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 0.002007/0.002007, allocations: 78.48 kB / 19.18 MB, free: 2.527 MB / 14.72 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 0.002305/0.002305, allocations: 168.5 kB / 22.46 MB, free: 5.359 MB / 14.72 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 1.462/1.462, allocations: 177.1 MB / 202.8 MB, free: 9.176 MB / 190.1 MB
"
[Timeout remaining time 178]
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 0.1281/0.1281, allocations: 17.45 MB / 276.6 MB, free: 15.21 MB / 270.1 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 3.988e-06/3.988e-06, allocations: 4 kB / 412.1 MB, free: 4.273 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.481e-05/2.88e-05, allocations: 2.281 kB / 412.1 MB, free: 4.27 MB / 334.1 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 0.03673/0.03676, allocations: 26.49 MB / 438.6 MB, free: 9.914 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.2386/0.2753, allocations: 14.7 MB / 453.3 MB, free: 31.38 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001171/0.2765, allocations: 17.97 kB / 453.3 MB, free: 31.38 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001178/0.2777, allocations: 315.3 kB / 453.6 MB, free: 31.37 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.006151/0.2838, allocations: 1.522 MB / 455.2 MB, free: 31.03 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.007626/0.2914, allocations: 2.077 MB / 457.2 MB, free: 30.46 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.003147/0.2946, allocations: 1.6 MB / 458.8 MB, free: 30.06 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001344/0.2959, allocations: 0.6966 MB / 459.5 MB, free: 29.88 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001637/0.2976, allocations: 1.068 MB / 460.6 MB, free: 29.52 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001452/0.299, allocations: 0.7022 MB / 461.3 MB, free: 29.39 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002769/0.2993, allocations: 135.3 kB / 461.4 MB, free: 29.39 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.007083/0.3064, allocations: 1.707 MB / 463.1 MB, free: 29.04 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0005403/0.3069, allocations: 338.9 kB / 463.5 MB, free: 28.86 MB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.001209/0.3081, allocations: 0.4987 MB / 464 MB, free: 28.67 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.009472/0.3176, allocations: 3.653 MB / 467.6 MB, free: 27.4 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.661e-06/0.3176, allocations: 0 / 467.6 MB, free: 27.4 MB / 366.1 MB
Notification: Performance of FrontEnd: time 1.472e-06/0.3176, allocations: 3.812 kB / 467.6 MB, free: 27.4 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 3.175e-05/0.3176, allocations: 0 / 467.6 MB, free: 27.4 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 0.003934/0.3216, allocations: 1.763 MB / 469.4 MB, free: 26.36 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.352e-05/0.3216, allocations: 9.719 kB / 469.4 MB, free: 26.36 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001349/0.323, allocations: 273.2 kB / 469.7 MB, free: 26.27 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001115/0.3241, allocations: 0.6079 MB / 470.3 MB, free: 25.91 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001086/0.3242, allocations: 138.2 kB / 470.4 MB, free: 25.8 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000185/0.3244, allocations: 112.5 kB / 470.5 MB, free: 25.77 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001978/0.3264, allocations: 1.339 MB / 471.9 MB, free: 24.98 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.563e-05/0.3264, allocations: 192 / 471.9 MB, free: 24.98 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001147/0.3265, allocations: 43.16 kB / 471.9 MB, free: 24.95 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.541e-05/0.3265, allocations: 32.7 kB / 471.9 MB, free: 24.94 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002465/0.329, allocations: 1.674 MB / 473.6 MB, free: 24.21 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 0.005694/0.3347, allocations: 3.382 MB / 477 MB, free: 21.95 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003035/0.3377, allocations: 1.873 MB / 478.9 MB, free: 21.06 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0006658/0.3384, allocations: 0.5299 MB / 479.4 MB, free: 20.53 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.005486/0.3439, allocations: 2.802 MB / 482.2 MB, free: 17.77 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.766e-05/0.3439, allocations: 43.22 kB / 482.2 MB, free: 17.71 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=78): time 4.007e-06/0.3439, allocations: 2.859 kB / 482.2 MB, free: 17.71 MB / 366.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01407/0.358, allocations: 3.421 MB / 485.7 MB, free: 14.3 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.461e-05/0.358, allocations: 64.41 kB / 485.7 MB, free: 14.22 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0005478/0.3586, allocations: 0.5728 MB / 486.3 MB, free: 13.64 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 7.301e-05/0.3586, allocations: 45.64 kB / 486.3 MB, free: 13.59 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002083/0.3588, allocations: 0.5516 MB / 486.9 MB, free: 13.04 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002048/0.3591, allocations: 343 kB / 487.2 MB, free: 12.7 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002887/0.3593, allocations: 237.5 kB / 487.5 MB, free: 12.47 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 9.461e-05/0.3594, allocations: 390.8 kB / 487.8 MB, free: 12.08 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005268/0.36, allocations: 358.4 kB / 488.2 MB, free: 11.73 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0006711/0.3606, allocations: 0.7516 MB / 488.9 MB, free: 10.8 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001307/0.3619, allocations: 1.2 MB / 490.1 MB, free: 9.445 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.881e-06/0.3619, allocations: 4 kB / 490.1 MB, free: 9.441 MB / 366.