Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Physiolibrary_Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Physiolibrary 3.0.0-master/package.mo", uses=false)
Using package Physiolibrary with version 3.0.0-beta1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Physiolibrary 3.0.0-master/package.mo)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Running command: translateModel(Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Physiolibrary_Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Physiolibrary_Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.00148/0.00148, allocations: 183.2 kB / 15.98 MB, free: 5.77 MB / 13.93 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.316/1.316, allocations: 222.9 MB / 239.7 MB, free: 11 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001268/0.001268, allocations: 114.6 kB / 289.9 MB, free: 10.94 MB / 234.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Physiolibrary 3.0.0-master/package.mo): time 0.3681/0.3681, allocations: 36.67 MB / 376.7 MB, free: 41.45 MB / 298.7 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001202/0.001203, allocations: 63.91 kB / 446.4 MB, free: 11.84 MB / 330.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1195/0.1207, allocations: 58.91 MB / 0.4935 GB, free: 0.875 MB / 378.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Physiolibrary 3.0.0-master/Chemical.mo:4671:7-4671:66:writable] Warning: An inner declaration for outer component system could not be found and was automatically generated.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Physiolibrary 3.0.0-master/Chemical.mo:4671:7-4671:66: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(Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis): time 0.2445/0.3652, allocations: 23.32 MB / 0.5163 GB, free: 33.81 MB / 378.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01664/0.3819, allocations: 16.49 MB / 0.5324 GB, free: 22.41 MB / 378.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001504/0.3834, allocations: 24.19 kB / 0.5324 GB, free: 22.39 MB / 378.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.001049/0.3845, allocations: 299 kB / 0.5327 GB, free: 22.24 MB / 378.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.004466/0.389, allocations: 1.269 MB / 0.5339 GB, free: 21.49 MB / 378.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.006001/0.395, allocations: 1.749 MB / 0.5356 GB, free: 20.46 MB / 378.7 MB
Notification: Performance of NFFlatten.flatten: time 0.002583/0.3976, allocations: 1.508 MB / 0.5371 GB, free: 19.75 MB / 378.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001012/0.3986, allocations: 0.7351 MB / 0.5378 GB, free: 19.43 MB / 378.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009813/0.3996, allocations: 0.7621 MB / 0.5385 GB, free: 19.2 MB / 378.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001064/0.4007, allocations: 0.8355 MB / 0.5394 GB, free: 18.88 MB / 378.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001972/0.4009, allocations: 88.66 kB / 0.5394 GB, free: 18.88 MB / 378.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.006337/0.4072, allocations: 1.695 MB / 0.5411 GB, free: 18.46 MB / 378.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0004698/0.4077, allocations: 291.4 kB / 0.5414 GB, free: 18.3 MB / 378.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.001102/0.4089, allocations: 0.6445 MB / 0.542 GB, free: 17.95 MB / 378.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.008221/0.4171, allocations: 3.181 MB / 0.5451 GB, free: 16.65 MB / 378.7 MB
Notification: Performance of FrontEnd - DAE generated: time 7.253e-06/0.4171, allocations: 1.125 kB / 0.5451 GB, free: 16.65 MB / 378.7 MB
Notification: Performance of FrontEnd: time 2.254e-06/0.4171, allocations: 0 / 0.5451 GB, free: 16.65 MB / 378.7 MB
