Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.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 0.001923/0.001923, allocations: 85.48 kB / 19.44 MB, free: 344 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 0.002047/0.002047, allocations: 173.2 kB / 22.76 MB, free: 1.664 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 1.548/1.548, allocations: 177.2 MB / 203.1 MB, free: 5.594 MB / 186.7 MB
"
[Timeout remaining time 178]
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 0.1525/0.1525, allocations: 17.45 MB / 277 MB, free: 11.59 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.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.603e-06/1.603e-06, allocations: 0 / 352.8 MB, free: 10.17 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.586e-05/2.746e-05, allocations: 2.312 kB / 352.8 MB, free: 10.16 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.ClimateChange.HydrogenotrophicMethanogenesis): time 0.04073/0.04076, allocations: 27.29 MB / 380.1 MB, free: 15.02 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.02544/0.0662, allocations: 16.76 MB / 396.9 MB, free: 14.2 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000831/0.06703, allocations: 15.88 kB / 396.9 MB, free: 14.18 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009842/0.06801, allocations: 317.4 kB / 397.2 MB, free: 13.87 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.004408/0.07242, allocations: 1.524 MB / 398.7 MB, free: 12.34 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005968/0.07839, allocations: 2.085 MB / 400.8 MB, free: 10.24 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.002532/0.08092, allocations: 1.591 MB / 402.4 MB, free: 8.641 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001093/0.08201, allocations: 0.7156 MB / 403.1 MB, free: 7.902 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001454/0.08347, allocations: 1.076 MB / 404.2 MB, free: 6.824 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.00132/0.08479, allocations: 0.721 MB / 404.9 MB, free: 6.102 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002795/0.08507, allocations: 136 kB / 405.1 MB, free: 5.969 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004894/0.08996, allocations: 1.708 MB / 406.8 MB, free: 4.258 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0004324/0.09039, allocations: 334.9 kB / 407.1 MB, free: 3.93 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0008225/0.09122, allocations: 0.4989 MB / 407.6 MB, free: 3.43 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.1689/0.2601, allocations: 3.665 MB / 411.3 MB, free: 42.92 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 7.644e-06/0.2601, allocations: 0 / 411.3 MB, free: 42.92 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.793e-06/0.2601, allocations: 1.094 kB / 411.3 MB, free: 42.92 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 7.857e-05/0.2602, allocations: 0 / 411.3 MB, free: 42.92 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: 276
 * Number of variables: 276
Notification: Performance of Generate backend data structure: time 0.003903/0.2641, allocations: 1.943 MB / 413.2 MB, free: 42.04 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.26e-05/0.2641, allocations: 10.44 kB / 413.2 MB, free: 42.04 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001526/0.2657, allocations: 451.5 kB / 413.7 MB, free: 41.88 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001231/0.2669, allocations: 0.6253 MB / 414.3 MB, free: 41.65 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001146/0.267, allocations: 138.5 kB / 414.4 MB, free: 41.59 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001966/0.2672, allocations: 114.8 kB / 414.5 MB, free: 41.58 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002387/0.2696, allocations: 1.364 MB / 415.9 MB, free: 41.45 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.895e-05/0.2696, allocations: 192 / 415.9 MB, free: 41.45 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001239/0.2697, allocations: 43.53 kB / 415.9 MB, free: 41.45 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.148e-05/0.2698, allocations: 29.06 kB / 416 MB, free: 41.44 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.003036/0.2728, allocations: 1.631 MB / 417.6 MB, free: 41.43 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 0.007275/0.2801, allocations: 3.931 MB / 421.5 MB, free: 40.33 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003247/0.2833, allocations: 1.83 MB / 423.4 MB, free: 40.25 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0007478/0.2841, allocations: 0.5066 MB / 423.9 MB, free: 40.21 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.005868/0.2899, allocations: 3.022 MB / 426.9 MB, free: 38.98 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.42e-05/0.29, allocations: 45.58 kB / 426.9 MB, free: 38.93 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 3.277e-06/0.29, allocations: 6.031 kB / 426.9 MB, free: 38.93 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.01455/0.3045, allocations: 3.477 MB / 430.4 MB, free: 37.76 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.058e-05/0.3046, allocations: 62.5 kB / 430.5 MB, free: 37.7 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0007106/0.3053, allocations: 0.7382 MB / 431.2 MB, free: 37.3 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 5.958e-05/0.3053, allocations: 42.3 kB / 431.2 MB, free: 37.26 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002997/0.3056, allocations: 0.6301 MB / 431.9 MB, free: 36.75 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002379/0.3059, allocations: 360.8 kB / 432.2 MB, free: 36.48 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003116/0.3062, allocations: 270.3 kB / 432.5 MB, free: 36.34 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001789/0.3064, allocations: 0.6102 MB / 433.1 MB, free: 35.79 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005034/0.3069, allocations: 354.3 kB / 433.5 MB, free: 35.69 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0007463/0.3076, allocations: 0.9304 MB / 434.4 MB, free: 34.86 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001392/0.309, allocations: 1.402 MB / 435.8 MB, free: 33.85 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.943e-06/0.309, allocations: 3.75 kB / 435.8 MB, free: 33.85 MB / 330.