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 0.00131/0.00131, allocations: 99.64 kB / 18.95 MB, free: 2.668 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 0.001521/0.001521, allocations: 207.6 kB / 22.24 MB, free: 5.262 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 1.401/1.401, allocations: 230.6 MB / 256 MB, free: 7.797 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 0.1388/0.1388, allocations: 24 MB / 336.4 MB, free: 10.84 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 0.002077/0.002077, allocations: 71.83 kB / 471.8 MB, free: 6.848 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2993/0.3013, allocations: 59.89 MB / 0.5192 GB, free: 9.746 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 0.06981/0.3711, allocations: 26.21 MB / 0.5448 GB, free: 13.24 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02136/0.3925, allocations: 14.71 MB / 0.5592 GB, free: 15.87 MB / 414.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001013/0.3935, allocations: 19.81 kB / 0.5592 GB, free: 15.85 MB / 414.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001163/0.3947, allocations: 308.7 kB / 0.5595 GB, free: 15.62 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.004563/0.3992, allocations: 1.471 MB / 0.5609 GB, free: 14.38 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005736/0.405, allocations: 2.019 MB / 0.5629 GB, free: 12.71 MB / 414.1 MB
Notification: Performance of NFFlatten.flatten: time 0.00252/0.4075, allocations: 1.547 MB / 0.5644 GB, free: 11.32 MB / 414.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001201/0.4087, allocations: 0.6925 MB / 0.5651 GB, free: 10.66 MB / 414.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001263/0.41, allocations: 0.7794 MB / 0.5659 GB, free: 9.879 MB / 414.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001465/0.4114, allocations: 0.7862 MB / 0.5666 GB, free: 9.09 MB / 414.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0003505/0.4118, allocations: 136 kB / 0.5668 GB, free: 8.957 MB / 414.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004918/0.4167, allocations: 1.697 MB / 0.5684 GB, free: 7.258 MB / 414.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0004548/0.4171, allocations: 331 kB / 0.5687 GB, free: 6.934 MB / 414.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0008787/0.418, allocations: 0.5758 MB / 0.5693 GB, free: 6.355 MB / 414.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.00753/0.4256, allocations: 3.432 MB / 0.5726 GB, free: 2.91 MB / 414.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.871e-06/0.4256, allocations: 3.938 kB / 0.5726 GB, free: 2.906 MB / 414.1 MB
Notification: Performance of FrontEnd: time 2.084e-06/0.4256, allocations: 0 / 0.5726 GB, free: 2.906 MB / 414.1 MB
Notification: Performance of Transformations before backend: time 5.862e-05/0.4256, allocations: 4 kB / 0.5726 GB, free: 2.902 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 0.003964/0.4296, allocations: 1.765 MB / 0.5744 GB, free: 1.098 MB / 414.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.108e-05/0.4296, allocations: 8.031 kB / 0.5744 GB, free: 1.09 MB / 414.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001311/0.4309, allocations: 283.7 kB / 0.5746 GB, free: 0.8125 MB / 414.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001283/0.4322, allocations: 0.6087 MB / 0.5752 GB, free: 184 kB / 414.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001461/0.4324, allocations: 142.1 kB / 0.5754 GB, free: 28 kB / 414.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002432/0.4326, allocations: 120.3 kB / 0.5755 GB, free: 15.91 MB / 430.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002381/0.435, allocations: 1.333 MB / 0.5768 GB, free: 14.53 MB / 430.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.855e-05/0.435, allocations: 0 / 0.5768 GB, free: 14.53 MB / 430.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001141/0.4351, allocations: 44 kB / 0.5768 GB, free: 14.48 MB / 430.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.679e-05/0.4352, allocations: 28 kB / 0.5769 GB, free: 14.46 MB / 430.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002914/0.4381, allocations: 1.675 MB / 0.5785 GB, free: 12.77 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 0.007072/0.4451, allocations: 3.386 MB / 0.5818 GB, free: 9.301 MB / 430.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003413/0.4486, allocations: 1.871 MB / 0.5836 GB, free: 7.434 MB / 430.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0008894/0.4494, allocations: 0.5338 MB / 0.5842 GB, free: 6.895 MB / 430.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006025/0.4555, allocations: 2.779 MB / 0.5869 GB, free: 4.09 MB / 430.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.721e-05/0.4555, allocations: 47.16 kB / 0.5869 GB, free: 4.035 MB / 430.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.765e-06/0.4555, allocations: 7.875 kB / 0.5869 GB, free: 4.027 MB / 430.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01402/0.4695, allocations: 3.422 MB / 0.5903 GB, free: 0.5664 MB / 430.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.725e-05/0.4696, allocations: 60.41 kB / 0.5903 GB, free: 0.4961 MB / 430.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0007849/0.4704, allocations: 0.5741 MB / 0.5909 GB, free: 15.91 MB / 446.1 MB
Notification: Performance of collectPreVariables (initialization): time 6.888e-05/0.4704, allocations: 41.7 kB / 0.5909 GB, free: 15.86 MB / 446.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004439/0.4709, allocations: 0.5622 MB / 0.5915 GB, free: 15.29 MB / 446.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003283/0.4712, allocations: 349.1 kB / 0.5918 GB, free: 14.95 MB / 446.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003464/0.4716, allocations: 230.8 kB / 0.592 GB, free: 14.71 MB / 446.1 MB
