Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_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 0.0008896/0.0008896, allocations: 93.06 kB / 19.65 MB, free: 280 kB / 13.93 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 0.002083/0.002083, allocations: 169.3 kB / 23.02 MB, free: 1.551 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 1.009/1.009, allocations: 177.1 MB / 203.4 MB, free: 5.625 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo): time 0.08662/0.08662, allocations: 17.38 MB / 277.3 MB, free: 11.64 MB / 266.7 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/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_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.154e-06/2.154e-06, allocations: 0 / 353.4 MB, free: 9.969 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 4.13e-05/4.345e-05, allocations: 2.312 kB / 353.4 MB, free: 9.965 MB / 282.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/Obsolete.mo:14337:7-14337:66: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 2.0.0/Obsolete.mo:14337:7-14337:66: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 0.04287/0.04292, allocations: 29.25 MB / 382.7 MB, free: 12.84 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01183/0.05475, allocations: 6.254 MB / 388.9 MB, free: 6.566 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001388/0.05614, allocations: 19.88 kB / 389 MB, free: 6.547 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0008226/0.05696, allocations: 182.2 kB / 389.1 MB, free: 6.367 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.003215/0.06018, allocations: 0.8572 MB / 390 MB, free: 5.504 MB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.003334/0.06351, allocations: 0.8595 MB / 390.9 MB, free: 4.641 MB / 314.7 MB
Notification: Performance of NFFlatten.flatten: time 0.002971/0.06648, allocations: 1.599 MB / 392.5 MB, free: 3.035 MB / 314.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.00132/0.0678, allocations: 0.7233 MB / 393.2 MB, free: 2.289 MB / 314.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.00174/0.06954, allocations: 1.076 MB / 394.3 MB, free: 1.211 MB / 314.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001391/0.07093, allocations: 0.7133 MB / 395 MB, free: 0.4961 MB / 314.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0003356/0.07127, allocations: 132 kB / 395.1 MB, free: 376 kB / 314.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.002319/0.07359, allocations: 0.5811 MB / 395.7 MB, free: 15.79 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0003579/0.07394, allocations: 346.8 kB / 396 MB, free: 15.45 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0008504/0.07479, allocations: 0.5028 MB / 396.5 MB, free: 14.94 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.003868/0.07866, allocations: 1.709 MB / 398.2 MB, free: 13.23 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 8.215e-06/0.07867, allocations: 0 / 398.2 MB, free: 13.23 MB / 330.7 MB
Notification: Performance of FrontEnd: time 2.655e-06/0.07867, allocations: 0 / 398.2 MB, free: 13.23 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 5.796e-05/0.07873, allocations: 0 / 398.2 MB, free: 13.23 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 0.003502/0.08223, allocations: 1.64 MB / 399.9 MB, free: 11.54 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 6.648e-05/0.0823, allocations: 12.03 kB / 399.9 MB, free: 11.53 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001494/0.08379, allocations: 446.6 kB / 400.3 MB, free: 11.09 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001314/0.08511, allocations: 0.6186 MB / 400.9 MB, free: 10.45 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001879/0.08529, allocations: 138.1 kB / 401.1 MB, free: 10.3 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002353/0.08553, allocations: 124.3 kB / 401.2 MB, free: 10.18 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002026/0.08756, allocations: 1.068 MB / 402.3 MB, free: 9.055 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.438e-05/0.08758, allocations: 192 / 402.3 MB, free: 9.055 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001006/0.08768, allocations: 52.12 kB / 402.3 MB, free: 9.004 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.457e-05/0.0877, allocations: 24 kB / 402.3 MB, free: 8.98 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001603/0.08931, allocations: 1.125 MB / 403.5 MB, free: 7.844 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 0.004687/0.09399, allocations: 3.317 MB / 406.8 MB, free: 4.434 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002362/0.09636, allocations: 2.071 MB / 408.9 MB, free: 2.359 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004431/0.0968, allocations: 377.5 kB / 409.2 MB, free: 1.984 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.1565/0.2533, allocations: 2.198 MB / 411.4 MB, free: 51.39 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.15e-05/0.2533, allocations: 53.95 kB / 411.5 MB, free: 51.35 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 2.535e-06/0.2533, allocations: 0 / 411.5 MB, free: 51.35 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.007688/0.261, allocations: 2.968 MB / 414.4 MB, free: 51.05 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.387e-05/0.2611, allocations: 62.03 kB / 414.5 MB, free: 50.98 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000513/0.2616, allocations: 0.6039 MB / 415.1 MB, free: 50.77 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.203e-05/0.2616, allocations: 44.8 kB / 415.1 MB, free: 50.74 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.000255/0.2619, allocations: 0.6069 MB / 415.8 MB, free: 50.43 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001826/0.262, allocations: 343 kB / 416.1 MB, free: 50.25 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000259/0.2623, allocations: 236.4 kB / 416.3 MB, free: 50.22 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001401/0.2624, allocations: 0.5652 MB / 416.9 MB, free: 49.73 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003829/0.2628, allocations: 228.5 kB / 417.1 MB, free: 49.72 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000533/0.2634, allocations: 0.7871 MB / 417.9 MB, free: 49.03 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001017/0.2644, allocations: 1.111 MB / 419 MB, free: 48.33 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.953e-06/0.2644, allocations: 9.781 kB / 419 MB, free: 48.33 MB / 330.