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.003772/0.3128, allocations: 1.535 MB / 437.3 MB, free: 32.75 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.707e-05/0.3128, allocations: 12 kB / 437.3 MB, free: 32.74 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.676e-05/0.3128, allocations: 15.94 kB / 437.3 MB, free: 32.73 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.003102/0.3159, allocations: 387.9 kB / 437.7 MB, free: 32.45 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001349/0.3173, allocations: 328.7 kB / 438 MB, free: 32.19 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.0049/0.3222, allocations: 4.811 MB / 442.9 MB, free: 27.2 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001013/0.3232, allocations: 42.66 kB / 442.9 MB, free: 27.16 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 9.957e-05/0.3233, allocations: 63.98 kB / 443 MB, free: 27.09 MB / 330.7 MB
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 58
 * 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 (152):
 * Single equations (assignments): 150
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
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 0.0004751/0.3238, allocations: 322.8 kB / 443.3 MB, free: 26.79 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002182/0.324, allocations: 111.5 kB / 443.4 MB, free: 26.68 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.003738/0.3277, allocations: 1.337 MB / 444.7 MB, free: 25.38 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.251e-05/0.3277, allocations: 12 kB / 444.7 MB, free: 25.36 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.011e-06/0.3277, allocations: 0 / 444.7 MB, free: 25.36 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.112e-05/0.3278, allocations: 3.984 kB / 444.7 MB, free: 25.36 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001273/0.329, allocations: 0.9393 MB / 445.7 MB, free: 24.4 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.021e-06/0.329, allocations: 6.656 kB / 445.7 MB, free: 24.39 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001152/0.3302, allocations: 211 kB / 445.9 MB, free: 24.2 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.003069/0.3333, allocations: 371.1 kB / 446.3 MB, free: 23.84 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001156/0.3334, allocations: 35.98 kB / 446.3 MB, free: 23.81 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004384/0.3378, allocations: 4.712 MB / 451 MB, free: 18.89 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.018e-06/0.3378, allocations: 3.984 kB / 451 MB, free: 18.89 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004058/0.3418, allocations: 1.809 MB / 452.8 MB, free: 17.05 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002742/0.3421, allocations: 89.97 kB / 452.9 MB, free: 16.96 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001195/0.3422, allocations: 20 kB / 452.9 MB, free: 16.94 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005112/0.3427, allocations: 16 kB / 452.9 MB, free: 16.93 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002098/0.3429, allocations: 88.78 kB / 453 MB, free: 16.84 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.163e-05/0.343, allocations: 39.98 kB / 453.1 MB, free: 16.8 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.0003969/0.3434, allocations: 439 kB / 453.5 MB, free: 16.38 MB / 330.7 MB
Notification: Performance of sort global known variables: time 6e-08/0.3434, allocations: 3.75 kB / 453.5 MB, free: 16.38 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.002105/0.3455, allocations: 0.6727 MB / 454.2 MB, free: 15.71 MB / 330.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 5
 * Number of states: 5 (solution.temperature,CH4.logn,CO2.logn,H2O.logn,H2.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 (98):
 * Single equations (assignments): 96
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
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 0.001406/0.3469, allocations: 0.8567 MB / 455 MB, free: 15 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.001972/0.3489, allocations: 1.373 MB / 456.4 MB, free: 13.64 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 3.367e-06/0.3489, allocations: 0 / 456.4 MB, free: 13.64 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0009305/0.3498, allocations: 0.8554 MB / 457.3 MB, free: 12.77 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001092/0.3509, allocations: 225.8 kB / 457.5 MB, free: 12.58 MB / 330.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00292/0.3538, allocations: 1.956 MB / 459.4 MB, free: 10.62 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003036/0.3541, allocations: 448.8 kB / 459.9 MB, free: 10.16 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 0.0007568/0.3549, allocations: 216.9 kB / 460.1 MB, free: 10.02 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003041/0.3552, allocations: 167.7 kB / 460.2 MB, free: 9.867 MB / 330.7 MB
Notification: Performance of SimCode: time 1.613e-06/0.3552, allocations: 0 / 460.2 MB, free: 9.867 MB / 330.7 MB
Notification: Performance of Templates: time 0.03935/0.3945, allocations: 24.3 MB / 484.5 MB, free: 2.695 MB / 346.7 MB
"
[Timeout remaining time 660]
make -j1 -f Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile [Timeout 660]
(rm -f Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis -abortSlowSimulation -alarm=240  -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 6.085601040045731]