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 0.001367/0.001367, allocations: 110.4 kB / 18.94 MB, free: 2.949 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 0.00154/0.00154, allocations: 218.7 kB / 22.25 MB, free: 5.125 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 1.466/1.466, allocations: 230.6 MB / 256 MB, free: 7.977 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 0.1364/0.1364, allocations: 23.89 MB / 336.3 MB, free: 11.16 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 0.003071/0.003071, allocations: 63.91 kB / 471.7 MB, free: 7.141 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3786/0.3816, allocations: 59.87 MB / 0.5191 GB, free: 9.816 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 0.03718/0.4188, allocations: 26.7 MB / 0.5452 GB, free: 13.08 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0224/0.4412, allocations: 16.81 MB / 0.5616 GB, free: 13.6 MB / 414.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0009593/0.4422, allocations: 15.88 kB / 0.5616 GB, free: 13.59 MB / 414.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009955/0.4432, allocations: 332 kB / 0.562 GB, free: 13.33 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.00451/0.4477, allocations: 1.514 MB / 0.5634 GB, free: 12.05 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0059/0.4536, allocations: 2.022 MB / 0.5654 GB, free: 10.38 MB / 414.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002934/0.4565, allocations: 1.55 MB / 0.5669 GB, free: 8.984 MB / 414.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001222/0.4577, allocations: 0.6948 MB / 0.5676 GB, free: 8.379 MB / 414.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001113/0.4589, allocations: 0.7833 MB / 0.5684 GB, free: 7.594 MB / 414.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001459/0.4603, allocations: 0.8643 MB / 0.5692 GB, free: 6.727 MB / 414.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002225/0.4605, allocations: 136 kB / 0.5693 GB, free: 6.594 MB / 414.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.006711/0.4673, allocations: 1.806 MB / 0.5711 GB, free: 4.785 MB / 414.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0005969/0.4678, allocations: 323.1 kB / 0.5714 GB, free: 4.469 MB / 414.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.001071/0.4689, allocations: 0.6845 MB / 0.5721 GB, free: 3.781 MB / 414.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.008751/0.4777, allocations: 3.455 MB / 0.5755 GB, free: 320 kB / 414.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.298e-06/0.4777, allocations: 4 kB / 0.5755 GB, free: 316 kB / 414.1 MB
Notification: Performance of FrontEnd: time 1.383e-06/0.4777, allocations: 0 / 0.5755 GB, free: 316 kB / 414.1 MB
Notification: Performance of Transformations before backend: time 1.976e-05/0.4777, allocations: 0 / 0.5755 GB, free: 316 kB / 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 0.003625/0.4813, allocations: 1.777 MB / 0.5772 GB, free: 14.49 MB / 430.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.89e-05/0.4814, allocations: 8.031 kB / 0.5772 GB, free: 14.48 MB / 430.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001277/0.4826, allocations: 275.8 kB / 0.5775 GB, free: 14.21 MB / 430.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001194/0.4838, allocations: 0.6087 MB / 0.5781 GB, free: 13.58 MB / 430.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001514/0.484, allocations: 142.1 kB / 0.5782 GB, free: 13.43 MB / 430.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002137/0.4842, allocations: 116.3 kB / 0.5783 GB, free: 13.31 MB / 430.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002314/0.4865, allocations: 1.341 MB / 0.5796 GB, free: 11.93 MB / 430.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.478e-05/0.4865, allocations: 0 / 0.5796 GB, free: 11.93 MB / 430.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001192/0.4867, allocations: 44 kB / 0.5797 GB, free: 11.88 MB / 430.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.179e-05/0.4867, allocations: 28 kB / 0.5797 GB, free: 11.86 MB / 430.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002877/0.4896, allocations: 1.695 MB / 0.5813 GB, free: 10.15 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 0.007744/0.4973, allocations: 4.245 MB / 0.5855 GB, free: 5.703 MB / 430.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003725/0.501, allocations: 1.914 MB / 0.5874 GB, free: 3.789 MB / 430.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0009153/0.5019, allocations: 0.5299 MB / 0.5879 GB, free: 3.254 MB / 430.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.00673/0.5087, allocations: 2.931 MB / 0.5907 GB, free: 304 kB / 430.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.085e-05/0.5087, allocations: 47.16 kB / 0.5908 GB, free: 248 kB / 430.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.224e-06/0.5087, allocations: 0 / 0.5908 GB, free: 248 kB / 430.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01588/0.5246, allocations: 3.445 MB / 0.5941 GB, free: 12.76 MB / 446.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.731e-05/0.5246, allocations: 60.41 kB / 0.5942 GB, free: 12.69 MB / 446.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0007866/0.5254, allocations: 0.5862 MB / 0.5948 GB, free: 12.09 MB / 446.1 MB
Notification: Performance of collectPreVariables (initialization): time 8.082e-05/0.5255, allocations: 41.7 kB / 0.5948 GB, free: 12.05 MB / 446.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004278/0.5259, allocations: 0.5468 MB / 0.5953 GB, free: 11.49 MB / 446.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003204/0.5263, allocations: 353 kB / 0.5957 GB, free: 11.14 MB / 446.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003462/0.5266, allocations: 234.8 kB / 0.5959 GB, free: 10.91 MB / 446.1 MB
