB, free: 5.816 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004955/0.05136, allocations: 2.609 MB / 408.4 MB, free: 3.191 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001777/0.05314, allocations: 2.043 MB / 410.5 MB, free: 1.141 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0007886/0.05393, allocations: 0.9555 MB / 411.4 MB, free: 164 kB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.1772/0.2311, allocations: 1.377 MB / 412.8 MB, free: 36.54 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001361/0.2325, allocations: 0.9484 MB / 413.7 MB, free: 36.54 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0003178/0.2328, allocations: 173.4 kB / 413.9 MB, free: 36.54 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004005/0.2368, allocations: 2.074 MB / 416 MB, free: 36.54 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002948/0.2371, allocations: 436.5 kB / 416.4 MB, free: 36.54 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.000739/0.2378, allocations: 0.6369 MB / 417 MB, free: 36.54 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.004831/0.2427, allocations: 3.9 MB / 420.9 MB, free: 36.2 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 5.611e-06/0.2427, allocations: 3.938 kB / 420.9 MB, free: 36.19 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.903e-06/0.2427, allocations: 0 / 420.9 MB, free: 36.19 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 7.144e-05/0.2427, allocations: 0 / 420.9 MB, free: 36.19 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 0.002929/0.2457, allocations: 2.261 MB / 423.2 MB, free: 35.09 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.632e-05/0.2457, allocations: 12.66 kB / 423.2 MB, free: 35.09 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0009979/0.2467, allocations: 0.5517 MB / 423.8 MB, free: 34.9 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0007905/0.2475, allocations: 0.7618 MB / 424.5 MB, free: 34.64 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 9.03e-05/0.2476, allocations: 206.9 kB / 424.7 MB, free: 34.51 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001543/0.2477, allocations: 138.3 kB / 424.9 MB, free: 34.51 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001043/0.2488, allocations: 1.24 MB / 426.1 MB, free: 34.34 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.033e-05/0.2488, allocations: 2.844 kB / 426.1 MB, free: 34.34 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 8.703e-05/0.2489, allocations: 52.44 kB / 426.2 MB, free: 34.34 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.623e-05/0.2489, allocations: 38.62 kB / 426.2 MB, free: 34.34 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001093/0.25, allocations: 1.224 MB / 427.4 MB, free: 34.29 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 0.003972/0.254, allocations: 4.081 MB / 431.5 MB, free: 32.95 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002606/0.2566, allocations: 2.937 MB / 434.4 MB, free: 32.48 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003429/0.2569, allocations: 420.8 kB / 434.9 MB, free: 32.43 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.003732/0.2607, allocations: 3.623 MB / 438.5 MB, free: 29.45 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.78e-05/0.2607, allocations: 47.25 kB / 438.5 MB, free: 29.39 MB / 330.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0002346/0.2609, allocations: 141 kB / 438.7 MB, free: 29.26 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=97): time 2.204e-06/0.2609, allocations: 0 / 438.7 MB, free: 29.26 MB / 330.7 MB
Notification: Performance of matching and sorting (n=116): time 0.006694/0.2676, allocations: 3.077 MB / 441.7 MB, free: 26.23 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.515e-05/0.2676, allocations: 68.34 kB / 441.8 MB, free: 26.15 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003385/0.268, allocations: 0.7344 MB / 442.5 MB, free: 25.52 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.902e-05/0.268, allocations: 45.7 kB / 442.6 MB, free: 25.47 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001779/0.2682, allocations: 0.7198 MB / 443.3 MB, free: 24.78 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001524/0.2683, allocations: 433.6 kB / 443.7 MB, free: 24.38 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002049/0.2685, allocations: 305.1 kB / 444 MB, free: 24.11 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 6.571e-05/0.2686, allocations: 0.5294 MB / 444.6 MB, free: 23.59 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002148/0.2688, allocations: 219.8 kB / 444.8 MB, free: 23.38 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.00042/0.2692, allocations: 0.9554 MB / 445.7 MB, free: 22.16 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0007285/0.27, allocations: 1.306 MB / 447 MB, free: 20.66 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.56e-06/0.27, allocations: 6.688 kB / 447 MB, free: 20.66 MB / 330.7 MB
