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 0.001212/0.001212, allocations: 108 kB / 15.6 MB, free: 132 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001167/0.001167, allocations: 193.5 kB / 16.53 MB, free: 6.391 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.183/1.183, allocations: 222.9 MB / 240.2 MB, free: 4.402 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.1702/0.1702, allocations: 15.32 MB / 305.7 MB, free: 15.23 MB / 254.1 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.00115/0.00115, allocations: 63.89 kB / 370.3 MB, free: 3.949 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.08858/0.08975, allocations: 53.6 MB / 423.9 MB, free: 14.3 MB / 366.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:4740:7-4740:66: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 1.4.1-master/package.mo:4740:7-4740:66: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.Examples.ClimateChange.HydrogenotrophicMethanogenesis): time 0.2976/0.3874, allocations: 25.4 MB / 449.3 MB, free: 39.37 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.012/0.3994, allocations: 16.66 MB / 466 MB, free: 30.77 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0006021/0.4, allocations: 13.41 kB / 466 MB, free: 30.77 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.000682/0.4007, allocations: 331.2 kB / 466.3 MB, free: 30.59 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.003021/0.4038, allocations: 1.473 MB / 467.8 MB, free: 29.79 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004275/0.408, allocations: 1.99 MB / 469.8 MB, free: 28.85 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0014/0.4095, allocations: 1.532 MB / 471.3 MB, free: 28.11 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0008897/0.4104, allocations: 0.8556 MB / 472.2 MB, free: 27.72 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009531/0.4113, allocations: 0.7676 MB / 473 MB, free: 27.45 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001306/0.4126, allocations: 0.8506 MB / 473.8 MB, free: 27.1 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0003479/0.413, allocations: 134.5 kB / 473.9 MB, free: 27.1 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004727/0.4177, allocations: 1.782 MB / 475.7 MB, free: 26.66 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0004279/0.4182, allocations: 329.2 kB / 476 MB, free: 26.46 MB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.001059/0.4192, allocations: 0.6794 MB / 476.7 MB, free: 26.06 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.006426/0.4257, allocations: 3.318 MB / 480 MB, free: 24.61 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.14e-06/0.4257, allocations: 0 / 480 MB, free: 24.61 MB / 366.1 MB
Notification: Performance of FrontEnd: time 1.423e-06/0.4257, allocations: 0 / 480 MB, free: 24.61 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 4.39e-05/0.4258, allocations: 1.156 kB / 480 MB, free: 24.61 MB / 366.1 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 0.003593/0.4294, allocations: 1.81 MB / 481.9 MB, free: 23.5 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.302e-05/0.4294, allocations: 9.312 kB / 481.9 MB, free: 23.5 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001194/0.4306, allocations: 275.1 kB / 482.1 MB, free: 23.42 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0009302/0.4315, allocations: 0.6494 MB / 482.8 MB, free: 22.98 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 9.398e-05/0.4316, allocations: 111 kB / 482.9 MB, free: 22.91 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.00018/0.4318, allocations: 117.4 kB / 483 MB, free: 22.86 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001805/0.4336, allocations: 1.332 MB / 484.3 MB, free: 22.32 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.979e-05/0.4337, allocations: 1.281 kB / 484.3 MB, free: 22.32 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001018/0.4338, allocations: 48.19 kB / 484.4 MB, free: 22.28 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.932e-05/0.4338, allocations: 30.03 kB / 484.4 MB, free: 22.28 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0023/0.4361, allocations: 1.689 MB / 486.1 MB, free: 21.79 MB / 366.1 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 0.005656/0.4418, allocations: 4.309 MB / 490.4 MB, free: 19.19 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003052/0.4448, allocations: 2.28 MB / 492.7 MB, free: 18.17 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0006729/0.4455, allocations: 0.5963 MB / 493.3 MB, free: 17.92 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.005179/0.4507, allocations: 5.402 MB / 498.7 MB, free: 13.66 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.611e-05/0.4507, allocations: 39.47 kB / 498.7 MB, free: 13.61 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.074e-06/0.4507, allocations: 0 / 498.7 MB, free: 13.61 MB / 366.