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 0.00132/0.00132, allocations: 104.3 kB / 19.7 MB, free: 2.156 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 0.001448/0.001448, allocations: 212.3 kB / 22.99 MB, free: 4.984 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 1.463/1.463, 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 0.143/0.143, 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 0.002105/0.002105, allocations: 67.91 kB / 472.4 MB, free: 7.035 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3125/0.3146, allocations: 59.86 MB / 0.5198 GB, free: 9.84 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 0.07059/0.3852, allocations: 26.04 MB / 0.5452 GB, free: 13.6 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02021/0.4054, allocations: 14.71 MB / 0.5596 GB, free: 228 kB / 398.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0008917/0.4063, allocations: 15.88 kB / 0.5596 GB, free: 212 kB / 398.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009795/0.4073, allocations: 308.3 kB / 0.5599 GB, free: 15.98 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.004067/0.4114, allocations: 1.472 MB / 0.5613 GB, free: 14.74 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005446/0.4168, allocations: 2.022 MB / 0.5633 GB, free: 13.07 MB / 414.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002218/0.419, allocations: 1.547 MB / 0.5648 GB, free: 11.68 MB / 414.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.000951/0.42, allocations: 0.7103 MB / 0.5655 GB, free: 11.02 MB / 414.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0008916/0.4209, allocations: 0.7832 MB / 0.5662 GB, free: 10.23 MB / 414.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001146/0.422, allocations: 0.8605 MB / 0.5671 GB, free: 9.367 MB / 414.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002129/0.4222, allocations: 132 kB / 0.5672 GB, free: 9.238 MB / 414.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004458/0.4267, allocations: 1.747 MB / 0.5689 GB, free: 7.488 MB / 414.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0003397/0.427, allocations: 331 kB / 0.5692 GB, free: 7.164 MB / 414.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0006343/0.4277, allocations: 0.5798 MB / 0.5698 GB, free: 6.582 MB / 414.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.005932/0.4336, allocations: 3.436 MB / 0.5732 GB, free: 3.133 MB / 414.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.118e-06/0.4336, allocations: 0 / 0.5732 GB, free: 3.133 MB / 414.1 MB
Notification: Performance of FrontEnd: time 4.679e-06/0.4336, allocations: 4 kB / 0.5732 GB, free: 3.129 MB / 414.1 MB
Notification: Performance of Transformations before backend: time 1.563e-05/0.4336, allocations: 0 / 0.5732 GB, free: 3.129 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 0.003446/0.4371, allocations: 1.777 MB / 0.5749 GB, free: 1.312 MB / 414.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.536e-05/0.4371, allocations: 8.031 kB / 0.5749 GB, free: 1.305 MB / 414.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001278/0.4384, allocations: 275.5 kB / 0.5752 GB, free: 1.035 MB / 414.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.00125/0.4396, allocations: 0.6127 MB / 0.5758 GB, free: 408 kB / 414.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001656/0.4398, allocations: 138.1 kB / 0.5759 GB, free: 256 kB / 414.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002333/0.44, allocations: 116.3 kB / 0.576 GB, free: 140 kB / 414.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002339/0.4424, allocations: 1.341 MB / 0.5773 GB, free: 14.75 MB / 430.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.585e-05/0.4424, allocations: 0 / 0.5773 GB, free: 14.75 MB / 430.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001228/0.4425, allocations: 44 kB / 0.5774 GB, free: 14.71 MB / 430.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.398e-05/0.4426, allocations: 27.94 kB / 0.5774 GB, free: 14.68 MB / 430.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002834/0.4454, allocations: 1.675 MB / 0.579 GB, free: 13 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 0.006713/0.4521, allocations: 3.387 MB / 0.5823 GB, free: 9.52 MB / 430.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003658/0.4558, allocations: 1.878 MB / 0.5842 GB, free: 7.648 MB / 430.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0008983/0.4567, allocations: 0.5377 MB / 0.5847 GB, free: 7.105 MB / 430.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.00644/0.4631, allocations: 2.779 MB / 0.5874 GB, free: 4.301 MB / 430.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.318e-05/0.4631, allocations: 43.16 kB / 0.5874 GB, free: 4.25 MB / 430.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.474e-06/0.4631, allocations: 0 / 0.5874 GB, free: 4.25 MB / 430.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01761/0.4807, allocations: 3.426 MB / 0.5908 GB, free: 0.7852 MB / 430.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.192e-05/0.4808, allocations: 60.41 kB / 0.5908 GB, free: 0.7148 MB / 430.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0006742/0.4815, allocations: 0.5701 MB / 0.5914 GB, free: 136 kB / 430.1 MB
Notification: Performance of collectPreVariables (initialization): time 7.178e-05/0.4815, allocations: 41.7 kB / 0.5914 GB, free: 88 kB / 430.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004251/0.482, allocations: 0.5546 MB / 0.592 GB, free: 15.52 MB / 446.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003058/0.4823, allocations: 353 kB / 0.5923 GB, free: 15.18 MB / 446.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003715/0.4826, allocations: 234.8 kB / 0.5925 GB, free: 14.94 MB / 446.1 MB