Notification: Performance of Transformations before backend: time 2.588e-05/0.4172, allocations: 3.938 kB / 0.5451 GB, free: 16.64 MB / 378.7 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 0.003514/0.4207, allocations: 1.794 MB / 0.5469 GB, free: 15.55 MB / 378.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.246e-05/0.4207, allocations: 10.53 kB / 0.5469 GB, free: 15.55 MB / 378.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001174/0.4219, allocations: 266.4 kB / 0.5471 GB, free: 15.47 MB / 378.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.00104/0.423, allocations: 0.6573 MB / 0.5478 GB, free: 15.02 MB / 378.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001146/0.4231, allocations: 115.6 kB / 0.5479 GB, free: 14.95 MB / 378.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001902/0.4233, allocations: 112.7 kB / 0.548 GB, free: 14.91 MB / 378.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001991/0.4253, allocations: 1.34 MB / 0.5493 GB, free: 14.36 MB / 378.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.332e-05/0.4253, allocations: 0 / 0.5493 GB, free: 14.36 MB / 378.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001034/0.4255, allocations: 48.28 kB / 0.5494 GB, free: 14.32 MB / 378.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.496e-05/0.4255, allocations: 27.41 kB / 0.5494 GB, free: 14.32 MB / 378.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002301/0.4278, allocations: 1.697 MB / 0.551 GB, free: 13.11 MB / 378.7 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 0.005908/0.4337, allocations: 4.308 MB / 0.5552 GB, free: 9.297 MB / 378.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002908/0.4366, allocations: 2.283 MB / 0.5575 GB, free: 7.145 MB / 378.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0007467/0.4374, allocations: 0.5961 MB / 0.5581 GB, free: 6.605 MB / 378.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.007014/0.4444, allocations: 5.412 MB / 0.5633 GB, free: 1.176 MB / 378.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.851e-05/0.4445, allocations: 39.22 kB / 0.5634 GB, free: 1.125 MB / 378.7 MB
Notification: Performance of pre-optimization done (n=78): time 3.807e-06/0.4445, allocations: 0 / 0.5634 GB, free: 1.125 MB / 378.7 MB
Notification: Performance of matching and sorting (n=95): time 0.01527/0.4598, allocations: 3.581 MB / 0.5669 GB, free: 13.93 MB / 394.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.277e-05/0.4599, allocations: 64.41 kB / 0.5669 GB, free: 13.86 MB / 394.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0007731/0.4607, allocations: 0.5897 MB / 0.5675 GB, free: 13.34 MB / 394.7 MB
Notification: Performance of collectPreVariables (initialization): time 8.296e-05/0.4608, allocations: 42.59 kB / 0.5676 GB, free: 13.3 MB / 394.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003502/0.4611, allocations: 0.5293 MB / 0.5681 GB, free: 12.81 MB / 394.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002832/0.4614, allocations: 334.1 kB / 0.5684 GB, free: 12.51 MB / 394.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003277/0.4617, allocations: 230.2 kB / 0.5686 GB, free: 12.3 MB / 394.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001924/0.4619, allocations: 394.7 kB / 0.569 GB, free: 11.93 MB / 394.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006796/0.4626, allocations: 359.2 kB / 0.5693 GB, free: 11.62 MB / 394.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0009387/0.4636, allocations: 0.7607 MB / 0.5701 GB, free: 10.75 MB / 394.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001627/0.4652, allocations: 1.214 MB / 0.5713 GB, free: 9.395 MB / 394.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.761e-06/0.4652, allocations: 4 kB / 0.5713 GB, free: 9.391 MB / 394.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004037/0.4693, allocations: 1.478 MB / 0.5727 GB, free: 8.074 MB / 394.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.523e-05/0.4693, allocations: 11.94 kB / 0.5727 GB, free: 8.062 MB / 394.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.795e-05/0.4693, allocations: 12 kB / 0.5727 GB, free: 8.051 MB / 394.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001966/0.4713, allocations: 252.2 kB / 0.573 GB, free: 7.863 MB / 394.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001618/0.473, allocations: 351.9 kB / 0.5733 GB, free: 7.551 MB / 394.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005191/0.4782, allocations: 3.491 MB / 0.5767 GB, free: 3.793 MB / 394.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001066/0.4793, allocations: 79.89 kB / 0.5768 GB, free: 3.715 MB / 394.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001101/0.4794, allocations: 63.98 kB / 0.5768 GB, free: 3.652 MB / 394.7 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 0.0004559/0.4798, allocations: 290.3 kB / 0.5771 GB, free: 3.359 MB / 394.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000166/0.48, allocations: 82.97 kB / 0.5772 GB, free: 3.277 MB / 394.