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01248/0.4632, allocations: 3.564 MB / 0.4905 GB, free: 12.09 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.006e-05/0.4633, allocations: 66.75 kB / 0.4906 GB, free: 12.03 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0006006/0.4639, allocations: 0.5864 MB / 0.4912 GB, free: 11.75 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 6.135e-05/0.464, allocations: 41.86 kB / 0.4912 GB, free: 11.71 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002107/0.4642, allocations: 0.53 MB / 0.4917 GB, free: 11.28 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001893/0.4644, allocations: 340.9 kB / 0.492 GB, free: 11.02 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002517/0.4646, allocations: 230.3 kB / 0.4923 GB, free: 10.91 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 9.144e-05/0.4647, allocations: 395.8 kB / 0.4926 GB, free: 10.55 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000508/0.4652, allocations: 357.7 kB / 0.493 GB, free: 10.43 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0006346/0.4659, allocations: 0.7524 MB / 0.4937 GB, free: 9.781 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001168/0.4671, allocations: 1.202 MB / 0.4949 GB, free: 8.867 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.511e-06/0.4671, allocations: 3.5 kB / 0.4949 GB, free: 8.867 MB / 366.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.003358/0.4704, allocations: 1.472 MB / 0.4963 GB, free: 8.277 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.761e-05/0.4705, allocations: 10.62 kB / 0.4963 GB, free: 8.277 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.254e-05/0.4705, allocations: 14.5 kB / 0.4963 GB, free: 8.277 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001719/0.4722, allocations: 241.8 kB / 0.4966 GB, free: 8.227 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001244/0.4735, allocations: 326.1 kB / 0.4969 GB, free: 8.195 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.00412/0.4776, allocations: 3.865 MB / 0.5007 GB, free: 4.734 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0007442/0.4783, allocations: 40.73 kB / 0.5007 GB, free: 4.715 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001038/0.4785, allocations: 69.19 kB / 0.5008 GB, free: 4.703 MB / 366.1 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 0.0003606/0.4788, allocations: 273.6 kB / 0.501 GB, free: 4.484 MB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000169/0.479, allocations: 86.88 kB / 0.5011 GB, free: 4.438 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.003512/0.4825, allocations: 1.344 MB / 0.5024 GB, free: 3.328 MB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.863e-06/0.4825, allocations: 11.94 kB / 0.5024 GB, free: 3.316 MB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.023e-06/0.4826, allocations: 4 kB / 0.5024 GB, free: 3.312 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.105e-05/0.4826, allocations: 9.375 kB / 0.5025 GB, free: 3.309 MB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001161/0.4837, allocations: 1.065 MB / 0.5035 GB, free: 2.383 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.25e-06/0.4837, allocations: 0 / 0.5035 GB, free: 2.383 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001038/0.4848, allocations: 219.3 kB / 0.5037 GB, free: 2.199 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001652/0.4865, allocations: 233.8 kB / 0.5039 GB, free: 2.031 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 6.938e-05/0.4865, allocations: 30.81 kB / 0.504 GB, free: 2.004 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.003982/0.4905, allocations: 3.765 MB / 0.5076 GB, free: 14.13 MB / 382.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.823e-06/0.4905, allocations: 4.062 kB / 0.5076 GB, free: 14.12 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00382/0.4944, allocations: 1.745 MB / 0.5093 GB, free: 12.37 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001868/0.4946, allocations: 144.1 kB / 0.5095 GB, free: 12.21 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001224/0.4947, allocations: 28.19 kB / 0.5095 GB, free: 12.18 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0004757/0.4952, allocations: 19.98 kB / 0.5095 GB, free: 12.16 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001781/0.4954, allocations: 80.89 kB / 0.5096 GB, free: 12.08 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.08e-05/0.4954, allocations: 43.92 kB / 0.5096 GB, free: 12.04 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0004259/0.4959, allocations: 391.1 kB / 0.51 GB, free: 11.66 MB / 382.1 MB
Notification: Performance of sort global known variables: time 1.1e-07/0.4959, allocations: 0 / 0.51 GB, free: 11.66 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.00189/0.4978, allocations: 0.6714 MB / 0.5107 GB, free: 10.98 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 0.001471/0.4993, allocations: 0.801 MB / 0.5115 GB, free: 10.17 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.002407/0.5017, allocations: 1.321 MB / 0.5127 GB, free: 8.832 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.807e-06/0.5017, allocations: 4.125 kB / 0.5127 GB, free: 8.828 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0009709/0.5027, allocations: 0.741 MB / 0.5135 GB, free: 8.062 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0008877/0.5036, allocations: 207.8 kB / 0.5137 GB, free: 7.867 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002916/0.5065, allocations: 1.992 MB / 0.5156 GB, free: 5.82 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005357/0.507, allocations: 1.034 MB / 0.5166 GB, free: 4.762 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.0008664/0.5079, allocations: 231.2 kB / 0.5168 GB, free: 4.531 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003008/0.5082, allocations: 161.8 kB / 0.517 GB, free: 4.379 MB / 382.1 MB
Notification: Performance of SimCode: time 2.41e-07/0.5082, allocations: 0 / 0.517 GB, free: 4.379 MB / 382.1 MB
Notification: Performance of Templates: time 0.03094/0.5392, allocations: 23.44 MB / 0.5399 GB, free: 13.03 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)