Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_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 0.001379/0.001379, 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 0.0009985/0.0009985, 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 0.9992/0.9992, allocations: 177.1 MB / 203.8 MB, free: 5.469 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo): time 0.09288/0.09288, allocations: 17.38 MB / 277.6 MB, free: 11.52 MB / 266.7 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/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_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.034e-06/2.034e-06, allocations: 1.375 kB / 300.7 MB, free: 1.828 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 9.017e-06/1.105e-05, allocations: 2.312 kB / 300.7 MB, free: 1.824 MB / 266.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/Obsolete.mo:14337:7-14337:66: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 2.0.0/Obsolete.mo:14337:7-14337:66: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 0.03255/0.03256, allocations: 35.03 MB / 335.7 MB, free: 1.508 MB / 298.7 MB
Notification: Performance of NFInst.instExpressions: time 0.00697/0.03953, allocations: 6.294 MB / 342 MB, free: 11.19 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0004806/0.04001, allocations: 19.88 kB / 342 MB, free: 11.17 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0005593/0.04057, allocations: 198.2 kB / 342.2 MB, free: 10.98 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.001825/0.0424, allocations: 0.8455 MB / 343.1 MB, free: 10.12 MB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.00141/0.04381, allocations: 0.8633 MB / 343.9 MB, free: 9.258 MB / 314.7 MB
Notification: Performance of NFFlatten.flatten: time 0.00132/0.04513, allocations: 1.591 MB / 345.5 MB, free: 7.66 MB / 314.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0007554/0.04588, allocations: 0.7272 MB / 346.2 MB, free: 6.902 MB / 314.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000935/0.04682, allocations: 1.072 MB / 347.3 MB, free: 5.828 MB / 314.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0007814/0.0476, allocations: 0.7016 MB / 348 MB, free: 5.125 MB / 314.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001709/0.04777, allocations: 136 kB / 348.1 MB, free: 4.992 MB / 314.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.001024/0.04879, allocations: 0.6006 MB / 348.7 MB, free: 4.391 MB / 314.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002128/0.04901, allocations: 334.9 kB / 349.1 MB, free: 4.062 MB / 314.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.000388/0.04939, allocations: 0.5028 MB / 349.6 MB, free: 3.559 MB / 314.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.001573/0.05097, allocations: 1.716 MB / 351.3 MB, free: 1.836 MB / 314.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.677e-06/0.05097, allocations: 0 / 351.3 MB, free: 1.836 MB / 314.7 MB
Notification: Performance of FrontEnd: time 1.573e-06/0.05097, allocations: 0 / 351.3 MB, free: 1.836 MB / 314.7 MB
Notification: Performance of Transformations before backend: time 1.658e-05/0.05099, allocations: 4 kB / 351.3 MB, free: 1.832 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 0.001681/0.05267, allocations: 1.508 MB / 352.8 MB, free: 300 kB / 314.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.102e-05/0.0527, allocations: 12.03 kB / 352.8 MB, free: 288 kB / 314.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0007926/0.05349, allocations: 439 kB / 353.2 MB, free: 15.85 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0006297/0.05412, allocations: 494.8 kB / 353.7 MB, free: 15.34 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001202/0.05424, allocations: 142.1 kB / 353.9 MB, free: 15.19 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001351/0.05438, allocations: 116.3 kB / 354 MB, free: 15.07 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0009373/0.05532, allocations: 0.9814 MB / 355 MB, free: 14.04 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.905e-05/0.05534, allocations: 192 / 355 MB, free: 14.04 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.348e-05/0.0554, allocations: 48.12 kB / 355 MB, free: 14 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.432e-05/0.05541, allocations: 24 kB / 355 MB, free: 13.97 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009265/0.05634, allocations: 0.8457 MB / 355.9 MB, free: 13.11 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 0.00312/0.05946, allocations: 2.623 MB / 358.5 MB, free: 10.41 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.001926/0.06139, allocations: 1.947 MB / 360.4 MB, free: 8.461 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.000273/0.06166, allocations: 274.7 kB / 360.7 MB, free: 8.184 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.002382/0.06404, allocations: 1.955 MB / 362.7 MB, free: 6.211 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.485e-05/0.06406, allocations: 43.22 kB / 362.7 MB, free: 6.16 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 1.763e-06/0.06407, allocations: 0 / 362.7 MB, free: 6.16 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.006466/0.07053, allocations: 2.715 MB / 365.4 MB, free: 3.414 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.313e-05/0.07057, allocations: 60.41 kB / 365.5 MB, free: 3.344 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003116/0.07088, allocations: 0.5347 MB / 366 MB, free: 2.793 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.389e-05/0.07092, allocations: 41.7 kB / 366.1 MB, free: 2.746 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002101/0.07113, allocations: 0.4893 MB / 366.5 MB, free: 2.246 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001852/0.07132, allocations: 349 kB / 366.9 MB, free: 1.902 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001986/0.07152, allocations: 234.7 kB / 367.1 MB, free: 1.668 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.000118/0.07163, allocations: 398.6 kB / 367.5 MB, free: 1.27 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001814/0.07181, allocations: 153.4 kB / 367.7 MB, free: 1.117 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003882/0.0722, allocations: 0.5524 MB / 368.2 MB, free: 392 kB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0007732/0.07298, allocations: 0.8548 MB / 369.1 MB, free: 15.35 MB / 346.