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.003707/0.3657, allocations: 1.469 MB / 491.6 MB, free: 7.969 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.377e-05/0.3657, allocations: 10.66 kB / 491.6 MB, free: 7.961 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.619e-05/0.3657, allocations: 22.62 kB / 491.6 MB, free: 7.941 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001918/0.3676, allocations: 241.8 kB / 491.9 MB, free: 7.707 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001416/0.369, allocations: 330.1 kB / 492.2 MB, free: 7.387 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.004623/0.3737, allocations: 3.583 MB / 495.8 MB, free: 3.621 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00112/0.3748, allocations: 42.77 kB / 495.8 MB, free: 3.582 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001158/0.3749, allocations: 63.98 kB / 495.9 MB, free: 3.52 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 0.0005332/0.3754, allocations: 277.3 kB / 496.2 MB, free: 3.238 MB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001855/0.3756, allocations: 86.14 kB / 496.2 MB, free: 3.156 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.003647/0.3793, allocations: 1.327 MB / 497.6 MB, free: 1.855 MB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.078e-05/0.3793, allocations: 14.62 kB / 497.6 MB, free: 1.844 MB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.012e-06/0.3793, allocations: 0 / 497.6 MB, free: 1.844 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.222e-05/0.3793, allocations: 3.984 kB / 497.6 MB, free: 1.84 MB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001221/0.3805, allocations: 0.7988 MB / 498.4 MB, free: 1.023 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.7e-06/0.3805, allocations: 0 / 498.4 MB, free: 1.023 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001167/0.3817, allocations: 215.8 kB / 498.6 MB, free: 0.8125 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001841/0.3835, allocations: 225.5 kB / 498.8 MB, free: 0.5938 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 8.237e-05/0.3836, allocations: 31.98 kB / 498.9 MB, free: 0.5625 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.005238/0.3888, allocations: 3.485 MB / 0.4906 GB, free: 12.89 MB / 382.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.488e-06/0.3888, allocations: 3.938 kB / 0.4906 GB, free: 12.89 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004776/0.3936, allocations: 1.737 MB / 0.4923 GB, free: 11.12 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002949/0.3939, allocations: 78.08 kB / 0.4923 GB, free: 11.05 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001301/0.394, allocations: 20.06 kB / 0.4924 GB, free: 11.03 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000541/0.3946, allocations: 20 kB / 0.4924 GB, free: 11.01 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002471/0.3948, allocations: 92.72 kB / 0.4925 GB, free: 10.92 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001116/0.3949, allocations: 39.98 kB / 0.4925 GB, free: 10.88 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0004844/0.3954, allocations: 363.1 kB / 0.4928 GB, free: 10.53 MB / 382.1 MB
Notification: Performance of sort global known variables: time 1e-07/0.3954, allocations: 0 / 0.4928 GB, free: 10.53 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.002462/0.3979, allocations: 0.6766 MB / 0.4935 GB, free: 9.852 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 0.001947/0.3998, allocations: 0.8581 MB / 0.4943 GB, free: 9.117 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.002444/0.4023, allocations: 1.19 MB / 0.4955 GB, free: 7.914 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.257e-06/0.4023, allocations: 0 / 0.4955 GB, free: 7.914 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001204/0.4035, allocations: 0.7006 MB / 0.4962 GB, free: 7.191 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001166/0.4047, allocations: 208.6 kB / 0.4964 GB, free: 7.016 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003554/0.4082, allocations: 1.898 MB / 0.4982 GB, free: 5.109 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004843/0.4087, allocations: 456.8 kB / 0.4987 GB, free: 4.648 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.0008094/0.4095, allocations: 221 kB / 0.4989 GB, free: 4.504 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003782/0.4099, allocations: 156.2 kB / 0.499 GB, free: 4.359 MB / 382.1 MB
Notification: Performance of SimCode: time 8.02e-07/0.4099, allocations: 0 / 0.499 GB, free: 4.359 MB / 382.1 MB
Notification: Performance of Templates: time 0.04236/0.4522, allocations: 23.96 MB / 0.5224 GB, free: 13.31 MB / 414.1 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=480 -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 5.7520542293787]
Failed to read output from testmodel.py, exit status != 0:
0.4620233289897442 0.47705152799999995 0.15610909499999995
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7fecff7dd1e0>