Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo", uses=false)
Using package Chemical with version 1.4.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: translateModel(Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001128/0.001128, allocations: 89.66 kB / 15.36 MB, free: 0.7383 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.008135/0.008135, allocations: 174 kB / 16.27 MB, free: 6.613 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.372/1.372, allocations: 223.3 MB / 240.3 MB, free: 5.332 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2037/0.2037, allocations: 15.27 MB / 306.7 MB, free: 15.71 MB / 254.1 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0003017/0.0003017, allocations: 12.28 kB / 372.1 MB, free: 3.617 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2749/0.2752, allocations: 54.62 MB / 426.7 MB, free: 40.39 MB / 350.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:3019:6-3019:65: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 1.4.1-master/package.mo:3019:6-3019:65: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.Examples.ClimateChange.HydrogenotrophicMethanogenesis): time 0.02439/0.2996, allocations: 24.71 MB / 451.4 MB, free: 32.17 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0177/0.3173, allocations: 16.44 MB / 467.9 MB, free: 21.03 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001292/0.3187, allocations: 23.22 kB / 467.9 MB, free: 21.02 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001129/0.3198, allocations: 305.4 kB / 468.2 MB, free: 20.86 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.004661/0.3245, allocations: 1.31 MB / 469.5 MB, free: 20.08 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005529/0.3301, allocations: 1.741 MB / 471.2 MB, free: 19.06 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002025/0.3321, allocations: 1.488 MB / 472.7 MB, free: 18.36 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001012/0.3331, allocations: 0.6989 MB / 473.4 MB, free: 18.05 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001561/0.3347, allocations: 0.7222 MB / 474.2 MB, free: 17.84 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001395/0.3361, allocations: 0.8021 MB / 475 MB, free: 17.55 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0003127/0.3364, allocations: 70.81 kB / 475 MB, free: 17.55 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.005376/0.3418, allocations: 1.725 MB / 476.8 MB, free: 16.19 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0003478/0.3422, allocations: 270.6 kB / 477 MB, free: 15.98 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0007721/0.343, allocations: 0.6359 MB / 477.7 MB, free: 15.39 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.00659/0.3496, allocations: 3.106 MB / 480.8 MB, free: 12.93 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.789e-06/0.3496, allocations: 0 / 480.8 MB, free: 12.93 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.914e-06/0.3496, allocations: 0 / 480.8 MB, free: 12.93 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 5.52e-05/0.3497, allocations: 0 / 480.8 MB, free: 12.93 MB / 350.1 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 0.002896/0.3526, allocations: 1.52 MB / 482.3 MB, free: 11.5 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.602e-05/0.3526, allocations: 12.03 kB / 482.3 MB, free: 11.49 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001151/0.3538, allocations: 277.2 kB / 482.6 MB, free: 11.26 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0008757/0.3547, allocations: 0.622 MB / 483.2 MB, free: 10.69 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 8.86e-05/0.3548, allocations: 109 kB / 483.3 MB, free: 10.57 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002052/0.355, allocations: 121.5 kB / 483.4 MB, free: 10.46 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002054/0.3571, allocations: 1.334 MB / 484.7 MB, free: 9.344 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.552e-05/0.3571, allocations: 0 / 484.7 MB, free: 9.344 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001095/0.3572, allocations: 48 kB / 484.8 MB, free: 9.297 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.65e-05/0.3572, allocations: 24 kB / 484.8 MB, free: 9.273 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002285/0.3595, allocations: 1.696 MB / 486.5 MB, free: 7.809 MB / 350.1 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 0.005851/0.3654, allocations: 4.247 MB / 490.8 MB, free: 4.051 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002927/0.3683, allocations: 2.278 MB / 493 MB, free: 1.898 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0007426/0.3691, allocations: 0.5923 MB / 493.6 MB, free: 1.355 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006801/0.3759, allocations: 5.289 MB / 498.9 MB, free: 12 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.238e-05/0.376, allocations: 39.97 kB / 499 MB, free: 11.95 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=78): time 3.687e-06/0.376, allocations: 7.984 kB / 499 MB, free: 11.95 MB / 366.