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 0.001198/0.001198, allocations: 88.2 kB / 20.19 MB, free: 4.359 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 0.001101/0.001101, allocations: 173 kB / 23.49 MB, free: 1.055 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 0.9951/0.9951, allocations: 177.1 MB / 203.8 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 0.09071/0.09071, allocations: 17.46 MB / 277.7 MB, free: 11.64 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 1.803e-06/1.803e-06, allocations: 0 / 353.6 MB, free: 10.21 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.525e-05/2.705e-05, allocations: 10.25 kB / 353.6 MB, free: 10.2 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 0.02804/0.02807, allocations: 30.51 MB / 384.1 MB, free: 11.81 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01633/0.0444, allocations: 19.55 MB / 403.6 MB, free: 8.191 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0009095/0.04531, allocations: 23.81 kB / 403.7 MB, free: 8.168 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.00116/0.04647, allocations: 384.9 kB / 404 MB, free: 7.789 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.003521/0.04999, allocations: 1.725 MB / 405.8 MB, free: 6.051 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004788/0.05478, allocations: 2.605 MB / 408.4 MB, free: 3.43 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.002207/0.05698, allocations: 2.035 MB / 410.4 MB, free: 1.387 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001099/0.05808, allocations: 0.9671 MB / 411.4 MB, free: 404 kB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.1334/0.1915, allocations: 1.379 MB / 412.7 MB, free: 36.14 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001762/0.1933, allocations: 0.9458 MB / 413.7 MB, free: 36.14 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0004837/0.1938, allocations: 175 kB / 413.9 MB, free: 36.14 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004684/0.1984, allocations: 2.07 MB / 415.9 MB, free: 36.14 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0004419/0.1989, allocations: 439.8 kB / 416.4 MB, free: 36.14 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.001049/0.1999, allocations: 0.6355 MB / 417 MB, free: 36.14 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.007743/0.2077, allocations: 3.896 MB / 420.9 MB, free: 35.8 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 6.733e-06/0.2077, allocations: 3.562 kB / 420.9 MB, free: 35.8 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.814e-06/0.2077, allocations: 0 / 420.9 MB, free: 35.8 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 5.115e-05/0.2077, allocations: 0 / 420.9 MB, free: 35.8 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 0.003387/0.2111, allocations: 2.26 MB / 423.2 MB, free: 34.69 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.882e-05/0.2112, allocations: 9.875 kB / 423.2 MB, free: 34.69 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001243/0.2124, allocations: 0.5501 MB / 423.7 MB, free: 34.5 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0009345/0.2133, allocations: 0.7716 MB / 424.5 MB, free: 34.24 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.000114/0.2135, allocations: 208 kB / 424.7 MB, free: 34.11 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001639/0.2136, allocations: 139.4 kB / 424.8 MB, free: 34.11 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001605/0.2152, allocations: 1.373 MB / 426.2 MB, free: 33.95 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.505e-05/0.2153, allocations: 192 / 426.2 MB, free: 33.95 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001056/0.2154, allocations: 51.5 kB / 426.2 MB, free: 33.95 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.044e-05/0.2154, allocations: 35.38 kB / 426.3 MB, free: 33.94 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001706/0.2171, allocations: 1.439 MB / 427.7 MB, free: 33.92 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 0.004843/0.2219, allocations: 4.214 MB / 431.9 MB, free: 32.31 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003037/0.225, allocations: 3.044 MB / 435 MB, free: 31.75 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0005848/0.2255, allocations: 494 kB / 435.5 MB, free: 31.66 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.004525/0.2301, allocations: 3.595 MB / 439.1 MB, free: 28.78 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.593e-05/0.2301, allocations: 42.39 kB / 439.1 MB, free: 28.73 MB / 330.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0003442/0.2304, allocations: 142.7 kB / 439.2 MB, free: 28.59 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=97): time 2.565e-06/0.2304, allocations: 0 / 439.2 MB, free: 28.59 MB / 330.7 MB
Notification: Performance of matching and sorting (n=116): time 0.008072/0.2385, allocations: 3.511 MB / 442.8 MB, free: 25.1 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.605e-05/0.2385, allocations: 64.41 kB / 442.8 MB, free: 25.02 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0005075/0.2391, allocations: 0.7372 MB / 443.6 MB, free: 24.27 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 5.162e-05/0.2391, allocations: 45.7 kB / 443.6 MB, free: 24.22 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002028/0.2393, allocations: 0.7158 MB / 444.3 MB, free: 23.5 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001679/0.2395, allocations: 430.5 kB / 444.7 MB, free: 23.09 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002221/0.2397, allocations: 295.8 kB / 445 MB, free: 22.79 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 6.544e-05/0.2398, allocations: 0.5277 MB / 445.5 MB, free: 22.26 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003931/0.2402, allocations: 283.8 kB / 445.8 MB, free: 21.98 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005352/0.2407, allocations: 1.013 MB / 446.8 MB, free: 20.67 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001092/0.2418, allocations: 1.417 MB / 448.3 MB, free: 19.03 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.981e-06/0.2418, allocations: 4 kB / 448.3 MB, free: 19.02 MB / 330.7 MB
