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 0.0008798/0.0008798, allocations: 81.17 kB / 19.87 MB, free: 4.621 MB / 18.57 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 0.0008916/0.0008916, allocations: 169 kB / 23.27 MB, free: 1.219 MB / 18.57 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 0.9406/0.9406, allocations: 177.1 MB / 203.7 MB, free: 5.492 MB / 186.7 MB
"
[Timeout remaining time 179]
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 0.08499/0.08499, allocations: 17.47 MB / 277.7 MB, free: 11.39 MB / 266.7 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: Performance of FrontEnd - loaded program: time 1.693e-06/1.693e-06, allocations: 0 / 354 MB, free: 9.555 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.449e-05/1.618e-05, allocations: 6.25 kB / 354 MB, free: 9.547 MB / 282.7 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 0.02543/0.02544, allocations: 29.22 MB / 383.2 MB, free: 12.46 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.005944/0.03139, allocations: 6.176 MB / 389.4 MB, free: 6.262 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002843/0.03167, allocations: 19.81 kB / 389.4 MB, free: 6.242 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0003572/0.03203, allocations: 190.2 kB / 389.6 MB, free: 6.055 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.001246/0.03328, allocations: 0.8494 MB / 390.5 MB, free: 5.199 MB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.001152/0.03443, allocations: 0.8517 MB / 391.3 MB, free: 4.344 MB / 314.7 MB
Notification: Performance of NFFlatten.flatten: time 0.000944/0.03537, allocations: 1.599 MB / 392.9 MB, free: 2.738 MB / 314.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005296/0.0359, allocations: 0.7233 MB / 393.6 MB, free: 1.992 MB / 314.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000699/0.0366, allocations: 1.076 MB / 394.7 MB, free: 0.9141 MB / 314.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0006098/0.03721, allocations: 0.7211 MB / 395.4 MB, free: 196 kB / 314.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001321/0.03734, allocations: 136 kB / 395.6 MB, free: 60 kB / 314.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0007188/0.03806, allocations: 0.5811 MB / 396.1 MB, free: 15.48 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.000199/0.03826, allocations: 338.9 kB / 396.5 MB, free: 15.14 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003209/0.03858, allocations: 0.5028 MB / 397 MB, free: 14.64 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.001273/0.03985, allocations: 1.712 MB / 398.7 MB, free: 12.92 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 2.385e-06/0.03986, allocations: 0 / 398.7 MB, free: 12.92 MB / 330.7 MB
Notification: Performance of FrontEnd: time 9.72e-07/0.03986, allocations: 4 kB / 398.7 MB, free: 12.92 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 8.677e-06/0.03987, allocations: 0 / 398.7 MB, free: 12.92 MB / 330.7 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 0.001621/0.04149, allocations: 1.644 MB / 400.3 MB, free: 11.23 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.204e-05/0.04152, allocations: 8.031 kB / 400.3 MB, free: 11.22 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0007418/0.04226, allocations: 458.3 kB / 400.8 MB, free: 10.77 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0006104/0.04287, allocations: 0.6108 MB / 401.4 MB, free: 10.13 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 8.713e-05/0.04296, allocations: 134.1 kB / 401.5 MB, free: 9.988 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001275/0.04309, allocations: 120.3 kB / 401.7 MB, free: 9.871 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.000954/0.04404, allocations: 0.9741 MB / 402.6 MB, free: 8.844 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.565e-05/0.04406, allocations: 192 / 402.6 MB, free: 8.844 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.968e-05/0.04413, allocations: 44.12 kB / 402.7 MB, free: 8.801 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.597e-05/0.04414, allocations: 28 kB / 402.7 MB, free: 8.773 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000944/0.04509, allocations: 0.9597 MB / 403.7 MB, free: 7.793 MB / 330.7 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 0.003395/0.04848, allocations: 3.2 MB / 406.9 MB, free: 4.508 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002056/0.05054, allocations: 1.996 MB / 408.9 MB, free: 2.512 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003333/0.05087, allocations: 313.4 kB / 409.2 MB, free: 2.199 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.1425/0.1934, allocations: 2.253 MB / 411.4 MB, free: 51.49 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.078e-05/0.1934, allocations: 42.3 kB / 411.5 MB, free: 51.45 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 2.494e-06/0.1934, allocations: 0 / 411.5 MB, free: 51.45 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.006845/0.2003, allocations: 2.658 MB / 414.1 MB, free: 51.23 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.626e-05/0.2003, allocations: 61.95 kB / 414.2 MB, free: 51.17 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0005682/0.2009, allocations: 0.6095 MB / 414.8 MB, free: 50.96 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.035e-05/0.2009, allocations: 40.3 kB / 414.8 MB, free: 50.93 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002414/0.2012, allocations: 0.6033 MB / 415.4 MB, free: 50.62 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001893/0.2013, allocations: 348.4 kB / 415.8 MB, free: 50.44 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002474/0.2016, allocations: 243.9 kB / 416 MB, free: 50.41 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001514/0.2017, allocations: 0.5736 MB / 416.6 MB, free: 49.91 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002547/0.202, allocations: 178 kB / 416.7 MB, free: 49.91 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004324/0.2024, allocations: 0.7396 MB / 417.5 MB, free: 49.21 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0007715/0.2032, allocations: 1.025 MB / 418.5 MB, free: 48.52 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.773e-06/0.2032, allocations: 3.75 kB / 418.5 MB, free: 48.52 MB / 330.