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 0.001249/0.001249, 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 0.001439/0.001439, 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 0.9099/0.9099, allocations: 177.1 MB / 203.7 MB, free: 5.512 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 0.08831/0.08831, allocations: 17.38 MB / 277.6 MB, free: 11.5 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 1.423e-06/1.423e-06, allocations: 0 / 353.9 MB, free: 9.699 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.835e-05/1.978e-05, allocations: 2.312 kB / 353.9 MB, free: 9.695 MB / 282.7 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 0.02472/0.02474, allocations: 29.21 MB / 383.1 MB, free: 12.62 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.005782/0.03052, allocations: 6.18 MB / 389.3 MB, free: 6.414 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0004289/0.03095, allocations: 15.88 kB / 389.3 MB, free: 6.398 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0004289/0.03138, allocations: 186.2 kB / 389.5 MB, free: 6.215 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.001514/0.03289, allocations: 0.8533 MB / 390.3 MB, free: 5.355 MB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.001423/0.03431, allocations: 0.8595 MB / 391.2 MB, free: 4.492 MB / 314.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001221/0.03554, allocations: 1.595 MB / 392.8 MB, free: 2.891 MB / 314.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006865/0.03622, allocations: 0.7233 MB / 393.5 MB, free: 2.145 MB / 314.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0008593/0.03708, allocations: 1.076 MB / 394.6 MB, free: 1.066 MB / 314.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0007172/0.0378, allocations: 0.7133 MB / 395.3 MB, free: 360 kB / 314.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001729/0.03797, allocations: 132 kB / 395.4 MB, free: 228 kB / 314.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.001001/0.03897, allocations: 0.5889 MB / 396 MB, free: 15.63 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001994/0.03917, allocations: 334.9 kB / 396.3 MB, free: 15.3 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003633/0.03953, allocations: 0.5028 MB / 396.8 MB, free: 14.8 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.001531/0.04106, allocations: 1.713 MB / 398.6 MB, free: 13.08 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.256e-06/0.04107, allocations: 0 / 398.6 MB, free: 13.08 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.002e-06/0.04107, allocations: 0 / 398.6 MB, free: 13.08 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 2.016e-05/0.04109, allocations: 0 / 398.6 MB, free: 13.08 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 0.001708/0.0428, allocations: 1.644 MB / 400.2 MB, free: 11.39 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.493e-05/0.04283, allocations: 16.03 kB / 400.2 MB, free: 11.38 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0007518/0.04358, allocations: 450.5 kB / 400.7 MB, free: 10.94 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0006461/0.04423, allocations: 0.6108 MB / 401.3 MB, free: 10.3 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 8.244e-05/0.04431, allocations: 138.1 kB / 401.4 MB, free: 10.15 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001228/0.04444, allocations: 120.2 kB / 401.5 MB, free: 10.03 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0009456/0.04538, allocations: 0.9741 MB / 402.5 MB, free: 9.004 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.659e-05/0.0454, allocations: 192 / 402.5 MB, free: 9.004 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.708e-05/0.04547, allocations: 56.11 kB / 402.5 MB, free: 8.949 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.466e-05/0.04549, allocations: 24 kB / 402.6 MB, free: 8.926 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009583/0.04645, allocations: 0.948 MB / 403.5 MB, free: 7.957 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 0.003444/0.04989, allocations: 3.219 MB / 406.7 MB, free: 4.652 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.001956/0.05185, allocations: 1.995 MB / 408.7 MB, free: 2.656 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003017/0.05215, allocations: 313.5 kB / 409 MB, free: 2.344 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.002512/0.05466, allocations: 2.252 MB / 411.3 MB, free: 84 kB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.416e-05/0.05469, allocations: 42.05 kB / 411.3 MB, free: 32 kB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 2.044e-06/0.05469, allocations: 0 / 411.3 MB, free: 32 kB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.1183/0.173, allocations: 2.65 MB / 414 MB, free: 52.25 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.184e-05/0.173, allocations: 62.92 kB / 414 MB, free: 52.18 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004079/0.1734, allocations: 0.6041 MB / 414.6 MB, free: 51.98 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.261e-05/0.1735, allocations: 41.19 kB / 414.7 MB, free: 51.95 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002225/0.1737, allocations: 0.6033 MB / 415.3 MB, free: 51.64 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001672/0.1739, allocations: 345.6 kB / 415.6 MB, free: 51.46 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002195/0.1741, allocations: 247.1 kB / 415.9 MB, free: 51.43 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001049/0.1742, allocations: 0.5814 MB / 416.5 MB, free: 50.93 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002419/0.1744, allocations: 174.2 kB / 416.6 MB, free: 50.93 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003794/0.1748, allocations: 0.7388 MB / 417.4 MB, free: 50.23 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0007023/0.1755, allocations: 1.031 MB / 418.4 MB, free: 49.53 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.342e-06/0.1755, allocations: 6.609 kB / 418.4 MB, free: 49.53 MB / 330.