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 0.001651/0.001651, allocations: 95.77 kB / 18.94 MB, free: 2.832 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 0.00188/0.00188, allocations: 217.1 kB / 22.25 MB, free: 5.105 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 1.474/1.474, allocations: 230.6 MB / 256 MB, free: 7.848 MB / 206.1 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 0.1389/0.1389, allocations: 23.92 MB / 336.3 MB, free: 11.1 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: 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 0.002141/0.002141, allocations: 59.91 kB / 471.7 MB, free: 7.039 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3272/0.3293, allocations: 59.87 MB / 0.5191 GB, free: 9.699 MB / 382.1 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 0.07081/0.4001, allocations: 26.09 MB / 0.5446 GB, free: 13.57 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02183/0.422, allocations: 14.72 MB / 0.5589 GB, free: 192 kB / 398.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001064/0.423, allocations: 19.81 kB / 0.559 GB, free: 172 kB / 398.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009833/0.424, allocations: 296.8 kB / 0.5592 GB, free: 15.95 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.004405/0.4284, allocations: 1.479 MB / 0.5607 GB, free: 14.7 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.00589/0.4343, allocations: 2.022 MB / 0.5627 GB, free: 13.03 MB / 414.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002613/0.4369, allocations: 1.543 MB / 0.5642 GB, free: 11.64 MB / 414.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001049/0.438, allocations: 0.7034 MB / 0.5649 GB, free: 11 MB / 414.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009987/0.439, allocations: 0.7833 MB / 0.5656 GB, free: 10.22 MB / 414.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001372/0.4403, allocations: 0.8644 MB / 0.5665 GB, free: 9.352 MB / 414.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002165/0.4406, allocations: 132 kB / 0.5666 GB, free: 9.223 MB / 414.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.00629/0.4468, allocations: 1.743 MB / 0.5683 GB, free: 7.477 MB / 414.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0004463/0.4473, allocations: 335 kB / 0.5686 GB, free: 7.148 MB / 414.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0008504/0.4481, allocations: 0.5681 MB / 0.5692 GB, free: 6.578 MB / 414.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.009951/0.4581, allocations: 3.443 MB / 0.5725 GB, free: 3.121 MB / 414.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.412e-06/0.4581, allocations: 0 / 0.5725 GB, free: 3.121 MB / 414.1 MB
Notification: Performance of FrontEnd: time 1.413e-06/0.4581, allocations: 0 / 0.5725 GB, free: 3.121 MB / 414.1 MB
Notification: Performance of Transformations before backend: time 3.65e-05/0.4581, allocations: 0 / 0.5725 GB, free: 3.121 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 0.003934/0.4621, allocations: 1.78 MB / 0.5743 GB, free: 1.301 MB / 414.1 MB
Notification: Performance of prepare preOptimizeDAE: time 6.272e-05/0.4621, allocations: 8.031 kB / 0.5743 GB, free: 1.293 MB / 414.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001299/0.4634, allocations: 279.7 kB / 0.5746 GB, free: 1.02 MB / 414.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001223/0.4647, allocations: 0.6127 MB / 0.5751 GB, free: 392 kB / 414.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001673/0.4648, allocations: 138.1 kB / 0.5753 GB, free: 240 kB / 414.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002196/0.465, allocations: 116.3 kB / 0.5754 GB, free: 124 kB / 414.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002363/0.4674, allocations: 1.333 MB / 0.5767 GB, free: 14.74 MB / 430.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.582e-05/0.4674, allocations: 0 / 0.5767 GB, free: 14.74 MB / 430.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001229/0.4676, allocations: 44 kB / 0.5767 GB, free: 14.7 MB / 430.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.225e-05/0.4676, allocations: 31.98 kB / 0.5768 GB, free: 14.66 MB / 430.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002881/0.4705, allocations: 1.679 MB / 0.5784 GB, free: 12.98 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 0.007102/0.4776, allocations: 3.375 MB / 0.5817 GB, free: 9.516 MB / 430.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003682/0.4812, allocations: 1.886 MB / 0.5835 GB, free: 7.633 MB / 430.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0009123/0.4822, allocations: 0.5299 MB / 0.5841 GB, free: 7.098 MB / 430.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006564/0.4887, allocations: 2.772 MB / 0.5868 GB, free: 4.301 MB / 430.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.55e-05/0.4888, allocations: 51.16 kB / 0.5868 GB, free: 4.242 MB / 430.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.915e-06/0.4888, allocations: 0 / 0.5868 GB, free: 4.242 MB / 430.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01709/0.5059, allocations: 3.422 MB / 0.5902 GB, free: 0.7812 MB / 430.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.016e-05/0.5059, allocations: 68.39 kB / 0.5902 GB, free: 0.7031 MB / 430.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0007364/0.5067, allocations: 0.5662 MB / 0.5908 GB, free: 128 kB / 430.1 MB
Notification: Performance of collectPreVariables (initialization): time 8.01e-05/0.5068, allocations: 45.64 kB / 0.5908 GB, free: 76 kB / 430.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004332/0.5072, allocations: 0.5545 MB / 0.5914 GB, free: 15.51 MB / 446.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003289/0.5075, allocations: 353.1 kB / 0.5917 GB, free: 15.16 MB / 446.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003725/0.5079, allocations: 234.8 kB / 0.5919 GB, free: 14.93 MB / 446.1 MB
