Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_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 0.001393/0.001393, allocations: 92.42 kB / 19.7 MB, free: 2.137 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 0.001556/0.001556, allocations: 207.2 kB / 22.99 MB, free: 4.953 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 1.48/1.48, allocations: 230.6 MB / 256.8 MB, free: 7.816 MB / 206.1 MB
"
[Timeout remaining time 178]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo): time 0.1484/0.1484, allocations: 23.88 MB / 337.1 MB, free: 10.99 MB / 270.1 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/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_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis") [Timeout 660]
"Notification: Chemical requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed.
Notification: Performance of FrontEnd - loaded program: time 0.002056/0.002056, allocations: 71.89 kB / 472.4 MB, free: 7.027 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3218/0.3239, allocations: 59.86 MB / 0.5198 GB, free: 9.812 MB / 382.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/Obsolete.mo:14337:7-14337:66: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 2.0.0/Obsolete.mo:14337:7-14337:66: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 0.07263/0.3965, allocations: 26.13 MB / 0.5453 GB, free: 13.52 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02165/0.4182, allocations: 14.7 MB / 0.5596 GB, free: 156 kB / 398.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001373/0.4196, allocations: 19.81 kB / 0.5597 GB, free: 136 kB / 398.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001263/0.4208, allocations: 308.4 kB / 0.5599 GB, free: 15.9 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.005569/0.4264, allocations: 1.472 MB / 0.5614 GB, free: 14.66 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.006545/0.4329, allocations: 2.019 MB / 0.5634 GB, free: 13 MB / 414.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002906/0.4358, allocations: 1.55 MB / 0.5649 GB, free: 11.6 MB / 414.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001331/0.4372, allocations: 0.7013 MB / 0.5656 GB, free: 10.98 MB / 414.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001178/0.4384, allocations: 0.7871 MB / 0.5663 GB, free: 10.19 MB / 414.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001421/0.4398, allocations: 0.8645 MB / 0.5672 GB, free: 9.32 MB / 414.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002722/0.44, allocations: 132 kB / 0.5673 GB, free: 9.191 MB / 414.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.005688/0.4457, allocations: 1.743 MB / 0.569 GB, free: 7.445 MB / 414.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0005613/0.4463, allocations: 339 kB / 0.5693 GB, free: 7.113 MB / 414.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0009003/0.4472, allocations: 0.5719 MB / 0.5699 GB, free: 6.539 MB / 414.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.008843/0.456, allocations: 3.44 MB / 0.5732 GB, free: 3.086 MB / 414.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.572e-06/0.456, allocations: 0 / 0.5732 GB, free: 3.086 MB / 414.1 MB
Notification: Performance of FrontEnd: time 1.713e-06/0.456, allocations: 0 / 0.5732 GB, free: 3.086 MB / 414.1 MB
Notification: Performance of Transformations before backend: time 3.545e-05/0.4561, allocations: 0 / 0.5732 GB, free: 3.086 MB / 414.1 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 0.003779/0.4599, allocations: 1.78 MB / 0.575 GB, free: 1.266 MB / 414.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.85e-05/0.4599, allocations: 8.031 kB / 0.575 GB, free: 1.258 MB / 414.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001233/0.4611, allocations: 279.5 kB / 0.5753 GB, free: 0.9844 MB / 414.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001291/0.4624, allocations: 0.6087 MB / 0.5758 GB, free: 360 kB / 414.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001433/0.4626, allocations: 142.1 kB / 0.576 GB, free: 204 kB / 414.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002224/0.4628, allocations: 124.3 kB / 0.5761 GB, free: 80 kB / 414.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002275/0.4651, allocations: 1.329 MB / 0.5774 GB, free: 14.7 MB / 430.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.976e-05/0.4651, allocations: 3.984 kB / 0.5774 GB, free: 14.7 MB / 430.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001156/0.4652, allocations: 47.94 kB / 0.5774 GB, free: 14.65 MB / 430.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.59e-05/0.4652, allocations: 28 kB / 0.5775 GB, free: 14.62 MB / 430.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002815/0.4681, allocations: 1.672 MB / 0.5791 GB, free: 12.95 MB / 430.1 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 0.00705/0.4751, allocations: 3.375 MB / 0.5824 GB, free: 9.48 MB / 430.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003597/0.4787, allocations: 1.882 MB / 0.5842 GB, free: 7.602 MB / 430.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0009152/0.4796, allocations: 0.5299 MB / 0.5848 GB, free: 7.066 MB / 430.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006685/0.4863, allocations: 2.791 MB / 0.5875 GB, free: 4.25 MB / 430.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.536e-05/0.4863, allocations: 47.16 kB / 0.5875 GB, free: 4.195 MB / 430.1 MB
Notification: Performance of pre-optimization done (n=78): time 3.276e-06/0.4863, allocations: 0 / 0.5875 GB, free: 4.195 MB / 430.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01464/0.501, allocations: 3.418 MB / 0.5909 GB, free: 0.7383 MB / 430.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.443e-05/0.501, allocations: 60.41 kB / 0.5909 GB, free: 0.668 MB / 430.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0008006/0.5018, allocations: 0.5701 MB / 0.5915 GB, free: 88 kB / 430.1 MB