Notification: Performance of setup shared object (initialization): time 0.0002182/0.5268, allocations: 390.8 kB / 0.5963 GB, free: 10.52 MB / 446.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006884/0.5275, allocations: 362.5 kB / 0.5966 GB, free: 10.16 MB / 446.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001044/0.5286, allocations: 0.7516 MB / 0.5974 GB, free: 9.234 MB / 446.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001843/0.5304, allocations: 1.2 MB / 0.5985 GB, free: 7.855 MB / 446.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.401e-05/0.5304, allocations: 4 kB / 0.5985 GB, free: 7.852 MB / 446.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.00434/0.5348, allocations: 1.475 MB / 0.6 GB, free: 6.363 MB / 446.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.284e-05/0.5348, allocations: 8 kB / 0.6 GB, free: 6.355 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.899e-05/0.5348, allocations: 16 kB / 0.6 GB, free: 6.34 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002123/0.5369, allocations: 245.5 kB / 0.6002 GB, free: 6.094 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001517/0.5384, allocations: 327.5 kB / 0.6005 GB, free: 5.773 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.006067/0.5445, allocations: 3.656 MB / 0.6041 GB, free: 1.891 MB / 446.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0008677/0.5454, allocations: 43.98 kB / 0.6042 GB, free: 1.848 MB / 446.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001316/0.5455, allocations: 67.98 kB / 0.6042 GB, free: 1.781 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 0.0004942/0.546, allocations: 277.6 kB / 0.6045 GB, free: 1.5 MB / 446.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002039/0.5462, allocations: 95.38 kB / 0.6046 GB, free: 1.406 MB / 446.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004509/0.5507, allocations: 1.339 MB / 0.6059 GB, free: 52 kB / 446.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.145e-05/0.5507, allocations: 11.94 kB / 0.6059 GB, free: 40 kB / 446.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.657e-06/0.5507, allocations: 0 / 0.6059 GB, free: 40 kB / 446.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.119e-05/0.5507, allocations: 3.984 kB / 0.6059 GB, free: 36 kB / 446.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001598/0.5523, allocations: 1.034 MB / 0.6069 GB, free: 14.93 MB / 462.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.439e-06/0.5523, allocations: 3.938 kB / 0.6069 GB, free: 14.93 MB / 462.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00125/0.5536, allocations: 215.8 kB / 0.6071 GB, free: 14.71 MB / 462.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.002063/0.5557, allocations: 229.6 kB / 0.6073 GB, free: 14.48 MB / 462.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.598e-05/0.5557, allocations: 31.98 kB / 0.6074 GB, free: 14.45 MB / 462.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.005469/0.5612, allocations: 3.561 MB / 0.6108 GB, free: 10.67 MB / 462.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.174e-06/0.5612, allocations: 4.062 kB / 0.6109 GB, free: 10.66 MB / 462.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00481/0.566, allocations: 1.744 MB / 0.6126 GB, free: 8.887 MB / 462.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002204/0.5662, allocations: 87.44 kB / 0.6126 GB, free: 8.801 MB / 462.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001211/0.5664, allocations: 16 kB / 0.6127 GB, free: 8.785 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005315/0.5669, allocations: 20 kB / 0.6127 GB, free: 8.766 MB / 462.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002235/0.5671, allocations: 92.72 kB / 0.6128 GB, free: 8.676 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.845e-05/0.5672, allocations: 43.92 kB / 0.6128 GB, free: 8.633 MB / 462.1 MB
Notification: Performance of sorting global known variables: time 0.0005755/0.5678, allocations: 395.1 kB / 0.6132 GB, free: 8.254 MB / 462.1 MB
Notification: Performance of sort global known variables: time 9e-08/0.5678, allocations: 0 / 0.6132 GB, free: 8.254 MB / 462.1 MB
Notification: Performance of remove unused functions: time 0.002133/0.5699, allocations: 0.6779 MB / 0.6138 GB, free: 7.574 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 0.001761/0.5717, allocations: 0.8219 MB / 0.6146 GB, free: 6.742 MB / 462.1 MB
Notification: Performance of simCode: created initialization part: time 0.002394/0.5741, allocations: 1.196 MB / 0.6158 GB, free: 5.523 MB / 462.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.546e-06/0.5741, allocations: 0 / 0.6158 GB, free: 5.523 MB / 462.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001226/0.5753, allocations: 0.6903 MB / 0.6165 GB, free: 4.805 MB / 462.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001121/0.5764, allocations: 202.6 kB / 0.6167 GB, free: 4.605 MB / 462.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003876/0.5803, allocations: 2.021 MB / 0.6187 GB, free: 2.551 MB / 462.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000811/0.5811, allocations: 1.034 MB / 0.6197 GB, free: 1.488 MB / 462.1 MB
Notification: Performance of simCode: alias equations: time 0.0009451/0.582, allocations: 226.1 kB / 0.6199 GB, free: 1.27 MB / 462.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0004102/0.5825, allocations: 162.1 kB / 0.62 GB, free: 1.113 MB / 462.1 MB
Notification: Performance of SimCode: time 1.192e-06/0.5825, allocations: 0 / 0.62 GB, free: 1.113 MB / 462.1 MB
Notification: Performance of Templates: time 0.0439/0.6263, allocations: 24.95 MB / 0.6444 GB, free: 8.266 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: 5.938952086027712]
Failed to read output from testmodel.py, exit status != 0:
0.6368114370852709 0.650908742 0.169807819
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7f4d0bae2f50>