Notification: Performance of matching and sorting (n=197) (initialization): time 0.002051/0.272, allocations: 1.48 MB / 448.5 MB, free: 19.29 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.653e-05/0.2721, allocations: 12 kB / 448.5 MB, free: 19.28 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.174e-05/0.2721, allocations: 18.69 kB / 448.6 MB, free: 19.26 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001435/0.2735, allocations: 468.4 kB / 449 MB, free: 18.82 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005448/0.274, allocations: 376.1 kB / 449.4 MB, free: 18.48 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002113/0.2762, allocations: 4.325 MB / 453.7 MB, free: 13.99 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0004253/0.2766, allocations: 52 kB / 453.8 MB, free: 13.94 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.839e-05/0.2766, allocations: 78.64 kB / 453.8 MB, free: 13.87 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 0.000197/0.2768, allocations: 259.6 kB / 454.1 MB, free: 13.63 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001328/0.277, allocations: 147.2 kB / 454.2 MB, free: 13.48 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.002041/0.279, allocations: 1.302 MB / 455.5 MB, free: 12.22 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.08e-06/0.279, allocations: 12 kB / 455.5 MB, free: 12.21 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.938e-06/0.279, allocations: 6.656 kB / 455.5 MB, free: 12.2 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.165e-06/0.279, allocations: 6.75 kB / 455.6 MB, free: 12.2 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007598/0.2798, allocations: 0.9269 MB / 456.5 MB, free: 11.37 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.62e-06/0.2798, allocations: 3.938 kB / 456.5 MB, free: 11.36 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004274/0.2802, allocations: 236.5 kB / 456.7 MB, free: 11.15 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001393/0.2816, allocations: 438.5 kB / 457.1 MB, free: 10.73 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 5.377e-05/0.2817, allocations: 39.97 kB / 457.2 MB, free: 10.69 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.001823/0.2835, allocations: 4.224 MB / 461.4 MB, free: 6.293 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.703e-06/0.2835, allocations: 4 kB / 461.4 MB, free: 6.289 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.002071/0.2856, allocations: 1.555 MB / 463 MB, free: 4.719 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002136/0.2858, allocations: 207.2 kB / 463.2 MB, free: 4.516 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 7.088e-05/0.2859, allocations: 24 kB / 463.2 MB, free: 4.492 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000272/0.2861, allocations: 27.98 kB / 463.2 MB, free: 4.465 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001215/0.2862, allocations: 116.1 kB / 463.3 MB, free: 4.355 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.654e-05/0.2863, allocations: 47.97 kB / 463.4 MB, free: 4.309 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.0001673/0.2865, allocations: 402.4 kB / 463.8 MB, free: 3.957 MB / 330.7 MB
Notification: Performance of sort global known variables: time 7e-08/0.2865, allocations: 2.656 kB / 463.8 MB, free: 3.957 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.001552/0.288, allocations: 0.8415 MB / 464.6 MB, free: 3.113 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 0.001017/0.289, allocations: 1.026 MB / 465.6 MB, free: 2.242 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.0009427/0.29, allocations: 1.234 MB / 466.9 MB, free: 1.051 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.352e-06/0.29, allocations: 0 / 466.9 MB, free: 1.051 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.000506/0.2905, allocations: 0.7965 MB / 467.7 MB, free: 256 kB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006268/0.2911, allocations: 268.5 kB / 467.9 MB, free: 16 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 0.003342/0.2945, allocations: 2.182 MB / 470.1 MB, free: 13.85 MB / 346.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001744/0.2946, allocations: 238.4 kB / 470.3 MB, free: 13.6 MB / 346.7 MB
Notification: Performance of simCode: alias equations: time 0.0006929/0.2953, allocations: 277 kB / 470.6 MB, free: 13.41 MB / 346.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000588/0.2959, allocations: 425.9 kB / 471 MB, free: 12.99 MB / 346.7 MB
Notification: Performance of SimCode: time 1.423e-06/0.2959, allocations: 0 / 471 MB, free: 12.99 MB / 346.7 MB
Notification: Performance of Templates: time 0.03499/0.3309, allocations: 32.93 MB / 0.4922 GB, free: 13.2 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: 3.5997608602046967]