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.003925/0.4839, allocations: 1.331 MB / 0.5785 GB, free: 1.934 MB / 394.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 9.327e-06/0.484, allocations: 12 kB / 0.5785 GB, free: 1.922 MB / 394.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.33e-06/0.484, allocations: 4 kB / 0.5785 GB, free: 1.918 MB / 394.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.036e-05/0.484, allocations: 7.969 kB / 0.5785 GB, free: 1.91 MB / 394.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001386/0.4854, allocations: 1.077 MB / 0.5796 GB, free: 0.7656 MB / 394.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.372e-06/0.4854, allocations: 4 kB / 0.5796 GB, free: 0.7617 MB / 394.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001365/0.4868, allocations: 239.8 kB / 0.5798 GB, free: 0.5273 MB / 394.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001844/0.4886, allocations: 221.5 kB / 0.58 GB, free: 312 kB / 394.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 8.636e-05/0.4887, allocations: 35.98 kB / 0.5801 GB, free: 276 kB / 394.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004544/0.4933, allocations: 3.394 MB / 0.5834 GB, free: 12.61 MB / 410.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.964e-06/0.4933, allocations: 0 / 0.5834 GB, free: 12.61 MB / 410.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.02075/0.5141, allocations: 8.362 MB / 0.5915 GB, free: 3.926 MB / 410.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001844/0.5143, allocations: 148.1 kB / 0.5917 GB, free: 3.762 MB / 410.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001111/0.5144, allocations: 23.94 kB / 0.5917 GB, free: 3.738 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005554/0.515, allocations: 43.94 kB / 0.5917 GB, free: 3.695 MB / 410.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002079/0.5152, allocations: 80.83 kB / 0.5918 GB, free: 3.617 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.655e-05/0.5153, allocations: 39.98 kB / 0.5919 GB, free: 3.578 MB / 410.7 MB
Notification: Performance of sorting global known variables: time 0.0004421/0.5157, allocations: 387.1 kB / 0.5922 GB, free: 3.203 MB / 410.7 MB
Notification: Performance of sort global known variables: time 1.4e-07/0.5157, allocations: 4 kB / 0.5922 GB, free: 3.199 MB / 410.7 MB
Notification: Performance of remove unused functions: time 0.002447/0.5182, allocations: 0.7808 MB / 0.593 GB, free: 2.418 MB / 410.7 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 0.001552/0.5197, allocations: 0.8049 MB / 0.5938 GB, free: 1.609 MB / 410.7 MB
Notification: Performance of simCode: created initialization part: time 0.002219/0.522, allocations: 1.259 MB / 0.595 GB, free: 336 kB / 410.7 MB
Notification: Performance of simCode: created event and clocks part: time 3.236e-06/0.522, allocations: 0 / 0.595 GB, free: 336 kB / 410.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.001176/0.5232, allocations: 0.7488 MB / 0.5957 GB, free: 15.55 MB / 426.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001122/0.5243, allocations: 190.6 kB / 0.5959 GB, free: 15.37 MB / 426.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.004227/0.5286, allocations: 3.129 MB / 0.599 GB, free: 12.18 MB / 426.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000625/0.5292, allocations: 1.061 MB / 0.6 GB, free: 11.08 MB / 426.7 MB
Notification: Performance of simCode: alias equations: time 0.001095/0.5303, allocations: 249.7 kB / 0.6003 GB, free: 10.84 MB / 426.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0004203/0.5307, allocations: 161 kB / 0.6004 GB, free: 10.69 MB / 426.7 MB
Notification: Performance of SimCode: time 6.91e-07/0.5307, allocations: 0 / 0.6004 GB, free: 10.69 MB / 426.7 MB
Notification: Performance of Templates: time 0.03654/0.5673, allocations: 25.89 MB / 0.6257 GB, free: 0.9219 MB / 442.7 MB
make -j1 -f Physiolibrary_Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile
(rm -f Physiolibrary_Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Physiolibrary_Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Physiolibrary_Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Physiolibrary_Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Physiolibrary_Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Physiolibrary_Physiolibrary.Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1)