Notification: Performance of setup shared object (initialization): time 0.0002117/0.4718, allocations: 390.8 kB / 0.5924 GB, free: 14.32 MB / 446.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000664/0.4724, allocations: 354.5 kB / 0.5927 GB, free: 13.98 MB / 446.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001009/0.4734, allocations: 0.7516 MB / 0.5935 GB, free: 13.05 MB / 446.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001819/0.4753, allocations: 1.204 MB / 0.5946 GB, free: 11.66 MB / 446.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.006e-05/0.4753, allocations: 4 kB / 0.5946 GB, free: 11.66 MB / 446.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004006/0.4793, allocations: 1.467 MB / 0.5961 GB, free: 10.18 MB / 446.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.329e-05/0.4793, allocations: 11.94 kB / 0.5961 GB, free: 10.17 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.287e-05/0.4793, allocations: 20.12 kB / 0.5961 GB, free: 10.15 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001827/0.4811, allocations: 237.5 kB / 0.5963 GB, free: 9.914 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001409/0.4826, allocations: 331.5 kB / 0.5967 GB, free: 9.59 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005492/0.488, allocations: 3.579 MB / 0.6001 GB, free: 5.809 MB / 446.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000765/0.4888, allocations: 43.94 kB / 0.6002 GB, free: 5.766 MB / 446.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001293/0.4889, allocations: 64.05 kB / 0.6003 GB, free: 5.703 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 0.0004831/0.4894, allocations: 277.4 kB / 0.6005 GB, free: 5.422 MB / 446.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002223/0.4896, allocations: 91.42 kB / 0.6006 GB, free: 5.332 MB / 446.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.003939/0.4936, allocations: 1.327 MB / 0.6019 GB, free: 3.988 MB / 446.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 8.997e-06/0.4936, allocations: 8 kB / 0.6019 GB, free: 3.98 MB / 446.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.262e-06/0.4936, allocations: 4 kB / 0.6019 GB, free: 3.977 MB / 446.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.507e-06/0.4936, allocations: 3.984 kB / 0.6019 GB, free: 3.973 MB / 446.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001267/0.4949, allocations: 0.7999 MB / 0.6027 GB, free: 3.117 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.739e-06/0.4949, allocations: 0 / 0.6027 GB, free: 3.117 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001157/0.496, allocations: 219.7 kB / 0.6029 GB, free: 2.902 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001789/0.4978, allocations: 229.7 kB / 0.6031 GB, free: 2.672 MB / 446.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 8.265e-05/0.4979, allocations: 31.98 kB / 0.6032 GB, free: 2.641 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.005095/0.503, allocations: 3.496 MB / 0.6066 GB, free: 14.94 MB / 462.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.003e-06/0.503, allocations: 0 / 0.6066 GB, free: 14.94 MB / 462.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004433/0.5074, allocations: 1.737 MB / 0.6083 GB, free: 13.17 MB / 462.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.000218/0.5077, allocations: 83.42 kB / 0.6083 GB, free: 13.09 MB / 462.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001495/0.5078, allocations: 20 kB / 0.6084 GB, free: 13.07 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005328/0.5083, allocations: 27.88 kB / 0.6084 GB, free: 13.04 MB / 462.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001885/0.5085, allocations: 84.84 kB / 0.6085 GB, free: 12.96 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.236e-05/0.5086, allocations: 39.98 kB / 0.6085 GB, free: 12.92 MB / 462.1 MB
Notification: Performance of sorting global known variables: time 0.0004996/0.5091, allocations: 363.1 kB / 0.6089 GB, free: 12.57 MB / 462.1 MB
Notification: Performance of sort global known variables: time 8e-08/0.5091, allocations: 0 / 0.6089 GB, free: 12.57 MB / 462.1 MB
Notification: Performance of remove unused functions: time 0.00212/0.5112, allocations: 0.6779 MB / 0.6095 GB, free: 11.89 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 0.001756/0.513, allocations: 0.8284 MB / 0.6103 GB, free: 11.06 MB / 462.1 MB
Notification: Performance of simCode: created initialization part: time 0.002418/0.5154, allocations: 1.192 MB / 0.6115 GB, free: 9.84 MB / 462.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.917e-06/0.5154, allocations: 0 / 0.6115 GB, free: 9.84 MB / 462.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001199/0.5166, allocations: 0.6941 MB / 0.6122 GB, free: 9.121 MB / 462.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001029/0.5176, allocations: 201.4 kB / 0.6124 GB, free: 8.926 MB / 462.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003625/0.5213, allocations: 2.001 MB / 0.6143 GB, free: 6.887 MB / 462.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005294/0.5218, allocations: 451.4 kB / 0.6147 GB, free: 6.414 MB / 462.1 MB
Notification: Performance of simCode: alias equations: time 0.0008275/0.5226, allocations: 222.7 kB / 0.615 GB, free: 6.195 MB / 462.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003574/0.523, allocations: 169.8 kB / 0.6151 GB, free: 6.035 MB / 462.1 MB
Notification: Performance of SimCode: time 1.303e-06/0.523, allocations: 0 / 0.6151 GB, free: 6.035 MB / 462.1 MB
Notification: Performance of Templates: time 0.03972/0.5627, allocations: 25.33 MB / 0.6399 GB, free: 12.9 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: 5.661201987415552]
Failed to read output from testmodel.py, exit status != 0:
0.5718637034296989 0.585854294 0.157100234
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7f71b8352fe0>