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 0.0008147/0.0008147, allocations: 80.75 kB / 19.94 MB, free: 4.547 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 0.0009383/0.0009383, allocations: 181 kB / 23.36 MB, free: 1.133 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 0.9044/0.9044, allocations: 177.1 MB / 203.8 MB, free: 5.473 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 0.08071/0.08071, allocations: 17.47 MB / 277.7 MB, free: 11.43 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 1.553e-06/1.553e-06, allocations: 0 / 300.7 MB, free: 1.77 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.28e-05/1.436e-05, allocations: 3.188 kB / 300.7 MB, free: 1.766 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.ClimateChange.HydrogenotrophicMethanogenesis): time 0.02769/0.0277, allocations: 35 MB / 335.7 MB, free: 1.371 MB / 298.7 MB
Notification: Performance of NFInst.instExpressions: time 0.00606/0.03376, allocations: 6.304 MB / 342 MB, free: 11.05 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003332/0.03409, allocations: 15.88 kB / 342.1 MB, free: 11.04 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0003791/0.03447, allocations: 186.2 kB / 342.2 MB, free: 10.85 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.001152/0.03562, allocations: 0.8688 MB / 343.1 MB, free: 9.977 MB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.001042/0.03667, allocations: 0.8672 MB / 344 MB, free: 9.105 MB / 314.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001018/0.03768, allocations: 1.595 MB / 345.6 MB, free: 7.504 MB / 314.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005327/0.03822, allocations: 0.7233 MB / 346.3 MB, free: 6.75 MB / 314.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0007062/0.03892, allocations: 1.076 MB / 347.4 MB, free: 5.672 MB / 314.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0006281/0.03955, allocations: 0.7055 MB / 348.1 MB, free: 4.965 MB / 314.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001289/0.03968, allocations: 136 kB / 348.2 MB, free: 4.832 MB / 314.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.000692/0.04037, allocations: 0.5889 MB / 348.8 MB, free: 4.242 MB / 314.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001989/0.04057, allocations: 338.9 kB / 349.1 MB, free: 3.91 MB / 314.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003374/0.04091, allocations: 0.4989 MB / 349.6 MB, free: 3.41 MB / 314.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.001269/0.04218, allocations: 1.72 MB / 351.3 MB, free: 1.684 MB / 314.7 MB
Notification: Performance of FrontEnd - DAE generated: time 1.804e-06/0.04218, allocations: 4 kB / 351.3 MB, free: 1.68 MB / 314.7 MB
Notification: Performance of FrontEnd: time 1.052e-06/0.04218, allocations: 0 / 351.3 MB, free: 1.68 MB / 314.7 MB
Notification: Performance of Transformations before backend: time 8.827e-06/0.04219, allocations: 0 / 351.3 MB, free: 1.68 MB / 314.7 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 0.00149/0.04368, allocations: 1.504 MB / 352.9 MB, free: 148 kB / 314.7 MB
Notification: Performance of prepare preOptimizeDAE: time 2.688e-05/0.04371, allocations: 8.031 kB / 352.9 MB, free: 140 kB / 314.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0006801/0.04439, allocations: 430.9 kB / 353.3 MB, free: 15.71 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0005482/0.04494, allocations: 0.491 MB / 353.8 MB, free: 15.2 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 8.765e-05/0.04502, allocations: 138.1 kB / 353.9 MB, free: 15.05 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001206/0.04514, allocations: 112.3 kB / 354 MB, free: 14.94 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0008729/0.04602, allocations: 0.9853 MB / 355 MB, free: 13.9 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.652e-05/0.04603, allocations: 4.188 kB / 355 MB, free: 13.9 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.876e-05/0.0461, allocations: 48.12 kB / 355.1 MB, free: 13.85 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.669e-05/0.04612, allocations: 31.98 kB / 355.1 MB, free: 13.82 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008514/0.04697, allocations: 0.8418 MB / 355.9 MB, free: 12.96 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 0.002959/0.04993, allocations: 2.623 MB / 358.5 MB, free: 10.26 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.001835/0.05176, allocations: 1.95 MB / 360.5 MB, free: 8.312 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002541/0.05202, allocations: 274.7 kB / 360.8 MB, free: 8.035 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.002244/0.05426, allocations: 1.951 MB / 362.7 MB, free: 6.066 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.21e-05/0.05428, allocations: 39.22 kB / 362.8 MB, free: 6.02 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 1.644e-06/0.05429, allocations: 0 / 362.8 MB, free: 6.02 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.005892/0.06018, allocations: 2.712 MB / 365.5 MB, free: 3.273 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.243e-05/0.06021, allocations: 64.41 kB / 365.5 MB, free: 3.199 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002891/0.0605, allocations: 0.5308 MB / 366.1 MB, free: 2.652 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.03e-05/0.06054, allocations: 37.7 kB / 366.1 MB, free: 2.609 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001827/0.06072, allocations: 0.4971 MB / 366.6 MB, free: 2.102 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001701/0.06089, allocations: 353 kB / 366.9 MB, free: 1.754 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001878/0.06108, allocations: 230.8 kB / 367.2 MB, free: 1.523 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001089/0.06119, allocations: 402.6 kB / 367.6 MB, free: 1.121 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000177/0.06137, allocations: 153.4 kB / 367.7 MB, free: 0.9688 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003481/0.06171, allocations: 0.5484 MB / 368.3 MB, free: 244 kB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0006368/0.06235, allocations: 0.8588 MB / 369.1 MB, free: 15.2 MB / 346.