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.001953/0.2052, allocations: 1.153 MB / 419.7 MB, free: 48.38 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.996e-05/0.2052, allocations: 13.38 kB / 419.7 MB, free: 48.38 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.618e-05/0.2052, allocations: 13.41 kB / 419.7 MB, free: 48.38 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001335/0.2065, allocations: 336.6 kB / 420 MB, free: 48.36 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007402/0.2073, allocations: 327.6 kB / 420.3 MB, free: 48.36 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002411/0.2097, allocations: 4.319 MB / 424.7 MB, free: 44.49 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003825/0.2101, allocations: 39.91 kB / 424.7 MB, free: 44.49 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.19e-05/0.2101, allocations: 57.53 kB / 424.8 MB, free: 44.49 MB / 330.7 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 0.0002015/0.2103, allocations: 235.4 kB / 425 MB, free: 44.33 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001256/0.2105, allocations: 117 kB / 425.1 MB, free: 44.29 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.001679/0.2121, allocations: 1.01 MB / 426.1 MB, free: 44.18 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.302e-06/0.2121, allocations: 9.781 kB / 426.1 MB, free: 44.18 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.199e-06/0.2122, allocations: 7.125 kB / 426.1 MB, free: 44.18 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.123e-06/0.2122, allocations: 9.312 kB / 426.1 MB, free: 44.18 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000659/0.2128, allocations: 0.7701 MB / 426.9 MB, free: 43.95 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.629e-06/0.2128, allocations: 0 / 426.9 MB, free: 43.95 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005343/0.2134, allocations: 214.7 kB / 427.1 MB, free: 43.95 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.00119/0.2145, allocations: 328.2 kB / 427.4 MB, free: 43.92 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.642e-05/0.2146, allocations: 31.19 kB / 427.5 MB, free: 43.92 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.00195/0.2165, allocations: 4.225 MB / 431.7 MB, free: 40.07 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.262e-06/0.2165, allocations: 1.656 kB / 431.7 MB, free: 40.07 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001644/0.2182, allocations: 1.253 MB / 433 MB, free: 39.73 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.864e-05/0.2182, allocations: 70.95 kB / 433 MB, free: 39.68 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.124e-05/0.2183, allocations: 25.41 kB / 433 MB, free: 39.68 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002148/0.2185, allocations: 33.03 kB / 433.1 MB, free: 39.68 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001114/0.2186, allocations: 82.02 kB / 433.2 MB, free: 39.67 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.924e-05/0.2187, allocations: 31.06 kB / 433.2 MB, free: 39.67 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.0001791/0.2189, allocations: 349.9 kB / 433.5 MB, free: 39.54 MB / 330.7 MB
Notification: Performance of sort global known variables: time 6.1e-08/0.2189, allocations: 0 / 433.5 MB, free: 39.54 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.0009029/0.2198, allocations: 401.5 kB / 433.9 MB, free: 39.54 MB / 330.7 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 0.0003977/0.2202, allocations: 345.2 kB / 434.3 MB, free: 39.45 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.0008368/0.221, allocations: 1.041 MB / 435.3 MB, free: 39.07 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.094e-06/0.221, allocations: 0 / 435.3 MB, free: 39.07 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0004186/0.2214, allocations: 0.6973 MB / 436 MB, free: 38.71 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000568/0.222, allocations: 231 kB / 436.2 MB, free: 38.71 MB / 330.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002031/0.224, allocations: 1.804 MB / 438 MB, free: 37.9 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000105/0.2241, allocations: 202.8 kB / 438.2 MB, free: 37.82 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 0.0004487/0.2246, allocations: 220.1 kB / 438.4 MB, free: 37.81 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0004483/0.225, allocations: 374.7 kB / 438.8 MB, free: 37.71 MB / 330.7 MB
Notification: Performance of SimCode: time 7.41e-07/0.225, allocations: 2.656 kB / 438.8 MB, free: 37.71 MB / 330.7 MB
Notification: Performance of Templates: time 0.01824/0.2433, allocations: 19.33 MB / 458.1 MB, free: 20.03 MB / 330.7 MB
"
[Timeout remaining time 660]
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=240  -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 3.22351152356714]