Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Physiolibrary_Physiolibrary.Chemical.Examples.SimpleReaction.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.SimpleReaction,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Physiolibrary_Physiolibrary.Chemical.Examples.SimpleReaction")
translateModel(Physiolibrary.Chemical.Examples.SimpleReaction,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Physiolibrary_Physiolibrary.Chemical.Examples.SimpleReaction")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001405/0.001405, 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 1.413/1.413, allocations: 222.9 MB / 239.7 MB, free: 10.99 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001127/0.001127, allocations: 108.8 kB / 289.9 MB, free: 10.93 MB / 234.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Physiolibrary 3.0.0-master/package.mo): time 0.3393/0.3393, allocations: 36.67 MB / 376.7 MB, free: 41.45 MB / 298.7 MB
Notification: Performance of FrontEnd - loaded program: time 0.001216/0.001216, allocations: 67.91 kB / 446.4 MB, free: 11.84 MB / 330.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1218/0.123, allocations: 58.93 MB / 0.4935 GB, free: 0.8594 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.SimpleReaction): time 0.2279/0.351, allocations: 21.44 MB / 0.5144 GB, free: 34.93 MB / 378.7 MB
Notification: Performance of NFInst.instExpressions: time 0.00871/0.3597, allocations: 7.907 MB / 0.5221 GB, free: 29.99 MB / 378.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0009538/0.3607, allocations: 16.31 kB / 0.5222 GB, free: 29.98 MB / 378.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0006017/0.3614, allocations: 162.8 kB / 0.5223 GB, free: 29.9 MB / 378.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.001835/0.3632, allocations: 0.5761 MB / 0.5229 GB, free: 29.55 MB / 378.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.00289/0.3661, allocations: 0.8988 MB / 0.5238 GB, free: 29.02 MB / 378.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001098/0.3672, allocations: 0.924 MB / 0.5247 GB, free: 28.57 MB / 378.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005133/0.3677, allocations: 449.8 kB / 0.5251 GB, free: 28.39 MB / 378.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0004013/0.3682, allocations: 424.6 kB / 0.5255 GB, free: 28.26 MB / 378.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0004832/0.3686, allocations: 492.1 kB / 0.526 GB, free: 28.07 MB / 378.7 MB
Notification: Performance of NFPackage.collectConstants: time 9.701e-05/0.3688, allocations: 51.06 kB / 0.526 GB, free: 28.07 MB / 378.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.002742/0.3715, allocations: 0.812 MB / 0.5268 GB, free: 27.86 MB / 378.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.000196/0.3717, allocations: 169.8 kB / 0.527 GB, free: 27.77 MB / 378.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003485/0.3721, allocations: 393.5 kB / 0.5273 GB, free: 27.55 MB / 378.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.00396/0.376, allocations: 1.676 MB / 0.529 GB, free: 26.86 MB / 378.7 MB
Notification: Performance of FrontEnd - DAE generated: time 6.112e-06/0.3761, allocations: 1.375 kB / 0.529 GB, free: 26.86 MB / 378.7 MB
Notification: Performance of FrontEnd: time 1.773e-06/0.3761, allocations: 4 kB / 0.529 GB, free: 26.86 MB / 378.7 MB
Notification: Performance of Transformations before backend: time 1.553e-05/0.3761, allocations: 0 / 0.529 GB, free: 26.86 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: 168
 * Number of variables: 168
Notification: Performance of Generate backend data structure: time 0.002551/0.3787, allocations: 1.159 MB / 0.5301 GB, free: 26.07 MB / 378.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.709e-05/0.3787, allocations: 9 kB / 0.5301 GB, free: 26.07 MB / 378.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0006524/0.3794, allocations: 152.2 kB / 0.5303 GB, free: 26.02 MB / 378.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0006624/0.3801, allocations: 469.2 kB / 0.5307 GB, free: 25.67 MB / 378.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001101/0.3802, allocations: 82.42 kB / 0.5308 GB, free: 25.62 MB / 378.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001219/0.3803, allocations: 72.5 kB / 0.5309 GB, free: 25.59 MB / 378.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001273/0.3816, allocations: 0.7792 MB / 0.5316 GB, free: 25.26 MB / 378.