Notification: Performance of setup shared object (initialization): time 0.0002095/0.4829, allocations: 390.7 kB / 0.5929 GB, free: 14.55 MB / 446.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006543/0.4835, allocations: 358.5 kB / 0.5933 GB, free: 14.2 MB / 446.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000991/0.4845, allocations: 0.7477 MB / 0.594 GB, free: 13.27 MB / 446.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001763/0.4863, allocations: 1.2 MB / 0.5952 GB, free: 11.89 MB / 446.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.326e-06/0.4863, allocations: 8 kB / 0.5952 GB, free: 11.89 MB / 446.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004615/0.4909, allocations: 1.47 MB / 0.5966 GB, free: 10.4 MB / 446.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.618e-05/0.4909, allocations: 12.88 kB / 0.5966 GB, free: 10.39 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.07e-05/0.4909, allocations: 16 kB / 0.5966 GB, free: 10.38 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002329/0.4933, allocations: 241.5 kB / 0.5969 GB, free: 10.13 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001585/0.4948, allocations: 327.5 kB / 0.5972 GB, free: 9.812 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.00614/0.501, allocations: 3.583 MB / 0.6007 GB, free: 6.027 MB / 446.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0008532/0.5018, allocations: 47.92 kB / 0.6007 GB, free: 5.98 MB / 446.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.000127/0.502, allocations: 71.92 kB / 0.6008 GB, free: 5.91 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 0.000492/0.5025, allocations: 273.6 kB / 0.601 GB, free: 5.633 MB / 446.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001934/0.5027, allocations: 87.48 kB / 0.6011 GB, free: 5.547 MB / 446.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004551/0.5072, allocations: 1.323 MB / 0.6024 GB, free: 4.207 MB / 446.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.306e-05/0.5072, allocations: 15.98 kB / 0.6024 GB, free: 4.191 MB / 446.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.757e-06/0.5072, allocations: 0 / 0.6024 GB, free: 4.191 MB / 446.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.102e-05/0.5072, allocations: 3.984 kB / 0.6024 GB, free: 4.188 MB / 446.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001288/0.5085, allocations: 0.7999 MB / 0.6032 GB, free: 3.332 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.072e-06/0.5085, allocations: 4.109 kB / 0.6032 GB, free: 3.328 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0013/0.5098, allocations: 215.8 kB / 0.6034 GB, free: 3.117 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.002233/0.5121, allocations: 233.5 kB / 0.6037 GB, free: 2.883 MB / 446.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.961e-05/0.5121, allocations: 27.98 kB / 0.6037 GB, free: 2.855 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.005522/0.5177, allocations: 3.492 MB / 0.6071 GB, free: 15.16 MB / 462.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.817e-06/0.5177, allocations: 3.938 kB / 0.6071 GB, free: 15.16 MB / 462.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004902/0.5226, allocations: 1.729 MB / 0.6088 GB, free: 13.39 MB / 462.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002169/0.5228, allocations: 83.45 kB / 0.6089 GB, free: 13.31 MB / 462.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001208/0.5229, allocations: 20 kB / 0.6089 GB, free: 13.29 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005554/0.5235, allocations: 31.92 kB / 0.6089 GB, free: 13.26 MB / 462.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002026/0.5237, allocations: 84.8 kB / 0.609 GB, free: 13.18 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.508e-05/0.5237, allocations: 35.98 kB / 0.609 GB, free: 13.14 MB / 462.1 MB
Notification: Performance of sorting global known variables: time 0.0004602/0.5242, allocations: 367.1 kB / 0.6094 GB, free: 12.79 MB / 462.1 MB
Notification: Performance of sort global known variables: time 9e-08/0.5242, allocations: 0 / 0.6094 GB, free: 12.79 MB / 462.1 MB
Notification: Performance of remove unused functions: time 0.002004/0.5262, allocations: 0.6779 MB / 0.61 GB, free: 12.11 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 0.001475/0.5277, allocations: 0.8185 MB / 0.6108 GB, free: 11.29 MB / 462.1 MB
Notification: Performance of simCode: created initialization part: time 0.002268/0.53, allocations: 1.188 MB / 0.612 GB, free: 10.07 MB / 462.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.675e-06/0.53, allocations: 0 / 0.612 GB, free: 10.07 MB / 462.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001195/0.5312, allocations: 0.7018 MB / 0.6127 GB, free: 9.344 MB / 462.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001014/0.5322, allocations: 214.3 kB / 0.6129 GB, free: 9.133 MB / 462.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003421/0.5356, allocations: 1.994 MB / 0.6148 GB, free: 7.105 MB / 462.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004775/0.5361, allocations: 459.4 kB / 0.6153 GB, free: 6.625 MB / 462.1 MB
Notification: Performance of simCode: alias equations: time 0.0007934/0.5369, allocations: 229.6 kB / 0.6155 GB, free: 6.402 MB / 462.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003611/0.5372, allocations: 158.3 kB / 0.6156 GB, free: 6.25 MB / 462.1 MB
Notification: Performance of SimCode: time 7.52e-07/0.5372, allocations: 0 / 0.6156 GB, free: 6.25 MB / 462.1 MB
Notification: Performance of Templates: time 0.04036/0.5776, allocations: 25.71 MB / 0.6407 GB, free: 12.74 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 -s gbode -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 5.920086443002219]
Failed to read output from testmodel.py, exit status != 0:
0.5866646540089278 0.60044067 0.16367340700000002
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7fd913412f50>