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/Chemical 1.4.0-master/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/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/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 Chemical with version 1.4.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/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/Chemical 1.4.0-master/package.mo): time 0.07974/0.07974, allocations: 15.29 MB / 31.09 MB, free: 3.105 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001129/0.001129, allocations: 198.1 kB / 36.14 MB, free: 2.141 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.317/1.317, allocations: 222.9 MB / 264 MB, free: 4.852 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0009775/0.0009778, allocations: 103.2 kB / 318.4 MB, free: 3.426 MB / 250.7 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0009786/0.0009787, allocations: 58.36 kB / 382.7 MB, free: 48.84 MB / 298.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.07618/0.07717, allocations: 53.62 MB / 436.3 MB, free: 1.02 MB / 298.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:4721:7-4721:66: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 1.4.0-master/package.mo:4721:7-4721:66: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 0.02898/0.1062, allocations: 23.3 MB / 459.6 MB, free: 9.816 MB / 330.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01623/0.1224, allocations: 16.48 MB / 476.1 MB, free: 9.277 MB / 346.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000922/0.1234, allocations: 27.81 kB / 476.2 MB, free: 9.25 MB / 346.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.001023/0.1244, allocations: 310 kB / 476.5 MB, free: 8.945 MB / 346.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.003586/0.128, allocations: 1.266 MB / 477.7 MB, free: 7.672 MB / 346.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005111/0.1332, allocations: 1.741 MB / 479.5 MB, free: 5.922 MB / 346.7 MB
Notification: Performance of NFFlatten.flatten: time 0.002086/0.1353, allocations: 1.502 MB / 481 MB, free: 4.414 MB / 346.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0009604/0.1362, allocations: 0.7286 MB / 481.7 MB, free: 3.664 MB / 346.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009801/0.1372, allocations: 0.7597 MB / 482.4 MB, free: 2.902 MB / 346.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0009862/0.1382, allocations: 0.8331 MB / 483.3 MB, free: 2.066 MB / 346.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001837/0.1384, allocations: 88 kB / 483.4 MB, free: 1.98 MB / 346.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.005962/0.1444, allocations: 1.696 MB / 485.1 MB, free: 288 kB / 346.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.00037/0.1448, allocations: 295 kB / 485.4 MB, free: 15.99 MB / 362.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0009734/0.1458, allocations: 0.6415 MB / 486 MB, free: 15.35 MB / 362.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.006003/0.1518, allocations: 3.098 MB / 489.1 MB, free: 12.24 MB / 362.7 MB
Notification: Performance of FrontEnd - DAE generated: time 4.589e-06/0.1518, allocations: 0 / 489.1 MB, free: 12.24 MB / 362.7 MB
Notification: Performance of FrontEnd: time 1.233e-06/0.1518, allocations: 0 / 489.1 MB, free: 12.24 MB / 362.7 MB
Notification: Performance of Transformations before backend: time 4.934e-05/0.1519, allocations: 0 / 489.1 MB, free: 12.24 MB / 362.7 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 0.003521/0.1554, allocations: 1.785 MB / 490.9 MB, free: 10.4 MB / 362.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.739e-05/0.1555, allocations: 8.875 kB / 490.9 MB, free: 10.39 MB / 362.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001159/0.1566, allocations: 263.1 kB / 491.1 MB, free: 10.13 MB / 362.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001064/0.1577, allocations: 0.653 MB / 491.8 MB, free: 9.438 MB / 362.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001156/0.1578, allocations: 124.4 kB / 491.9 MB, free: 9.309 MB / 362.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001893/0.158, allocations: 112.4 kB / 492 MB, free: 9.199 MB / 362.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002049/0.1601, allocations: 1.337 MB / 493.4 MB, free: 7.816 MB / 362.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.963e-05/0.1601, allocations: 0 / 493.4 MB, free: 7.816 MB / 362.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001004/0.1602, allocations: 44 kB / 493.4 MB, free: 7.773 MB / 362.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.886e-05/0.1603, allocations: 28 kB / 493.4 MB, free: 7.746 MB / 362.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002396/0.1627, allocations: 1.691 MB / 495.1 MB, free: 6.047 MB / 362.7 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 0.006283/0.169, allocations: 4.298 MB / 499.4 MB, free: 1.539 MB / 362.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003291/0.1723, allocations: 2.284 MB / 0.4899 GB, free: 15.18 MB / 378.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0008593/0.1731, allocations: 0.5967 MB / 0.4905 GB, free: 14.58 MB / 378.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006756/0.1799, allocations: 5.396 MB / 0.4958 GB, free: 8.551 MB / 378.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.367e-05/0.1799, allocations: 39.22 kB / 0.4958 GB, free: 8.504 MB / 378.7 MB
Notification: Performance of pre-optimization done (n=78): time 2.474e-06/0.18, allocations: 0 / 0.4958 GB, free: 8.504 MB / 378.7 MB
Notification: Performance of matching and sorting (n=95): time 0.0144/0.1944, allocations: 3.573 MB / 0.4993 GB, free: 4.859 MB / 378.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.308e-05/0.1944, allocations: 64.34 kB / 0.4994 GB, free: 4.785 MB / 378.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000717/0.1952, allocations: 0.59 MB / 0.5 GB, free: 4.188 MB / 378.7 MB