Notification: Performance of setup shared object (initialization): time 0.0002105/0.5081, allocations: 390.7 kB / 0.5923 GB, free: 14.54 MB / 446.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006918/0.5088, allocations: 358.5 kB / 0.5926 GB, free: 14.19 MB / 446.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0009939/0.5098, allocations: 0.7438 MB / 0.5934 GB, free: 13.27 MB / 446.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001888/0.5117, allocations: 1.204 MB / 0.5945 GB, free: 11.88 MB / 446.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.002e-05/0.5117, allocations: 0 / 0.5945 GB, free: 11.88 MB / 446.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004545/0.5162, allocations: 1.474 MB / 0.596 GB, free: 10.39 MB / 446.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.567e-05/0.5163, allocations: 12 kB / 0.596 GB, free: 10.38 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.72e-05/0.5163, allocations: 12 kB / 0.596 GB, free: 10.37 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002269/0.5185, allocations: 242.3 kB / 0.5962 GB, free: 10.13 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001587/0.5201, allocations: 327.5 kB / 0.5965 GB, free: 9.809 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.006262/0.5264, allocations: 3.591 MB / 0.6001 GB, free: 6.016 MB / 446.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0008941/0.5273, allocations: 48.11 kB / 0.6001 GB, free: 5.969 MB / 446.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001313/0.5274, allocations: 63.98 kB / 0.6002 GB, free: 5.906 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 0.0004955/0.5279, allocations: 281.4 kB / 0.6004 GB, free: 5.621 MB / 446.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001992/0.5281, allocations: 83.48 kB / 0.6005 GB, free: 5.539 MB / 446.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004642/0.5328, allocations: 1.324 MB / 0.6018 GB, free: 4.199 MB / 446.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.186e-05/0.5328, allocations: 8 kB / 0.6018 GB, free: 4.191 MB / 446.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.462e-06/0.5328, allocations: 7.938 kB / 0.6018 GB, free: 4.184 MB / 446.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.263e-05/0.5328, allocations: 7.969 kB / 0.6018 GB, free: 4.176 MB / 446.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001463/0.5343, allocations: 0.7884 MB / 0.6026 GB, free: 3.332 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 8.025e-06/0.5343, allocations: 3.938 kB / 0.6026 GB, free: 3.328 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001386/0.5356, allocations: 219.9 kB / 0.6028 GB, free: 3.113 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.002329/0.538, allocations: 229.4 kB / 0.603 GB, free: 2.883 MB / 446.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.000114/0.5381, allocations: 35.98 kB / 0.6031 GB, free: 2.848 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.00574/0.5438, allocations: 3.496 MB / 0.6065 GB, free: 15.15 MB / 462.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.715e-06/0.5438, allocations: 0 / 0.6065 GB, free: 15.15 MB / 462.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.005199/0.549, allocations: 1.733 MB / 0.6082 GB, free: 13.38 MB / 462.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002482/0.5493, allocations: 75.45 kB / 0.6082 GB, free: 13.31 MB / 462.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001738/0.5495, allocations: 20 kB / 0.6083 GB, free: 13.29 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0006545/0.5501, allocations: 35.86 kB / 0.6083 GB, free: 13.25 MB / 462.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002197/0.5503, allocations: 80.86 kB / 0.6084 GB, free: 13.18 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001118/0.5504, allocations: 39.98 kB / 0.6084 GB, free: 13.14 MB / 462.1 MB
Notification: Performance of sorting global known variables: time 0.0005161/0.551, allocations: 367.1 kB / 0.6088 GB, free: 12.79 MB / 462.1 MB
Notification: Performance of sort global known variables: time 7e-08/0.551, allocations: 0 / 0.6088 GB, free: 12.79 MB / 462.1 MB
Notification: Performance of remove unused functions: time 0.002175/0.5531, allocations: 0.6779 MB / 0.6094 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 0.001908/0.555, allocations: 0.8185 MB / 0.6102 GB, free: 11.28 MB / 462.1 MB
Notification: Performance of simCode: created initialization part: time 0.002523/0.5576, allocations: 1.192 MB / 0.6114 GB, free: 10.06 MB / 462.1 MB
Notification: Performance of simCode: created event and clocks part: time 4.188e-06/0.5576, allocations: 4 kB / 0.6114 GB, free: 10.06 MB / 462.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001265/0.5588, allocations: 0.6902 MB / 0.6121 GB, free: 9.34 MB / 462.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001213/0.56, allocations: 211.6 kB / 0.6123 GB, free: 9.137 MB / 462.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003869/0.5639, allocations: 2.001 MB / 0.6142 GB, free: 7.102 MB / 462.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000566/0.5645, allocations: 463.4 kB / 0.6147 GB, free: 6.617 MB / 462.1 MB
Notification: Performance of simCode: alias equations: time 0.0008837/0.5654, allocations: 226.4 kB / 0.6149 GB, free: 6.395 MB / 462.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003932/0.5658, allocations: 161.5 kB / 0.615 GB, free: 6.242 MB / 462.1 MB
Notification: Performance of SimCode: time 8.12e-07/0.5658, allocations: 0 / 0.615 GB, free: 6.242 MB / 462.1 MB
Notification: Performance of Templates: time 0.04253/0.6083, allocations: 25.7 MB / 0.6401 GB, free: 12.74 MB / 494.1 MB
"
[Timeout remaining time 659]
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: 6.184158458840102]
Failed to read output from testmodel.py, exit status != 0:
0.6172718219459057 0.631905359 0.17047922799999995
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7f3c4fdc2f50>