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.001866/0.1774, allocations: 1.153 MB / 419.6 MB, free: 49.4 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.128e-05/0.1774, allocations: 10.94 kB / 419.6 MB, free: 49.4 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.512e-05/0.1774, allocations: 11.91 kB / 419.6 MB, free: 49.4 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.00133/0.1788, allocations: 345.7 kB / 419.9 MB, free: 49.38 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007397/0.1795, allocations: 326.7 kB / 420.2 MB, free: 49.38 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002402/0.1819, allocations: 4.311 MB / 424.5 MB, free: 45.52 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003945/0.1823, allocations: 44.28 kB / 424.6 MB, free: 45.52 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.911e-05/0.1824, allocations: 56.19 kB / 424.6 MB, free: 45.52 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 0.000194/0.1826, allocations: 240.1 kB / 424.9 MB, free: 45.35 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001244/0.1827, allocations: 111 kB / 425 MB, free: 45.31 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.001662/0.1843, allocations: 1.016 MB / 426 MB, free: 45.2 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.911e-06/0.1843, allocations: 10.22 kB / 426 MB, free: 45.2 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.178e-06/0.1843, allocations: 2.688 kB / 426 MB, free: 45.2 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.684e-06/0.1844, allocations: 4.266 kB / 426 MB, free: 45.2 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007308/0.1851, allocations: 0.7681 MB / 426.8 MB, free: 44.96 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 8.276e-06/0.1851, allocations: 5.328 kB / 426.8 MB, free: 44.96 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005517/0.1856, allocations: 218.8 kB / 427 MB, free: 44.96 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001208/0.1869, allocations: 333.3 kB / 427.3 MB, free: 44.94 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 5.122e-05/0.1869, allocations: 32.11 kB / 427.4 MB, free: 44.94 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.001934/0.1888, allocations: 4.22 MB / 431.6 MB, free: 41.09 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.673e-06/0.1888, allocations: 2.938 kB / 431.6 MB, free: 41.09 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001658/0.1905, allocations: 1.249 MB / 432.8 MB, free: 40.75 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 7.359e-05/0.1906, allocations: 83.17 kB / 432.9 MB, free: 40.7 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.899e-05/0.1906, allocations: 19.81 kB / 432.9 MB, free: 40.7 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002119/0.1908, allocations: 20.06 kB / 433 MB, free: 40.7 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001054/0.1909, allocations: 87.08 kB / 433 MB, free: 40.7 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.941e-05/0.191, allocations: 35.31 kB / 433.1 MB, free: 40.7 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.000151/0.1911, allocations: 341 kB / 433.4 MB, free: 40.56 MB / 330.7 MB
Notification: Performance of sort global known variables: time 1.2e-07/0.1911, allocations: 0 / 433.4 MB, free: 40.56 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.0009156/0.1921, allocations: 403.3 kB / 433.8 MB, free: 40.56 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 0.0003944/0.1925, allocations: 347 kB / 434.1 MB, free: 40.47 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.000941/0.1934, allocations: 1.042 MB / 435.2 MB, free: 40.09 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.154e-06/0.1934, allocations: 0 / 435.2 MB, free: 40.09 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003944/0.1938, allocations: 0.6939 MB / 435.9 MB, free: 39.73 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005561/0.1943, allocations: 226 kB / 436.1 MB, free: 39.7 MB / 330.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002124/0.1965, allocations: 1.802 MB / 437.9 MB, free: 38.8 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 9.982e-05/0.1966, allocations: 202.9 kB / 438.1 MB, free: 38.72 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 0.000451/0.197, allocations: 226.9 kB / 438.3 MB, free: 38.71 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.00042/0.1974, allocations: 369.2 kB / 438.7 MB, free: 38.47 MB / 330.7 MB
Notification: Performance of SimCode: time 8.02e-07/0.1974, allocations: 0 / 438.7 MB, free: 38.47 MB / 330.7 MB
Notification: Performance of Templates: time 0.01703/0.2145, allocations: 19.34 MB / 458 MB, free: 20.61 MB / 330.7 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  -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 3.104937548749149]