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 0.0008668/0.0008668, allocations: 69.89 kB / 20.65 MB, free: 3.852 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 0.0009157/0.0009157, allocations: 173 kB / 24.06 MB, free: 456 kB / 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 0.9353/0.9353, allocations: 177.1 MB / 204.5 MB, free: 5.531 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 0.0924/0.0924, allocations: 17.46 MB / 278.5 MB, free: 11.44 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 1.452e-06/1.452e-06, allocations: 0 / 354.8 MB, free: 10.48 MB / 330.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.64e-05/1.785e-05, allocations: 2.312 kB / 354.8 MB, free: 10.48 MB / 330.7 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 0.02932/0.02934, allocations: 29.18 MB / 384 MB, free: 13.39 MB / 362.7 MB
Notification: Performance of NFInst.instExpressions: time 0.00739/0.03673, allocations: 6.184 MB / 390.2 MB, free: 7.184 MB / 362.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003921/0.03712, allocations: 23.81 kB / 390.2 MB, free: 7.16 MB / 362.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0004636/0.03759, allocations: 190.2 kB / 390.4 MB, free: 6.973 MB / 362.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.00151/0.0391, allocations: 0.8533 MB / 391.2 MB, free: 6.113 MB / 362.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.001495/0.04059, allocations: 0.8478 MB / 392.1 MB, free: 5.262 MB / 362.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001354/0.04194, allocations: 1.602 MB / 393.7 MB, free: 3.652 MB / 362.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0007387/0.04268, allocations: 0.731 MB / 394.4 MB, free: 2.902 MB / 362.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009717/0.04365, allocations: 1.076 MB / 395.5 MB, free: 1.824 MB / 362.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0008215/0.04448, allocations: 0.7172 MB / 396.2 MB, free: 1.105 MB / 362.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001593/0.04464, allocations: 132 kB / 396.3 MB, free: 0.9766 MB / 362.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0009534/0.04559, allocations: 0.5889 MB / 396.9 MB, free: 396 kB / 362.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002503/0.04584, allocations: 334.9 kB / 397.2 MB, free: 60 kB / 362.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0004664/0.04631, allocations: 0.4991 MB / 397.7 MB, free: 15.55 MB / 378.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.001746/0.04805, allocations: 1.716 MB / 399.5 MB, free: 13.83 MB / 378.7 MB
Notification: Performance of FrontEnd - DAE generated: time 4.379e-06/0.04806, allocations: 0 / 399.5 MB, free: 13.83 MB / 378.7 MB
Notification: Performance of FrontEnd: time 1.172e-06/0.04806, allocations: 4 kB / 399.5 MB, free: 13.83 MB / 378.7 MB
Notification: Performance of Transformations before backend: time 1.135e-05/0.04807, allocations: 0 / 399.5 MB, free: 13.83 MB / 378.7 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 0.002046/0.05011, allocations: 1.641 MB / 401.1 MB, free: 12.14 MB / 378.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.291e-05/0.05015, allocations: 12.03 kB / 401.1 MB, free: 12.13 MB / 378.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001043/0.05119, allocations: 446.5 kB / 401.5 MB, free: 11.7 MB / 378.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0008056/0.052, allocations: 0.6186 MB / 402.2 MB, free: 11.05 MB / 378.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001162/0.05211, allocations: 138.1 kB / 402.3 MB, free: 10.9 MB / 378.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001668/0.05228, allocations: 112.3 kB / 402.4 MB, free: 10.79 MB / 378.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001238/0.05352, allocations: 0.9702 MB / 403.4 MB, free: 9.766 MB / 378.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.236e-05/0.05354, allocations: 4.172 kB / 403.4 MB, free: 9.762 MB / 378.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 9.88e-05/0.05364, allocations: 48.12 kB / 403.4 MB, free: 9.715 MB / 378.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.033e-05/0.05366, allocations: 28 kB / 403.5 MB, free: 9.688 MB / 378.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001291/0.05495, allocations: 0.9558 MB / 404.4 MB, free: 8.711 MB / 378.7 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 0.004281/0.05923, allocations: 3.215 MB / 407.6 MB, free: 5.41 MB / 378.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002694/0.06192, allocations: 1.985 MB / 409.6 MB, free: 3.422 MB / 378.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004085/0.06233, allocations: 313.5 kB / 409.9 MB, free: 3.109 MB / 378.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.003233/0.06556, allocations: 2.214 MB / 412.1 MB, free: 0.8711 MB / 378.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.088e-05/0.0656, allocations: 50.05 kB / 412.2 MB, free: 0.8125 MB / 378.7 MB
Notification: Performance of pre-optimization done (n=78): time 2.094e-06/0.0656, allocations: 0 / 412.2 MB, free: 0.8125 MB / 378.7 MB