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.002262/0.2666, allocations: 1.261 MB / 420.3 MB, free: 48.2 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.413e-05/0.2667, allocations: 12.19 kB / 420.3 MB, free: 48.2 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.713e-05/0.2667, allocations: 15.31 kB / 420.3 MB, free: 48.2 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.00149/0.2682, allocations: 343.8 kB / 420.6 MB, free: 48.18 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0008232/0.269, allocations: 332.5 kB / 421 MB, free: 48.17 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002708/0.2717, allocations: 4.371 MB / 425.3 MB, free: 44.26 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0004181/0.2721, allocations: 43.97 kB / 425.4 MB, free: 44.26 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 9.379e-05/0.2722, allocations: 65.7 kB / 425.4 MB, free: 44.26 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 0.0002041/0.2724, allocations: 235.6 kB / 425.7 MB, free: 44.1 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001226/0.2726, allocations: 125.4 kB / 425.8 MB, free: 44.05 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.00183/0.2744, allocations: 1.104 MB / 426.9 MB, free: 43.94 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.141e-06/0.2744, allocations: 12.34 kB / 426.9 MB, free: 43.94 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.597e-06/0.2744, allocations: 0 / 426.9 MB, free: 43.94 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.959e-06/0.2744, allocations: 5.484 kB / 426.9 MB, free: 43.94 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007121/0.2751, allocations: 0.7466 MB / 427.7 MB, free: 43.71 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.282e-06/0.2751, allocations: 5.594 kB / 427.7 MB, free: 43.71 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000599/0.2757, allocations: 216.9 kB / 427.9 MB, free: 43.71 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001361/0.2771, allocations: 333.1 kB / 428.2 MB, free: 43.68 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 6.438e-05/0.2771, allocations: 32.52 kB / 428.2 MB, free: 43.68 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002332/0.2795, allocations: 4.272 MB / 432.5 MB, free: 39.66 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.003e-06/0.2795, allocations: 3.875 kB / 432.5 MB, free: 39.66 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00201/0.2815, allocations: 1.385 MB / 433.9 MB, free: 39.12 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 6.634e-05/0.2816, allocations: 72.83 kB / 434 MB, free: 39.08 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.371e-05/0.2816, allocations: 21.94 kB / 434 MB, free: 39.06 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002243/0.2818, allocations: 21.23 kB / 434 MB, free: 39.05 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001179/0.282, allocations: 83.69 kB / 434.1 MB, free: 39.04 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.675e-05/0.282, allocations: 48.38 kB / 434.1 MB, free: 39.03 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.0002088/0.2822, allocations: 365.9 kB / 434.5 MB, free: 38.84 MB / 330.7 MB
Notification: Performance of sort global known variables: time 8e-08/0.2822, allocations: 0 / 434.5 MB, free: 38.84 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.0008873/0.2831, allocations: 404.2 kB / 434.9 MB, free: 38.8 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 0.000426/0.2835, allocations: 324.6 kB / 435.2 MB, free: 38.7 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.001065/0.2846, allocations: 1.143 MB / 436.4 MB, free: 38.23 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.304e-06/0.2846, allocations: 0 / 436.4 MB, free: 38.23 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0004757/0.2851, allocations: 0.7315 MB / 437.1 MB, free: 37.82 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005731/0.2856, allocations: 228.6 kB / 437.3 MB, free: 37.76 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 0.002255/0.2879, allocations: 1.828 MB / 439.1 MB, free: 36.79 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 9.276e-05/0.288, allocations: 205.1 kB / 439.3 MB, free: 36.61 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 0.0004247/0.2884, allocations: 225.5 kB / 439.6 MB, free: 36.5 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002115/0.2886, allocations: 158.4 kB / 439.7 MB, free: 36.38 MB / 330.7 MB
Notification: Performance of SimCode: time 6.12e-07/0.2886, allocations: 4 kB / 439.7 MB, free: 36.37 MB / 330.7 MB
Notification: Performance of Templates: time 0.0157/0.3043, allocations: 17.08 MB / 456.8 MB, free: 20.74 MB / 330.7 MB
"
[Timeout remaining time 660]
make -j1 -f Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile [Timeout 660]
(rm -f Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis -abortSlowSimulation -alarm=240  -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 3.6728353798389435]