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.706e-05/0.3816, allocations: 0 / 0.5316 GB, free: 25.26 MB / 378.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.051e-05/0.3817, allocations: 26.19 kB / 0.5316 GB, free: 25.24 MB / 378.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.019e-05/0.3817, allocations: 15.97 kB / 0.5317 GB, free: 25.24 MB / 378.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001327/0.383, allocations: 0.8835 MB / 0.5325 GB, free: 24.99 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 0.003814/0.3869, allocations: 2.585 MB / 0.535 GB, free: 23.34 MB / 378.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.001486/0.3884, allocations: 1.022 MB / 0.536 GB, free: 22.82 MB / 378.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004649/0.3889, allocations: 317.5 kB / 0.5363 GB, free: 22.68 MB / 378.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.003481/0.3923, allocations: 2.85 MB / 0.5391 GB, free: 20.41 MB / 378.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.182e-05/0.3924, allocations: 41.06 kB / 0.5392 GB, free: 20.36 MB / 378.7 MB
Notification: Performance of pre-optimization done (n=41): time 1.984e-06/0.3924, allocations: 0 / 0.5392 GB, free: 20.36 MB / 378.7 MB
Notification: Performance of matching and sorting (n=46): time 0.002629/0.395, allocations: 1.249 MB / 0.5404 GB, free: 19.66 MB / 378.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.652e-05/0.3951, allocations: 56.47 kB / 0.5404 GB, free: 19.6 MB / 378.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004032/0.3955, allocations: 420 kB / 0.5408 GB, free: 19.39 MB / 378.7 MB
Notification: Performance of collectPreVariables (initialization): time 2.495e-05/0.3955, allocations: 31.95 kB / 0.5409 GB, free: 19.36 MB / 378.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001689/0.3957, allocations: 368.1 kB / 0.5412 GB, free: 19.06 MB / 378.7 MB
Notification: Performance of collectInitialBindings (initialization): time 8.807e-05/0.3958, allocations: 160.5 kB / 0.5414 GB, free: 18.94 MB / 378.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001502/0.3959, allocations: 126.5 kB / 0.5415 GB, free: 18.87 MB / 378.7 MB
Notification: Performance of setup shared object (initialization): time 7.766e-05/0.396, allocations: 363.7 kB / 0.5418 GB, free: 18.54 MB / 378.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002812/0.3963, allocations: 152.1 kB / 0.542 GB, free: 18.48 MB / 378.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004054/0.3967, allocations: 397.6 kB / 0.5424 GB, free: 18.12 MB / 378.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0007104/0.3974, allocations: 0.5797 MB / 0.5429 GB, free: 17.65 MB / 378.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.386e-06/0.3975, allocations: 2.844 kB / 0.5429 GB, free: 17.65 MB / 378.7 MB
Notification: Performance of matching and sorting (n=83) (initialization): time 0.000917/0.3984, allocations: 0.6186 MB / 0.5435 GB, free: 17.39 MB / 378.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.323e-05/0.3984, allocations: 13.97 kB / 0.5436 GB, free: 17.39 MB / 378.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.272e-05/0.3984, allocations: 11.28 kB / 0.5436 GB, free: 17.38 MB / 378.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.672e-05/0.3985, allocations: 16.28 kB / 0.5436 GB, free: 17.38 MB / 378.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0008435/0.3993, allocations: 222.3 kB / 0.5438 GB, free: 17.37 MB / 378.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.916e-05/0.3993, allocations: 22.41 kB / 0.5438 GB, free: 17.36 MB / 378.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003988/0.3997, allocations: 43.94 kB / 0.5439 GB, free: 17.34 MB / 378.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.573e-05/0.3998, allocations: 36.16 kB / 0.5439 GB, free: 17.34 MB / 378.7 MB
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 35
 * 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 (83):
 * Single equations (assignments): 83