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01611/0.3921, allocations: 3.597 MB / 0.4908 GB, free: 8.746 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.963e-05/0.3922, allocations: 61.16 kB / 0.4908 GB, free: 8.676 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.001063/0.3932, allocations: 0.5895 MB / 0.4914 GB, free: 8.164 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 0.0001091/0.3934, allocations: 45.7 kB / 0.4915 GB, free: 8.113 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0005215/0.3939, allocations: 0.5304 MB / 0.492 GB, free: 7.625 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003809/0.3943, allocations: 329.7 kB / 0.4923 GB, free: 7.328 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001755/0.3945, allocations: 101.3 kB / 0.4924 GB, free: 7.238 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0002132/0.3947, allocations: 398.3 kB / 0.4928 GB, free: 6.867 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006684/0.3954, allocations: 358.4 kB / 0.4931 GB, free: 6.562 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0009335/0.3963, allocations: 0.7454 MB / 0.4938 GB, free: 5.691 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001824/0.3982, allocations: 1.214 MB / 0.495 GB, free: 4.34 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.135e-05/0.3982, allocations: 3.938 kB / 0.495 GB, free: 4.336 MB / 366.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004382/0.4026, allocations: 1.493 MB / 0.4965 GB, free: 2.824 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.75e-05/0.4026, allocations: 12 kB / 0.4965 GB, free: 2.812 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.012e-05/0.4026, allocations: 12 kB / 0.4965 GB, free: 2.801 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002184/0.4048, allocations: 254.2 kB / 0.4967 GB, free: 2.547 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001467/0.4063, allocations: 331.5 kB / 0.4971 GB, free: 2.223 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.0057/0.412, allocations: 3.511 MB / 0.5005 GB, free: 14.45 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001026/0.4131, allocations: 79.86 kB / 0.5006 GB, free: 14.37 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001486/0.4132, allocations: 67.98 kB / 0.5006 GB, free: 14.3 MB / 382.1 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 0.0005442/0.4138, allocations: 277.3 kB / 0.5009 GB, free: 14.02 MB / 382.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001823/0.414, allocations: 82.97 kB / 0.501 GB, free: 13.94 MB / 382.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004458/0.4185, allocations: 1.348 MB / 0.5023 GB, free: 12.57 MB / 382.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 9.327e-06/0.4185, allocations: 8 kB / 0.5023 GB, free: 12.57 MB / 382.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.285e-06/0.4185, allocations: 4 kB / 0.5023 GB, free: 12.56 MB / 382.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.309e-05/0.4185, allocations: 7.984 kB / 0.5023 GB, free: 12.55 MB / 382.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001591/0.4201, allocations: 1.077 MB / 0.5034 GB, free: 11.41 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 7.744e-06/0.4201, allocations: 0 / 0.5034 GB, free: 11.41 MB / 382.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001229/0.4214, allocations: 219.9 kB / 0.5036 GB, free: 11.19 MB / 382.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.00219/0.4236, allocations: 245.4 kB / 0.5038 GB, free: 10.95 MB / 382.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 9.162e-05/0.4237, allocations: 27.98 kB / 0.5038 GB, free: 10.92 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.005077/0.4288, allocations: 3.421 MB / 0.5072 GB, free: 7.227 MB / 382.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.088e-06/0.4288, allocations: 3.938 kB / 0.5072 GB, free: 7.223 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004678/0.4335, allocations: 1.752 MB / 0.5089 GB, free: 5.434 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002896/0.4338, allocations: 152.3 kB / 0.509 GB, free: 5.266 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001412/0.4339, allocations: 16 kB / 0.5091 GB, free: 5.25 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0006051/0.4346, allocations: 35.97 kB / 0.5091 GB, free: 5.215 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.000207/0.4348, allocations: 92.75 kB / 0.5092 GB, free: 5.121 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.13e-05/0.4349, allocations: 39.98 kB / 0.5092 GB, free: 5.082 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0004795/0.4353, allocations: 387.1 kB / 0.5096 GB, free: 4.711 MB / 382.1 MB
Notification: Performance of sort global known variables: time 1.9e-07/0.4354, allocations: 0 / 0.5096 GB, free: 4.711 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.002032/0.4374, allocations: 0.6675 MB / 0.5102 GB, free: 4.043 MB / 382.1 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 0.001649/0.4391, allocations: 0.8011 MB / 0.511 GB, free: 3.234 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.002351/0.4414, allocations: 1.25 MB / 0.5122 GB, free: 1.961 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 5.5e-06/0.4414, allocations: 4 kB / 0.5122 GB, free: 1.957 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001235/0.4427, allocations: 0.7457 MB / 0.513 GB, free: 1.188 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.00128/0.444, allocations: 184.1 kB / 0.5131 GB, free: 1.008 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003694/0.4477, allocations: 2.524 MB / 0.5156 GB, free: 14.45 MB / 398.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0006259/0.4483, allocations: 1.049 MB / 0.5166 GB, free: 13.37 MB / 398.1 MB
Notification: Performance of simCode: alias equations: time 0.00106/0.4494, allocations: 235.3 kB / 0.5169 GB, free: 13.13 MB / 398.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003775/0.4498, allocations: 156.1 kB / 0.517 GB, free: 12.98 MB / 398.1 MB
Notification: Performance of SimCode: time 6.41e-07/0.4498, allocations: 4 kB / 0.517 GB, free: 12.98 MB / 398.1 MB
Notification: Performance of Templates: time 0.03769/0.4875, allocations: 22.62 MB / 0.5391 GB, free: 6.453 MB / 414.1 MB
make -j1 -f Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile
(rm -f Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1)