Notification: Performance of collectPreVariables (initialization): time 7.003e-05/0.1952, allocations: 37.7 kB / 0.5 GB, free: 4.145 MB / 378.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003242/0.1956, allocations: 0.5295 MB / 0.5005 GB, free: 3.605 MB / 378.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.000273/0.1959, allocations: 335.2 kB / 0.5008 GB, free: 3.273 MB / 378.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003193/0.1962, allocations: 226.8 kB / 0.5011 GB, free: 3.047 MB / 378.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001832/0.1964, allocations: 402.7 kB / 0.5014 GB, free: 2.645 MB / 378.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006447/0.197, allocations: 358.5 kB / 0.5018 GB, free: 2.293 MB / 378.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000871/0.1979, allocations: 0.7401 MB / 0.5025 GB, free: 1.375 MB / 378.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.1754/0.3733, allocations: 1.205 MB / 0.5037 GB, free: 70.1 MB / 378.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.659e-05/0.3734, allocations: 3.5 kB / 0.5037 GB, free: 70.1 MB / 378.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004515/0.3779, allocations: 1.47 MB / 0.5051 GB, free: 70.04 MB / 378.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.59e-05/0.378, allocations: 11.41 kB / 0.5051 GB, free: 70.04 MB / 378.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.993e-05/0.378, allocations: 15.83 kB / 0.5051 GB, free: 70.04 MB / 378.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001888/0.3799, allocations: 246.9 kB / 0.5054 GB, free: 70.02 MB / 378.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001412/0.3813, allocations: 326.2 kB / 0.5057 GB, free: 70.02 MB / 378.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.004417/0.3858, allocations: 3.482 MB / 0.5091 GB, free: 67.36 MB / 378.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0009385/0.3867, allocations: 73.05 kB / 0.5092 GB, free: 67.36 MB / 378.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001619/0.3869, allocations: 69.83 kB / 0.5092 GB, free: 67.36 MB / 378.7 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 0.0004538/0.3874, allocations: 277 kB / 0.5095 GB, free: 67.25 MB / 378.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002071/0.3876, allocations: 85.8 kB / 0.5096 GB, free: 67.25 MB / 378.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004051/0.3916, allocations: 1.334 MB / 0.5109 GB, free: 67.15 MB / 378.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.277e-05/0.3917, allocations: 9.344 kB / 0.5109 GB, free: 67.15 MB / 378.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.706e-06/0.3917, allocations: 3.781 kB / 0.5109 GB, free: 67.15 MB / 378.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.237e-05/0.3917, allocations: 4.922 kB / 0.5109 GB, free: 67.15 MB / 378.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001572/0.3933, allocations: 1.061 MB / 0.5119 GB, free: 66.88 MB / 378.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.474e-05/0.3933, allocations: 5 kB / 0.5119 GB, free: 66.88 MB / 378.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00119/0.3945, allocations: 219.9 kB / 0.5121 GB, free: 66.86 MB / 378.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001829/0.3963, allocations: 233.4 kB / 0.5124 GB, free: 66.85 MB / 378.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 9.472e-05/0.3965, allocations: 30.47 kB / 0.5124 GB, free: 66.85 MB / 378.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004038/0.4005, allocations: 3.399 MB / 0.5157 GB, free: 64.18 MB / 378.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.226e-06/0.4005, allocations: 5.062 kB / 0.5157 GB, free: 64.18 MB / 378.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.02152/0.422, allocations: 8.353 MB / 0.5239 GB, free: 60.76 MB / 378.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0003693/0.4225, allocations: 150.9 kB / 0.524 GB, free: 60.62 MB / 378.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0003317/0.4228, allocations: 22.47 kB / 0.524 GB, free: 60.6 MB / 378.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0008081/0.4236, allocations: 45.33 kB / 0.5241 GB, free: 60.58 MB / 378.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0003513/0.424, allocations: 80.12 kB / 0.5242 GB, free: 60.57 MB / 378.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001565/0.4242, allocations: 38.67 kB / 0.5242 GB, free: 60.56 MB / 378.7 MB
Notification: Performance of sorting global known variables: time 0.0007317/0.4249, allocations: 392.6 kB / 0.5246 GB, free: 60.39 MB / 378.7 MB
Notification: Performance of sort global known variables: time 2.1e-07/0.4249, allocations: 2.656 kB / 0.5246 GB, free: 60.39 MB / 378.7 MB
Notification: Performance of remove unused functions: time 0.003376/0.4283, allocations: 0.7773 MB / 0.5253 GB, free: 60.3 MB / 378.7 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 0.001974/0.4303, allocations: 0.7765 MB / 0.5261 GB, free: 60.15 MB / 378.7 MB
Notification: Performance of simCode: created initialization part: time 0.00257/0.4329, allocations: 1.253 MB / 0.5273 GB, free: 59.57 MB / 378.7 MB
Notification: Performance of simCode: created event and clocks part: time 4.538e-06/0.4329, allocations: 0 / 0.5273 GB, free: 59.57 MB / 378.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.001173/0.4341, allocations: 0.7436 MB / 0.528 GB, free: 59.16 MB / 378.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001077/0.4352, allocations: 190.4 kB / 0.5282 GB, free: 59.09 MB / 378.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.004667/0.4399, allocations: 3.128 MB / 0.5313 GB, free: 57.15 MB / 378.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0006453/0.4405, allocations: 1.064 MB / 0.5323 GB, free: 56.44 MB / 378.7 MB
Notification: Performance of simCode: alias equations: time 0.001243/0.4418, allocations: 244.1 kB / 0.5326 GB, free: 56.43 MB / 378.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003867/0.4422, allocations: 165.4 kB / 0.5327 GB, free: 56.41 MB / 378.7 MB
Notification: Performance of SimCode: time 4.81e-07/0.4422, allocations: 0 / 0.5327 GB, free: 56.41 MB / 378.7 MB
Notification: Performance of Templates: time 0.03065/0.4728, allocations: 25.55 MB / 0.5577 GB, free: 35.52 MB / 378.7 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)