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.542e-06/0.07298, allocations: 4 kB / 369.1 MB, free: 15.35 MB / 346.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.001583/0.07457, allocations: 0.9249 MB / 370 MB, free: 14.41 MB / 346.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.236e-05/0.07459, allocations: 15.94 kB / 370 MB, free: 14.39 MB / 346.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.263e-05/0.0746, allocations: 12 kB / 370 MB, free: 14.38 MB / 346.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001208/0.07581, allocations: 338.1 kB / 370.4 MB, free: 14.04 MB / 346.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007596/0.07657, allocations: 363.5 kB / 370.7 MB, free: 13.69 MB / 346.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002412/0.07898, allocations: 3.014 MB / 373.7 MB, free: 10.5 MB / 346.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003296/0.07931, allocations: 43.98 kB / 373.8 MB, free: 10.46 MB / 346.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.155e-05/0.07937, allocations: 56.02 kB / 373.8 MB, free: 10.4 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 0.000188/0.07956, allocations: 192.2 kB / 374 MB, free: 10.2 MB / 346.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001008/0.07966, allocations: 79.88 kB / 374.1 MB, free: 10.12 MB / 346.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.001497/0.08116, allocations: 0.8764 MB / 375 MB, free: 9.238 MB / 346.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.651e-06/0.08116, allocations: 8 kB / 375 MB, free: 9.23 MB / 346.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.896e-06/0.08117, allocations: 0 / 375 MB, free: 9.23 MB / 346.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.035e-06/0.08117, allocations: 11.97 kB / 375 MB, free: 9.219 MB / 346.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006344/0.08181, allocations: 0.6688 MB / 375.6 MB, free: 8.504 MB / 346.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.829e-06/0.08181, allocations: 0 / 375.6 MB, free: 8.504 MB / 346.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0006001/0.08241, allocations: 239.7 kB / 375.9 MB, free: 8.27 MB / 346.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001146/0.08356, allocations: 321.5 kB / 376.2 MB, free: 7.949 MB / 346.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 5.132e-05/0.08361, allocations: 27.98 kB / 376.2 MB, free: 7.922 MB / 346.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002083/0.08569, allocations: 2.914 MB / 379.1 MB, free: 4.84 MB / 346.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.262e-06/0.0857, allocations: 0 / 379.1 MB, free: 4.84 MB / 346.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001678/0.08737, allocations: 1.058 MB / 380.2 MB, free: 3.75 MB / 346.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 6.139e-05/0.08743, allocations: 71.42 kB / 380.3 MB, free: 3.68 MB / 346.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.697e-05/0.0875, allocations: 23.94 kB / 380.3 MB, free: 3.656 MB / 346.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002044/0.08771, allocations: 16 kB / 380.3 MB, free: 3.641 MB / 346.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001326/0.08784, allocations: 88.78 kB / 380.4 MB, free: 3.551 MB / 346.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.434e-05/0.08788, allocations: 31.98 kB / 380.4 MB, free: 3.52 MB / 346.7 MB
Notification: Performance of sorting global known variables: time 0.0001619/0.08804, allocations: 228.6 kB / 380.6 MB, free: 3.297 MB / 346.7 MB
Notification: Performance of sort global known variables: time 4e-08/0.08804, allocations: 0 / 380.6 MB, free: 3.297 MB / 346.7 MB
Notification: Performance of remove unused functions: time 0.0008248/0.08887, allocations: 407.5 kB / 381 MB, free: 2.898 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 0.0004563/0.08933, allocations: 319.6 kB / 381.4 MB, free: 2.574 MB / 346.7 MB
Notification: Performance of simCode: created initialization part: time 0.0008719/0.0902, allocations: 0.8673 MB / 382.2 MB, free: 1.684 MB / 346.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.806e-05/0.09022, allocations: 16.5 kB / 382.2 MB, free: 1.668 MB / 346.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0004513/0.09067, allocations: 0.5648 MB / 382.8 MB, free: 1.078 MB / 346.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005374/0.0912, allocations: 227.2 kB / 383 MB, free: 0.8555 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 0.002351/0.09356, allocations: 1.801 MB / 384.8 MB, free: 15 MB / 362.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001381/0.09369, allocations: 197 kB / 385 MB, free: 14.79 MB / 362.7 MB
Notification: Performance of simCode: alias equations: time 0.0004923/0.09419, allocations: 218.4 kB / 385.2 MB, free: 14.57 MB / 362.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0004943/0.09468, allocations: 334.8 kB / 385.6 MB, free: 14.25 MB / 362.7 MB
Notification: Performance of SimCode: time 9.12e-07/0.09468, allocations: 0 / 385.6 MB, free: 14.25 MB / 362.7 MB
Notification: Performance of Templates: time 0.02155/0.1162, allocations: 19.3 MB / 404.9 MB, free: 11.14 MB / 378.7 MB
"
[Timeout remaining time 660]
make -j1 -f Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile [Timeout 660]
(rm -f Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis -abortSlowSimulation -alarm=240 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 3.2049152427352965]