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 0.0009449/0.0009449, allocations: 93.06 kB / 19.65 MB, free: 280 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 0.0009761/0.0009761, allocations: 169.3 kB / 23.02 MB, free: 1.551 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 0.9503/0.9503, allocations: 177.1 MB / 203.4 MB, free: 5.633 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 0.08817/0.08817, allocations: 17.46 MB / 277.4 MB, free: 11.55 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 1.563e-06/1.563e-06, allocations: 3.938 kB / 353.6 MB, free: 9.836 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.89e-05/2.046e-05, allocations: 5.406 kB / 353.6 MB, free: 9.832 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 0.0354/0.03542, allocations: 29.25 MB / 382.8 MB, free: 12.71 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.006648/0.04207, allocations: 6.25 MB / 389.1 MB, free: 6.441 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003647/0.04243, allocations: 19.81 kB / 389.1 MB, free: 6.422 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0004186/0.04285, allocations: 190.2 kB / 389.3 MB, free: 6.234 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.001225/0.04408, allocations: 0.8572 MB / 390.1 MB, free: 5.371 MB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.001194/0.04527, allocations: 0.8556 MB / 391 MB, free: 4.512 MB / 314.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001182/0.04645, allocations: 1.595 MB / 392.6 MB, free: 2.91 MB / 314.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0007167/0.04717, allocations: 0.7233 MB / 393.3 MB, free: 2.164 MB / 314.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000872/0.04804, allocations: 1.076 MB / 394.4 MB, free: 1.086 MB / 314.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0007882/0.04883, allocations: 0.7172 MB / 395.1 MB, free: 376 kB / 314.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001617/0.04899, allocations: 132 kB / 395.2 MB, free: 244 kB / 314.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0009063/0.0499, allocations: 0.5851 MB / 395.8 MB, free: 15.65 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002261/0.05013, allocations: 338.9 kB / 396.1 MB, free: 15.32 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003664/0.05049, allocations: 0.495 MB / 396.6 MB, free: 14.82 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.001529/0.05202, allocations: 1.724 MB / 398.4 MB, free: 13.09 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 6.933e-06/0.05203, allocations: 0 / 398.4 MB, free: 13.09 MB / 330.7 MB
Notification: Performance of FrontEnd: time 3.446e-06/0.05203, allocations: 0 / 398.4 MB, free: 13.09 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 1.84e-05/0.05205, allocations: 0 / 398.4 MB, free: 13.09 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 0.001911/0.05396, allocations: 1.64 MB / 400 MB, free: 11.41 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.257e-05/0.054, allocations: 12.03 kB / 400 MB, free: 11.4 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0007862/0.05479, allocations: 450.3 kB / 400.4 MB, free: 10.96 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000709/0.0555, allocations: 0.6147 MB / 401.1 MB, free: 10.31 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.000113/0.05561, allocations: 142.1 kB / 401.2 MB, free: 10.16 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001327/0.05575, allocations: 116.3 kB / 401.3 MB, free: 10.05 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001221/0.05697, allocations: 1.068 MB / 402.4 MB, free: 8.926 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.036e-05/0.05699, allocations: 4.188 kB / 402.4 MB, free: 8.922 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.808e-05/0.05706, allocations: 52.11 kB / 402.4 MB, free: 8.871 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.036e-05/0.05709, allocations: 28 kB / 402.5 MB, free: 8.844 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.00136/0.05844, allocations: 1.121 MB / 403.6 MB, free: 7.711 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 0.00372/0.06216, allocations: 3.313 MB / 406.9 MB, free: 4.305 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002244/0.06441, allocations: 2.067 MB / 409 MB, free: 2.234 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004307/0.06484, allocations: 369.5 kB / 409.3 MB, free: 1.867 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.1356/0.2004, allocations: 2.211 MB / 411.5 MB, free: 51.14 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.002e-05/0.2005, allocations: 42.98 kB / 411.6 MB, free: 51.1 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 3.737e-06/0.2005, allocations: 0 / 411.6 MB, free: 51.1 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.008111/0.2086, allocations: 2.975 MB / 414.6 MB, free: 50.8 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.285e-05/0.2086, allocations: 64.69 kB / 414.6 MB, free: 50.73 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0005716/0.2092, allocations: 0.6029 MB / 415.2 MB, free: 50.53 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.576e-05/0.2092, allocations: 43.73 kB / 415.3 MB, free: 50.5 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002621/0.2095, allocations: 0.6022 MB / 415.9 MB, free: 50.18 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002258/0.2097, allocations: 349.4 kB / 416.2 MB, free: 50 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002828/0.21, allocations: 239.3 kB / 416.4 MB, free: 49.97 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001596/0.2102, allocations: 0.5638 MB / 417 MB, free: 49.48 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003918/0.2106, allocations: 233.6 kB / 417.2 MB, free: 49.47 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005665/0.2111, allocations: 0.7792 MB / 418 MB, free: 48.78 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001015/0.2122, allocations: 1.111 MB / 419.1 MB, free: 48.08 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.636e-06/0.2122, allocations: 7.281 kB / 419.1 MB, free: 48.08 MB / 330.