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 0.001169/0.001169, allocations: 104.3 kB / 19.7 MB, free: 2.152 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 0.001407/0.001407, allocations: 214.6 kB / 22.99 MB, free: 4.965 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 1.391/1.391, allocations: 230.6 MB / 256.8 MB, free: 7.805 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 0.1442/0.1442, allocations: 23.92 MB / 337.1 MB, free: 11.03 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 0.002026/0.002026, allocations: 67.91 kB / 472.4 MB, free: 6.977 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3425/0.3445, allocations: 59.87 MB / 0.5198 GB, free: 9.734 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 0.07306/0.4175, allocations: 26.04 MB / 0.5453 GB, free: 13.53 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02147/0.439, allocations: 14.72 MB / 0.5596 GB, free: 160 kB / 398.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001261/0.4403, allocations: 15.88 kB / 0.5596 GB, free: 144 kB / 398.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001158/0.4414, allocations: 304.6 kB / 0.5599 GB, free: 15.91 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.004697/0.4461, allocations: 1.475 MB / 0.5614 GB, free: 14.66 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005906/0.452, allocations: 2.026 MB / 0.5634 GB, free: 12.99 MB / 414.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002379/0.4544, allocations: 1.547 MB / 0.5649 GB, free: 11.61 MB / 414.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001001/0.4554, allocations: 0.7016 MB / 0.5655 GB, free: 10.99 MB / 414.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0008863/0.4563, allocations: 0.7833 MB / 0.5663 GB, free: 10.21 MB / 414.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.00112/0.4574, allocations: 0.8605 MB / 0.5672 GB, free: 9.344 MB / 414.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002028/0.4576, allocations: 136 kB / 0.5673 GB, free: 9.211 MB / 414.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004913/0.4625, allocations: 1.739 MB / 0.569 GB, free: 7.469 MB / 414.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0003452/0.4629, allocations: 335 kB / 0.5693 GB, free: 7.141 MB / 414.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0006574/0.4635, allocations: 0.572 MB / 0.5699 GB, free: 6.566 MB / 414.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.00664/0.4702, allocations: 3.451 MB / 0.5732 GB, free: 3.102 MB / 414.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.759e-06/0.4702, allocations: 0 / 0.5732 GB, free: 3.102 MB / 414.1 MB
Notification: Performance of FrontEnd: time 1.292e-06/0.4702, allocations: 0 / 0.5732 GB, free: 3.102 MB / 414.1 MB
Notification: Performance of Transformations before backend: time 1.682e-05/0.4702, allocations: 0 / 0.5732 GB, free: 3.102 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 0.003473/0.4737, allocations: 1.769 MB / 0.575 GB, free: 1.293 MB / 414.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.82e-05/0.4737, allocations: 8.031 kB / 0.575 GB, free: 1.285 MB / 414.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.00124/0.475, allocations: 279.8 kB / 0.5752 GB, free: 1.012 MB / 414.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001173/0.4761, allocations: 0.6165 MB / 0.5758 GB, free: 380 kB / 414.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001587/0.4763, allocations: 138.1 kB / 0.576 GB, free: 228 kB / 414.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002186/0.4765, allocations: 120.3 kB / 0.5761 GB, free: 108 kB / 414.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002263/0.4788, allocations: 1.333 MB / 0.5774 GB, free: 14.73 MB / 430.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.431e-05/0.4788, allocations: 3.938 kB / 0.5774 GB, free: 14.72 MB / 430.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001197/0.4789, allocations: 52 kB / 0.5774 GB, free: 14.67 MB / 430.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.62e-05/0.4789, allocations: 24 kB / 0.5775 GB, free: 14.65 MB / 430.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002704/0.4816, allocations: 1.675 MB / 0.5791 GB, free: 12.96 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 0.006568/0.4882, allocations: 3.386 MB / 0.5824 GB, free: 9.488 MB / 430.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003474/0.4917, allocations: 1.871 MB / 0.5842 GB, free: 7.617 MB / 430.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.000875/0.4926, allocations: 0.5338 MB / 0.5848 GB, free: 7.078 MB / 430.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006356/0.4989, allocations: 2.764 MB / 0.5875 GB, free: 4.289 MB / 430.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.948e-05/0.499, allocations: 59.08 kB / 0.5875 GB, free: 4.223 MB / 430.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.625e-06/0.499, allocations: 0 / 0.5875 GB, free: 4.223 MB / 430.1 MB
Notification: Performance of matching and sorting (n=95): time 0.0165/0.5155, allocations: 3.421 MB / 0.5908 GB, free: 0.7656 MB / 430.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.63e-05/0.5155, allocations: 64.41 kB / 0.5909 GB, free: 0.6914 MB / 430.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0007584/0.5163, allocations: 0.5662 MB / 0.5915 GB, free: 116 kB / 430.1 MB
Notification: Performance of collectPreVariables (initialization): time 7.183e-05/0.5164, allocations: 41.7 kB / 0.5915 GB, free: 68 kB / 430.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004669/0.5168, allocations: 0.5585 MB / 0.592 GB, free: 15.5 MB / 446.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003299/0.5172, allocations: 353 kB / 0.5924 GB, free: 15.15 MB / 446.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003447/0.5175, allocations: 226.8 kB / 0.5926 GB, free: 14.92 MB / 446.1 MB