Notification: Performance of matching and sorting (n=95): time 0.0072/0.0728, allocations: 2.678 MB / 414.9 MB, free: 14.09 MB / 394.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.589e-05/0.07284, allocations: 64.41 kB / 414.9 MB, free: 14.02 MB / 394.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004375/0.07328, allocations: 0.6042 MB / 415.5 MB, free: 13.4 MB / 394.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.841e-05/0.07333, allocations: 37.7 kB / 415.6 MB, free: 13.36 MB / 394.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.000317/0.07365, allocations: 0.604 MB / 416.2 MB, free: 12.74 MB / 394.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002031/0.07385, allocations: 345 kB / 416.5 MB, free: 12.4 MB / 394.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002264/0.07408, allocations: 240.4 kB / 416.7 MB, free: 12.16 MB / 394.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001779/0.07425, allocations: 0.5741 MB / 417.3 MB, free: 11.57 MB / 394.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002072/0.07446, allocations: 174.5 kB / 417.5 MB, free: 11.4 MB / 394.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004749/0.07494, allocations: 0.7437 MB / 418.2 MB, free: 10.41 MB / 394.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0007441/0.07568, allocations: 1.024 MB / 419.3 MB, free: 9.148 MB / 394.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.079e-06/0.07568, allocations: 4 kB / 419.3 MB, free: 9.145 MB / 394.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.001752/0.07744, allocations: 1.148 MB / 420.4 MB, free: 7.977 MB / 394.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.376e-05/0.07746, allocations: 18.48 kB / 420.4 MB, free: 7.961 MB / 394.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.396e-05/0.07747, allocations: 12.84 kB / 420.4 MB, free: 7.949 MB / 394.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001327/0.0788, allocations: 350.9 kB / 420.8 MB, free: 7.598 MB / 394.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006995/0.0795, allocations: 327.5 kB / 421.1 MB, free: 7.277 MB / 394.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002934/0.08243, allocations: 4.312 MB / 425.4 MB, free: 2.746 MB / 394.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000333/0.08277, allocations: 40 kB / 425.4 MB, free: 2.707 MB / 394.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.563e-05/0.08283, allocations: 59.98 kB / 425.5 MB, free: 2.648 MB / 394.7 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 0.0002143/0.08305, allocations: 236.2 kB / 425.7 MB, free: 2.406 MB / 394.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001306/0.08318, allocations: 123.4 kB / 425.9 MB, free: 2.285 MB / 394.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.00169/0.08487, allocations: 1.025 MB / 426.9 MB, free: 1.242 MB / 394.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.64e-06/0.08487, allocations: 8 kB / 426.9 MB, free: 1.234 MB / 394.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.865e-06/0.08488, allocations: 0 / 426.9 MB, free: 1.234 MB / 394.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.115e-06/0.08489, allocations: 7.984 kB / 426.9 MB, free: 1.227 MB / 394.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006998/0.08558, allocations: 0.7481 MB / 427.6 MB, free: 428 kB / 394.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.027e-06/0.08559, allocations: 4.125 kB / 427.7 MB, free: 424 kB / 394.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005555/0.08614, allocations: 219.7 kB / 427.9 MB, free: 204 kB / 394.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001265/0.08741, allocations: 327 kB / 428.2 MB, free: 15.87 MB / 410.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.579e-05/0.08746, allocations: 35.92 kB / 428.2 MB, free: 15.84 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002533/0.08999, allocations: 4.217 MB / 432.4 MB, free: 11.39 MB / 410.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.292e-06/0.08999, allocations: 0 / 432.4 MB, free: 11.39 MB / 410.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001763/0.09175, allocations: 1.253 MB / 433.7 MB, free: 10.1 MB / 410.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 8.337e-05/0.09184, allocations: 83.31 kB / 433.8 MB, free: 10.02 MB / 410.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 7.296e-05/0.09191, allocations: 23.98 kB / 433.8 MB, free: 9.992 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002212/0.09213, allocations: 24 kB / 433.8 MB, free: 9.969 MB / 410.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001117/0.09224, allocations: 84.8 kB / 433.9 MB, free: 9.883 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.085e-05/0.09228, allocations: 27.98 kB / 433.9 MB, free: 9.855 MB / 410.7 MB
Notification: Performance of sorting global known variables: time 0.0001871/0.09247, allocations: 346.9 kB / 434.3 MB, free: 9.523 MB / 410.7 MB
Notification: Performance of sort global known variables: time 7e-08/0.09247, allocations: 0 / 434.3 MB, free: 9.523 MB / 410.7 MB
Notification: Performance of remove unused functions: time 0.000888/0.09336, allocations: 407.5 kB / 434.7 MB, free: 9.125 MB / 410.7 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 0.0004177/0.09378, allocations: 338.5 kB / 435 MB, free: 8.781 MB / 410.7 MB
Notification: Performance of simCode: created initialization part: time 0.0008968/0.09467, allocations: 1.041 MB / 436 MB, free: 7.711 MB / 410.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.944e-06/0.09467, allocations: 3.938 kB / 436 MB, free: 7.707 MB / 410.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0005472/0.09522, allocations: 0.694 MB / 436.7 MB, free: 6.973 MB / 410.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006228/0.09584, allocations: 231.1 kB / 437 MB, free: 6.75 MB / 410.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00235/0.09819, allocations: 1.809 MB / 438.8 MB, free: 4.879 MB / 410.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001344/0.09833, allocations: 197 kB / 439 MB, free: 4.668 MB / 410.7 MB
Notification: Performance of simCode: alias equations: time 0.0004664/0.0988, allocations: 214.4 kB / 439.2 MB, free: 4.457 MB / 410.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0004584/0.09925, allocations: 364.8 kB / 439.5 MB, free: 4.102 MB / 410.7 MB
Notification: Performance of SimCode: time 7.62e-07/0.09925, allocations: 0 / 439.5 MB, free: 4.102 MB / 410.7 MB
Notification: Performance of Templates: time 0.1412/0.2405, allocations: 19.64 MB / 459.2 MB, free: 107 MB / 410.7 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: 3.5594594748690724]