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.002322/0.2145, allocations: 1.259 MB / 420.4 MB, free: 47.95 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.944e-05/0.2145, allocations: 10.39 kB / 420.4 MB, free: 47.95 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.051e-05/0.2145, allocations: 20.75 kB / 420.4 MB, free: 47.95 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001534/0.2161, allocations: 347 kB / 420.8 MB, free: 47.93 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0008503/0.2169, allocations: 326.8 kB / 421.1 MB, free: 47.93 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002957/0.2199, allocations: 4.374 MB / 425.5 MB, free: 44.01 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0005959/0.2205, allocations: 40.84 kB / 425.5 MB, free: 44.01 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001002/0.2206, allocations: 67.84 kB / 425.6 MB, free: 44.01 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 0.0003237/0.2209, allocations: 241.9 kB / 425.8 MB, free: 43.85 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000155/0.221, allocations: 117.8 kB / 425.9 MB, free: 43.8 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.001925/0.223, allocations: 1.109 MB / 427 MB, free: 43.7 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.172e-06/0.223, allocations: 9.594 kB / 427 MB, free: 43.7 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.28e-06/0.223, allocations: 0 / 427 MB, free: 43.7 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.668e-06/0.223, allocations: 12.59 kB / 427 MB, free: 43.7 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008032/0.2238, allocations: 0.7479 MB / 427.8 MB, free: 43.46 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.042e-06/0.2238, allocations: 2.938 kB / 427.8 MB, free: 43.46 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005903/0.2244, allocations: 217.8 kB / 428 MB, free: 43.46 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001377/0.2258, allocations: 324 kB / 428.3 MB, free: 43.42 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 6.754e-05/0.2258, allocations: 38.81 kB / 428.4 MB, free: 43.41 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002304/0.2281, allocations: 4.264 MB / 432.6 MB, free: 39.35 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.216e-06/0.2281, allocations: 8.562 kB / 432.6 MB, free: 39.35 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.002123/0.2303, allocations: 1.383 MB / 434 MB, free: 38.82 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001301/0.2304, allocations: 73.86 kB / 434.1 MB, free: 38.77 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.483e-05/0.2305, allocations: 23.91 kB / 434.1 MB, free: 38.76 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000243/0.2307, allocations: 26.83 kB / 434.1 MB, free: 38.75 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001353/0.2308, allocations: 87.88 kB / 434.2 MB, free: 38.73 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.641e-05/0.2309, allocations: 37.2 kB / 434.3 MB, free: 38.72 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.000236/0.2311, allocations: 362 kB / 434.6 MB, free: 38.54 MB / 330.7 MB
Notification: Performance of sort global known variables: time 8e-08/0.2311, allocations: 0 / 434.6 MB, free: 38.54 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.001077/0.2322, allocations: 403.6 kB / 435 MB, free: 38.5 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 0.0004811/0.2327, allocations: 340.6 kB / 435.3 MB, free: 38.4 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.001283/0.234, allocations: 1.128 MB / 436.5 MB, free: 37.92 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.946e-06/0.234, allocations: 0 / 436.5 MB, free: 37.92 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0005324/0.2345, allocations: 0.7381 MB / 437.2 MB, free: 37.52 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006331/0.2351, allocations: 216.6 kB / 437.4 MB, free: 37.46 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 0.002698/0.2378, allocations: 1.843 MB / 439.3 MB, free: 36.52 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001141/0.2379, allocations: 203.8 kB / 439.5 MB, free: 36.44 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 0.0004983/0.2384, allocations: 221.6 kB / 439.7 MB, free: 36.33 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002273/0.2387, allocations: 155.6 kB / 439.8 MB, free: 36.21 MB / 330.7 MB
Notification: Performance of SimCode: time 1.563e-06/0.2387, allocations: 0 / 439.8 MB, free: 36.21 MB / 330.7 MB
Notification: Performance of Templates: time 0.01902/0.2577, allocations: 17.09 MB / 456.9 MB, free: 20.55 MB / 330.7 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: 3.5341672520153224]