Notification: Performance of setup shared object (initialization): time 0.000223/0.5177, allocations: 394.7 kB / 0.593 GB, free: 14.53 MB / 446.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006345/0.5184, allocations: 362.5 kB / 0.5933 GB, free: 14.18 MB / 446.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0009693/0.5193, allocations: 0.7477 MB / 0.5941 GB, free: 13.25 MB / 446.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001892/0.5212, allocations: 1.2 MB / 0.5952 GB, free: 11.87 MB / 446.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 9.808e-06/0.5212, allocations: 4 kB / 0.5952 GB, free: 11.87 MB / 446.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004473/0.5257, allocations: 1.478 MB / 0.5967 GB, free: 10.38 MB / 446.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.962e-05/0.5257, allocations: 12 kB / 0.5967 GB, free: 10.36 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.586e-05/0.5258, allocations: 12 kB / 0.5967 GB, free: 10.35 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002206/0.528, allocations: 242 kB / 0.5969 GB, free: 10.11 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001501/0.5295, allocations: 335.5 kB / 0.5972 GB, free: 9.781 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.0057/0.5352, allocations: 3.583 MB / 0.6007 GB, free: 5.996 MB / 446.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0008024/0.536, allocations: 43.94 kB / 0.6008 GB, free: 5.953 MB / 446.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001179/0.5361, allocations: 63.98 kB / 0.6008 GB, free: 5.891 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 0.0004409/0.5365, allocations: 277.4 kB / 0.6011 GB, free: 5.609 MB / 446.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001734/0.5367, allocations: 79.48 kB / 0.6012 GB, free: 5.531 MB / 446.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004343/0.541, allocations: 1.335 MB / 0.6025 GB, free: 4.18 MB / 446.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.053e-05/0.541, allocations: 12 kB / 0.6025 GB, free: 4.168 MB / 446.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.018e-06/0.5411, allocations: 3.938 kB / 0.6025 GB, free: 4.164 MB / 446.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.718e-06/0.5411, allocations: 3.984 kB / 0.6025 GB, free: 4.16 MB / 446.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001206/0.5423, allocations: 0.7961 MB / 0.6033 GB, free: 3.309 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.897e-06/0.5423, allocations: 3.938 kB / 0.6033 GB, free: 3.305 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001258/0.5435, allocations: 219.9 kB / 0.6035 GB, free: 3.09 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.0022/0.5457, allocations: 225.5 kB / 0.6037 GB, free: 2.863 MB / 446.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.358e-05/0.5458, allocations: 31.98 kB / 0.6037 GB, free: 2.832 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.005297/0.5511, allocations: 3.484 MB / 0.6071 GB, free: 15.15 MB / 462.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.933e-06/0.5511, allocations: 64 / 0.6071 GB, free: 15.15 MB / 462.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004752/0.5559, allocations: 1.74 MB / 0.6088 GB, free: 13.37 MB / 462.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001822/0.556, allocations: 87.44 kB / 0.6089 GB, free: 13.29 MB / 462.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001168/0.5562, allocations: 16 kB / 0.6089 GB, free: 13.27 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005375/0.5567, allocations: 28.12 kB / 0.609 GB, free: 13.24 MB / 462.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.000184/0.5569, allocations: 84.78 kB / 0.6091 GB, free: 13.16 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.138e-05/0.557, allocations: 43.97 kB / 0.6091 GB, free: 13.12 MB / 462.1 MB
Notification: Performance of sorting global known variables: time 0.0004203/0.5574, allocations: 363.1 kB / 0.6094 GB, free: 12.77 MB / 462.1 MB
Notification: Performance of sort global known variables: time 7e-08/0.5574, allocations: 0 / 0.6094 GB, free: 12.77 MB / 462.1 MB
Notification: Performance of remove unused functions: time 0.002018/0.5594, allocations: 0.6857 MB / 0.6101 GB, free: 12.08 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 0.001403/0.5608, allocations: 0.8106 MB / 0.6109 GB, free: 11.26 MB / 462.1 MB
Notification: Performance of simCode: created initialization part: time 0.002116/0.5629, allocations: 1.181 MB / 0.6121 GB, free: 10.06 MB / 462.1 MB
Notification: Performance of simCode: created event and clocks part: time 4.839e-06/0.5629, allocations: 11.94 kB / 0.6121 GB, free: 10.05 MB / 462.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001115/0.564, allocations: 0.6982 MB / 0.6128 GB, free: 9.32 MB / 462.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0009527/0.565, allocations: 197.4 kB / 0.6129 GB, free: 9.125 MB / 462.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003274/0.5683, allocations: 2.005 MB / 0.6149 GB, free: 7.086 MB / 462.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004588/0.5687, allocations: 455.4 kB / 0.6153 GB, free: 6.609 MB / 462.1 MB
Notification: Performance of simCode: alias equations: time 0.0007445/0.5695, allocations: 233.8 kB / 0.6156 GB, free: 6.383 MB / 462.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003488/0.5698, allocations: 156.5 kB / 0.6157 GB, free: 6.234 MB / 462.1 MB
Notification: Performance of SimCode: time 5.91e-07/0.5698, allocations: 4 kB / 0.6157 GB, free: 6.23 MB / 462.1 MB
Notification: Performance of Templates: time 0.03843/0.6082, allocations: 25.7 MB / 0.6408 GB, free: 12.73 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 -s cvode -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 5.786588255999959]
Failed to read output from testmodel.py, exit status != 0:
0.6170498150022468 0.6312757729999999 0.15796593399999995
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7f14eaa4af50>