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.449e-06/0.06236, allocations: 4 kB / 369.1 MB, free: 15.2 MB / 346.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.001423/0.06378, allocations: 0.9216 MB / 370 MB, free: 14.26 MB / 346.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.75e-05/0.0638, allocations: 9.719 kB / 370.1 MB, free: 14.25 MB / 346.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.174e-05/0.06381, allocations: 20.16 kB / 370.1 MB, free: 14.23 MB / 346.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001119/0.06493, allocations: 333.3 kB / 370.4 MB, free: 13.9 MB / 346.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006522/0.06558, allocations: 323.5 kB / 370.7 MB, free: 13.59 MB / 346.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002264/0.06784, allocations: 3.01 MB / 373.7 MB, free: 10.4 MB / 346.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000292/0.06814, allocations: 40 kB / 373.8 MB, free: 10.36 MB / 346.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.801e-05/0.06819, allocations: 60.02 kB / 373.8 MB, free: 10.3 MB / 346.7 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 0.0001761/0.06837, allocations: 192.2 kB / 374 MB, free: 10.11 MB / 346.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.679e-05/0.06847, allocations: 79.88 kB / 374.1 MB, free: 10.03 MB / 346.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.001625/0.07009, allocations: 0.8646 MB / 375 MB, free: 9.152 MB / 346.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.39e-06/0.0701, allocations: 8 kB / 375 MB, free: 9.145 MB / 346.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.364e-06/0.0701, allocations: 3.938 kB / 375 MB, free: 9.141 MB / 346.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.264e-06/0.07011, allocations: 3.984 kB / 375 MB, free: 9.137 MB / 346.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005884/0.07069, allocations: 0.6727 MB / 375.6 MB, free: 8.418 MB / 346.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.765e-06/0.0707, allocations: 0 / 375.6 MB, free: 8.418 MB / 346.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005276/0.07122, allocations: 211.7 kB / 375.8 MB, free: 8.211 MB / 346.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001088/0.07231, allocations: 321.5 kB / 376.2 MB, free: 7.891 MB / 346.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.967e-05/0.07235, allocations: 31.98 kB / 376.2 MB, free: 7.859 MB / 346.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.001887/0.07424, allocations: 2.91 MB / 379.1 MB, free: 4.781 MB / 346.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.914e-06/0.07424, allocations: 3.984 kB / 379.1 MB, free: 4.777 MB / 346.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00143/0.07567, allocations: 1.042 MB / 380.1 MB, free: 3.703 MB / 346.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 6.001e-05/0.07573, allocations: 75.61 kB / 380.2 MB, free: 3.629 MB / 346.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.877e-05/0.0758, allocations: 23.94 kB / 380.2 MB, free: 3.605 MB / 346.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002014/0.076, allocations: 24.06 kB / 380.3 MB, free: 3.582 MB / 346.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001076/0.07611, allocations: 88.77 kB / 380.4 MB, free: 3.492 MB / 346.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.887e-05/0.07615, allocations: 31.98 kB / 380.4 MB, free: 3.461 MB / 346.7 MB
Notification: Performance of sorting global known variables: time 0.0001386/0.07629, allocations: 220.6 kB / 380.6 MB, free: 3.246 MB / 346.7 MB
Notification: Performance of sort global known variables: time 5e-08/0.07629, allocations: 0 / 380.6 MB, free: 3.246 MB / 346.7 MB
Notification: Performance of remove unused functions: time 0.0007237/0.07701, allocations: 411.5 kB / 381 MB, free: 2.844 MB / 346.7 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 0.0003567/0.07737, allocations: 319.6 kB / 381.3 MB, free: 2.52 MB / 346.7 MB
Notification: Performance of simCode: created initialization part: time 0.001001/0.07837, allocations: 0.8795 MB / 382.2 MB, free: 1.617 MB / 346.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.306e-05/0.07838, allocations: 12.5 kB / 382.2 MB, free: 1.605 MB / 346.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.000401/0.07878, allocations: 0.5525 MB / 382.8 MB, free: 1.027 MB / 346.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004853/0.07927, allocations: 235.2 kB / 383 MB, free: 0.7969 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 0.002046/0.08131, allocations: 1.805 MB / 384.8 MB, free: 14.94 MB / 362.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001128/0.08143, allocations: 197 kB / 385 MB, free: 14.73 MB / 362.7 MB
Notification: Performance of simCode: alias equations: time 0.0004292/0.08185, allocations: 214.5 kB / 385.2 MB, free: 14.52 MB / 362.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0004377/0.08229, allocations: 331.1 kB / 385.5 MB, free: 14.2 MB / 362.7 MB
Notification: Performance of SimCode: time 8.32e-07/0.08229, allocations: 0 / 385.5 MB, free: 14.2 MB / 362.7 MB
Notification: Performance of Templates: time 0.01968/0.102, allocations: 19.29 MB / 404.8 MB, free: 11.08 MB / 378.7 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: 3.0638345777988434]