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0002127/0.4, allocations: 202.3 kB / 0.5441 GB, free: 17.16 MB / 378.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 7.706e-05/0.4001, allocations: 53.83 kB / 0.5441 GB, free: 17.13 MB / 378.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0009486/0.4011, allocations: 0.5035 MB / 0.5446 GB, free: 16.91 MB / 378.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.472e-06/0.4011, allocations: 5.938 kB / 0.5446 GB, free: 16.91 MB / 378.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.539e-06/0.4011, allocations: 0 / 0.5446 GB, free: 16.91 MB / 378.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.362e-06/0.4011, allocations: 3.516 kB / 0.5446 GB, free: 16.91 MB / 378.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006993/0.4018, allocations: 0.6237 MB / 0.5452 GB, free: 16.5 MB / 378.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.818e-06/0.4018, allocations: 1.719 kB / 0.5452 GB, free: 16.5 MB / 378.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0007332/0.4026, allocations: 173 kB / 0.5454 GB, free: 16.48 MB / 378.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 5.791e-06/0.4026, allocations: 6.125 kB / 0.5454 GB, free: 16.48 MB / 378.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.355e-05/0.4026, allocations: 20.19 kB / 0.5454 GB, free: 16.47 MB / 378.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.138e-06/0.4026, allocations: 2.75 kB / 0.5454 GB, free: 16.47 MB / 378.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.514e-06/0.4026, allocations: 1.375 kB / 0.5454 GB, free: 16.47 MB / 378.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004438/0.4071, allocations: 3.14 MB / 0.5485 GB, free: 14.29 MB / 378.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001733/0.4073, allocations: 170.3 kB / 0.5487 GB, free: 14.12 MB / 378.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.556e-05/0.4073, allocations: 12 kB / 0.5487 GB, free: 14.11 MB / 378.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002623/0.4076, allocations: 19.42 kB / 0.5487 GB, free: 14.09 MB / 378.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.786e-05/0.4077, allocations: 42.45 kB / 0.5487 GB, free: 14.06 MB / 378.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.035e-05/0.4077, allocations: 16 kB / 0.5488 GB, free: 14.05 MB / 378.7 MB
Notification: Performance of sorting global known variables: time 0.0002182/0.408, allocations: 282 kB / 0.549 GB, free: 13.81 MB / 378.7 MB
Notification: Performance of sort global known variables: time 1.2e-07/0.408, allocations: 0 / 0.549 GB, free: 13.81 MB / 378.7 MB
Notification: Performance of remove unused functions: time 0.001105/0.4091, allocations: 374.7 kB / 0.5494 GB, free: 13.45 MB / 378.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 5
 * Number of states: 3 (solution.temperature,A.logn,B.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 (53):
 * Single equations (assignments): 53
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.000718/0.4098, allocations: 428.2 kB / 0.5498 GB, free: 13.06 MB / 378.7 MB
Notification: Performance of simCode: created initialization part: time 0.0006176/0.4104, allocations: 433.7 kB / 0.5502 GB, free: 12.68 MB / 378.7 MB
Notification: Performance of simCode: created event and clocks part: time 3.035e-06/0.4104, allocations: 1.938 kB / 0.5502 GB, free: 12.68 MB / 378.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002336/0.4107, allocations: 211.2 kB / 0.5504 GB, free: 12.49 MB / 378.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006859/0.4114, allocations: 124.5 kB / 0.5505 GB, free: 12.39 MB / 378.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001879/0.4133, allocations: 1.787 MB / 0.5523 GB, free: 10.65 MB / 378.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.00032/0.4136, allocations: 0.901 MB / 0.5532 GB, free: 9.805 MB / 378.7 MB
Notification: Performance of simCode: alias equations: time 0.0004828/0.4141, allocations: 128.5 kB / 0.5533 GB, free: 9.699 MB / 378.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000155/0.4143, allocations: 77.66 kB / 0.5533 GB, free: 9.633 MB / 378.7 MB
Notification: Performance of SimCode: time 4.61e-07/0.4143, allocations: 0 / 0.5533 GB, free: 9.633 MB / 378.7 MB
Notification: Performance of Templates: time 0.01575/0.43, allocations: 10.63 MB / 0.5637 GB, free: 1.73 MB / 378.7 MB
make -j1 -f Physiolibrary_Physiolibrary.Chemical.Examples.SimpleReaction.makefile
(rm -f Physiolibrary_Physiolibrary.Chemical.Examples.SimpleReaction.pipe ; mkfifo Physiolibrary_Physiolibrary.Chemical.Examples.SimpleReaction.pipe ; head -c 1048576 < Physiolibrary_Physiolibrary.Chemical.Examples.SimpleReaction.pipe >> ../files/Physiolibrary_Physiolibrary.Chemical.Examples.SimpleReaction.sim & ./Physiolibrary_Physiolibrary.Chemical.Examples.SimpleReaction  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Physiolibrary_Physiolibrary.Chemical.Examples.SimpleReaction.pipe 2>&1)