Notification: Performance of matching and sorting (n=197) (initialization): time 0.002657/0.2444, allocations: 1.625 MB / 449.9 MB, free: 17.51 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.333e-05/0.2445, allocations: 15.94 kB / 449.9 MB, free: 17.5 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.435e-05/0.2445, allocations: 16 kB / 449.9 MB, free: 17.48 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001674/0.2462, allocations: 459.9 kB / 450.4 MB, free: 17.04 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006502/0.2468, allocations: 375.2 kB / 450.7 MB, free: 16.7 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.00274/0.2495, allocations: 4.385 MB / 455.1 MB, free: 12.12 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0006554/0.2502, allocations: 51.98 kB / 455.2 MB, free: 12.07 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 8.748e-05/0.2503, allocations: 87.97 kB / 455.3 MB, free: 11.98 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 0.0003434/0.2506, allocations: 267.6 kB / 455.5 MB, free: 11.74 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001771/0.2508, allocations: 144.5 kB / 455.7 MB, free: 11.6 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.002585/0.2534, allocations: 1.407 MB / 457.1 MB, free: 10.23 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 8.145e-06/0.2534, allocations: 12 kB / 457.1 MB, free: 10.22 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.849e-06/0.2534, allocations: 0 / 457.1 MB, free: 10.22 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.909e-06/0.2534, allocations: 14.62 kB / 457.1 MB, free: 10.21 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001011/0.2544, allocations: 0.9085 MB / 458 MB, free: 9.273 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 7.404e-06/0.2544, allocations: 0 / 458 MB, free: 9.273 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004785/0.2549, allocations: 230.7 kB / 458.2 MB, free: 9.059 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001604/0.2565, allocations: 455.5 kB / 458.7 MB, free: 8.633 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.558e-05/0.2566, allocations: 39.98 kB / 458.7 MB, free: 8.594 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002343/0.2589, allocations: 4.28 MB / 463 MB, free: 4.109 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.845e-06/0.2589, allocations: 3.469 kB / 463 MB, free: 4.109 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00284/0.2618, allocations: 1.723 MB / 464.7 MB, free: 2.348 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0004421/0.2622, allocations: 203.2 kB / 464.9 MB, free: 2.148 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 9.986e-05/0.2623, allocations: 31.94 kB / 464.9 MB, free: 2.117 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003204/0.2626, allocations: 27.98 kB / 465 MB, free: 2.09 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001937/0.2628, allocations: 111.5 kB / 465.1 MB, free: 1.984 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.929e-05/0.2629, allocations: 51.97 kB / 465.1 MB, free: 1.934 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.0003238/0.2632, allocations: 426.9 kB / 465.5 MB, free: 1.523 MB / 330.7 MB
Notification: Performance of sort global known variables: time 6e-08/0.2632, allocations: 0 / 465.5 MB, free: 1.523 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.001923/0.2651, allocations: 0.8415 MB / 466.4 MB, free: 0.6797 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 0.00134/0.2665, allocations: 0.9871 MB / 467.4 MB, free: 15.84 MB / 346.7 MB
Notification: Performance of simCode: created initialization part: time 0.001785/0.2683, allocations: 1.345 MB / 468.7 MB, free: 14.52 MB / 346.7 MB
Notification: Performance of simCode: created event and clocks part: time 3.397e-06/0.2683, allocations: 3.844 kB / 468.7 MB, free: 14.52 MB / 346.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0008527/0.2691, allocations: 0.843 MB / 469.6 MB, free: 13.65 MB / 346.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0008191/0.2699, allocations: 270.6 kB / 469.8 MB, free: 13.42 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 0.003585/0.2735, allocations: 2.209 MB / 472 MB, free: 11.2 MB / 346.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001819/0.2737, allocations: 238.4 kB / 472.3 MB, free: 10.95 MB / 346.7 MB
Notification: Performance of simCode: alias equations: time 0.0007359/0.2744, allocations: 290.4 kB / 472.6 MB, free: 10.75 MB / 346.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000299/0.2747, allocations: 183.1 kB / 472.7 MB, free: 10.57 MB / 346.7 MB
Notification: Performance of SimCode: time 1.493e-06/0.2747, allocations: 0 / 472.7 MB, free: 10.57 MB / 346.7 MB
Notification: Performance of Templates: time 0.03196/0.3067, allocations: 29.05 MB / 0.49 GB, free: 14.7 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: 3.9173494949936867]