Notification: Performance of collectPreVariables (initialization): time 0.0001286/0.502, allocations: 41.7 kB / 0.5915 GB, free: 40 kB / 430.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004677/0.5024, allocations: 0.5584 MB / 0.5921 GB, free: 15.47 MB / 446.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003735/0.5028, allocations: 353.1 kB / 0.5924 GB, free: 15.12 MB / 446.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003553/0.5032, allocations: 230.8 kB / 0.5926 GB, free: 14.89 MB / 446.1 MB
Notification: Performance of setup shared object (initialization): time 0.0002399/0.5034, allocations: 394.7 kB / 0.593 GB, free: 14.5 MB / 446.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006631/0.5041, allocations: 354.5 kB / 0.5933 GB, free: 14.15 MB / 446.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001057/0.5051, allocations: 0.7438 MB / 0.5941 GB, free: 13.23 MB / 446.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001905/0.507, allocations: 1.208 MB / 0.5952 GB, free: 11.84 MB / 446.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.752e-05/0.507, allocations: 8 kB / 0.5952 GB, free: 11.84 MB / 446.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004144/0.5112, allocations: 1.463 MB / 0.5967 GB, free: 10.36 MB / 446.1 MB
Notification: Performance of prepare postOptimizeDAE: time 4.162e-05/0.5112, allocations: 15.59 kB / 0.5967 GB, free: 10.35 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.331e-05/0.5113, allocations: 12 kB / 0.5967 GB, free: 10.34 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001842/0.5131, allocations: 249.4 kB / 0.5969 GB, free: 10.09 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001555/0.5147, allocations: 331.5 kB / 0.5973 GB, free: 9.762 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005844/0.5205, allocations: 3.595 MB / 0.6008 GB, free: 5.965 MB / 446.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0009196/0.5214, allocations: 43.94 kB / 0.6008 GB, free: 5.922 MB / 446.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001521/0.5216, allocations: 63.98 kB / 0.6009 GB, free: 5.859 MB / 446.1 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 0.0005102/0.5221, allocations: 277.5 kB / 0.6011 GB, free: 5.578 MB / 446.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002153/0.5223, allocations: 83.48 kB / 0.6012 GB, free: 5.496 MB / 446.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.00404/0.5263, allocations: 1.331 MB / 0.6025 GB, free: 4.148 MB / 446.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.401e-05/0.5263, allocations: 8 kB / 0.6025 GB, free: 4.141 MB / 446.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.586e-06/0.5264, allocations: 4 kB / 0.6025 GB, free: 4.137 MB / 446.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.882e-05/0.5264, allocations: 3.984 kB / 0.6025 GB, free: 4.133 MB / 446.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001455/0.5278, allocations: 0.8 MB / 0.6033 GB, free: 3.277 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.41e-06/0.5278, allocations: 4.125 kB / 0.6033 GB, free: 3.273 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00125/0.5291, allocations: 219.7 kB / 0.6035 GB, free: 3.059 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001827/0.5309, allocations: 221.5 kB / 0.6037 GB, free: 2.836 MB / 446.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001591/0.5311, allocations: 35.98 kB / 0.6038 GB, free: 2.801 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.005175/0.5362, allocations: 3.492 MB / 0.6072 GB, free: 15.11 MB / 462.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.689e-06/0.5363, allocations: 4 kB / 0.6072 GB, free: 15.11 MB / 462.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004519/0.5408, allocations: 1.733 MB / 0.6089 GB, free: 13.34 MB / 462.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002457/0.541, allocations: 83.44 kB / 0.609 GB, free: 13.25 MB / 462.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001218/0.5411, allocations: 16 kB / 0.609 GB, free: 13.24 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005124/0.5417, allocations: 27.94 kB / 0.609 GB, free: 13.21 MB / 462.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001972/0.5418, allocations: 84.84 kB / 0.6091 GB, free: 13.13 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.872e-05/0.5419, allocations: 39.98 kB / 0.6091 GB, free: 13.09 MB / 462.1 MB
Notification: Performance of sorting global known variables: time 0.0004503/0.5424, allocations: 359.1 kB / 0.6095 GB, free: 12.75 MB / 462.1 MB
Notification: Performance of sort global known variables: time 8e-08/0.5424, allocations: 0 / 0.6095 GB, free: 12.75 MB / 462.1 MB
Notification: Performance of remove unused functions: time 0.002027/0.5444, allocations: 0.6779 MB / 0.6101 GB, free: 12.07 MB / 462.1 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 0.001501/0.5459, allocations: 0.8301 MB / 0.6109 GB, free: 11.23 MB / 462.1 MB
Notification: Performance of simCode: created initialization part: time 0.002244/0.5482, allocations: 1.188 MB / 0.6121 GB, free: 10.02 MB / 462.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.306e-06/0.5482, allocations: 0 / 0.6121 GB, free: 10.02 MB / 462.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001155/0.5493, allocations: 0.6941 MB / 0.6128 GB, free: 9.293 MB / 462.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001014/0.5503, allocations: 201.9 kB / 0.613 GB, free: 9.094 MB / 462.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003497/0.5538, allocations: 2.038 MB / 0.615 GB, free: 7.016 MB / 462.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004874/0.5543, allocations: 459.4 kB / 0.6154 GB, free: 6.535 MB / 462.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0005023/0.5548, allocations: 201.8 kB / 0.6156 GB, free: 6.344 MB / 462.1 MB
Notification: Performance of SimCode: time 8.52e-07/0.5548, allocations: 0 / 0.6156 GB, free: 6.344 MB / 462.1 MB
Notification: Performance of Templates: time 0.0382/0.593, allocations: 27.12 MB / 0.6421 GB, free: 11.27 MB / 494.1 MB
"
[Timeout remaining time 659]
make -j1 -f Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile [Timeout 660]
(rm -f Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 9.744286425993778]
Failed to read output from testmodel.py, exit status != 0:
0.6029055480030365 0.618218808 0.15865181
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7fcf4f4f2f50>