Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.conf.json
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/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/Chemical 1.4.0-master/package.mo", uses=false)
Using package Chemical with version 1.4.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/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)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: translateModel(Chemical.Examples.Hemoglobin.HemoglobinCarboxylation,tolerance=1e-05,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation")
translateModel(Chemical.Examples.Hemoglobin.HemoglobinCarboxylation,tolerance=1e-05,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001021/0.001021, allocations: 99.7 kB / 15.05 MB, free: 1.105 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.00118/0.00118, allocations: 177.3 kB / 15.94 MB, free: 228 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.386/1.386, allocations: 223.2 MB / 239.9 MB, free: 5.332 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo): time 0.2298/0.2298, allocations: 15.26 MB / 306.2 MB, free: 15.79 MB / 254.1 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0003284/0.0003286, allocations: 8 kB / 371.4 MB, free: 4.004 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.363/0.3634, allocations: 54.63 MB / 426 MB, free: 40.08 MB / 350.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65: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 1.4.0-master/package.mo:3011:6-3011:65: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.Examples.Hemoglobin.HemoglobinCarboxylation): time 0.01579/0.3792, allocations: 20.03 MB / 446 MB, free: 29.13 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.06885/0.4481, allocations: 61.33 MB / 0.4955 GB, free: 1.039 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.006438/0.4546, allocations: 103.2 kB / 0.4956 GB, free: 0.9844 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.006534/0.4611, allocations: 1.496 MB / 0.497 GB, free: 184 kB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.02435/0.4855, allocations: 5.736 MB / 0.5026 GB, free: 12.41 MB / 382.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0338/0.5193, allocations: 8.802 MB / 0.5112 GB, free: 4.539 MB / 382.1 MB
Notification: Performance of NFFlatten.flatten: time 0.02354/0.5429, allocations: 15.92 MB / 0.5268 GB, free: 4.594 MB / 398.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.01895/0.5619, allocations: 16.06 MB / 0.5424 GB, free: 4.453 MB / 414.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.02487/0.5868, allocations: 14.53 MB / 0.5566 GB, free: 5.875 MB / 430.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.02446/0.6113, allocations: 13.07 MB / 0.5694 GB, free: 8.766 MB / 446.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.007897/0.6193, allocations: 1.426 MB / 0.5708 GB, free: 7.34 MB / 446.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.6366/1.256, allocations: 9.958 MB / 0.5805 GB, free: 36.64 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.01261/1.269, allocations: 4.858 MB / 0.5853 GB, free: 36.64 MB / 446.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.01029/1.279, allocations: 3.226 MB / 0.5884 GB, free: 36.61 MB / 446.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.05078/1.33, allocations: 30.24 MB / 0.6179 GB, free: 31.71 MB / 446.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.709e-06/1.33, allocations: 1.969 kB / 0.6179 GB, free: 31.71 MB / 446.1 MB
Notification: Performance of FrontEnd: time 2.304e-06/1.33, allocations: 0 / 0.6179 GB, free: 31.71 MB / 446.1 MB
Notification: Performance of Transformations before backend: time 0.001579/1.331, allocations: 0 / 0.6179 GB, free: 31.71 MB / 446.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 3808
 * Number of variables: 3808
Notification: Performance of Generate backend data structure: time 0.07784/1.409, allocations: 20.27 MB / 0.6377 GB, free: 21.7 MB / 446.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.274e-05/1.409, allocations: 12.41 kB / 0.6378 GB, free: 21.7 MB / 446.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02626/1.436, allocations: 3.89 MB / 0.6416 GB, free: 18.47 MB / 446.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.03264/1.468, allocations: 10.88 MB / 0.6522 GB, free: 11.09 MB / 446.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.001843/1.47, allocations: 2.134 MB / 0.6543 GB, free: 9.238 MB / 446.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.01074/1.481, allocations: 1.528 MB / 0.6558 GB, free: 8.211 MB / 446.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.09824/1.579, allocations: 34.56 MB / 0.6895 GB, free: 396 kB / 462.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0009605/1.58, allocations: 10.28 kB / 0.6895 GB, free: 392 kB / 462.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01518/1.595, allocations: 0.5855 MB / 0.6901 GB, free: 268 kB / 462.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0004334/1.596, allocations: 360 kB / 0.6904 GB, free: 15.91 MB / 478.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.1052/1.701, allocations: 46.74 MB / 0.7361 GB, free: 9.336 MB / 0.4982 GB
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 0.619/2.32, allocations: 127 MB / 0.8601 GB, free: 83.82 MB / 0.5294 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.839/3.159, allocations: 275.9 MB / 1.13 GB, free: 126 MB / 0.5763 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.1824/3.342, allocations: 86.93 MB / 1.214 GB, free: 41.12 MB / 0.5763 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 8.594e-05/3.342, allocations: 134.4 kB / 1.215 GB, free: 40.98 MB / 0.5763 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.02433/3.366, allocations: 4.441 MB / 1.219 GB, free: 36.62 MB / 0.5763 GB
Notification: Performance of pre-optimization done (n=995): time 4.257e-05/3.366, allocations: 7.938 kB / 1.219 GB, free: 36.62 MB / 0.5763 GB
Notification: Performance of matching and sorting (n=1129): time 1.027/4.393, allocations: 136.2 MB / 1.352 GB, free: 171.2 MB / 0.5763 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001622/4.394, allocations: 164.2 kB / 1.352 GB, free: 171 MB / 0.5763 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.02166/4.415, allocations: 10.08 MB / 1.362 GB, free: 161 MB / 0.5763 GB
Notification: Performance of collectPreVariables (initialization): time 0.005683/4.421, allocations: 213.7 kB / 1.362 GB, free: 160.8 MB / 0.5763 GB
Notification: Performance of collectInitialEqns (initialization): time 0.00711/4.428, allocations: 6.881 MB / 1.369 GB, free: 153.9 MB / 0.5763 GB
Notification: Performance of collectInitialBindings (initialization): time 0.01054/4.439, allocations: 3.908 MB / 1.373 GB, free: 150 MB / 0.5763 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.007158/4.446, allocations: 296 kB / 1.373 GB, free: 149.7 MB / 0.5763 GB
Notification: Performance of setup shared object (initialization): time 0.002013/4.448, allocations: 0.9061 MB / 1.374 GB, free: 148.8 MB / 0.5763 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.02571/4.474, allocations: 11.77 MB / 1.385 GB, free: 137 MB / 0.5763 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.02811/4.502, allocations: 16.44 MB / 1.401 GB, free: 118.5 MB / 0.5763 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.03002/4.532, allocations: 14.09 MB / 1.415 GB, free: 104.4 MB / 0.5763 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002192/4.532, allocations: 44 kB / 1.415 GB, free: 104.3 MB / 0.5763 GB
Notification: Performance of matching and sorting (n=1889) (initialization): time 0.7572/5.289, allocations: 81.41 MB / 1.495 GB, free: 190.5 MB / 0.5763 GB
Notification: Performance of prepare postOptimizeDAE: time 0.000227/5.29, allocations: 73.42 kB / 1.495 GB, free: 190.5 MB / 0.5763 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0003073/5.29, allocations: 147.2 kB / 1.495 GB, free: 190.5 MB / 0.5763 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.06138/5.351, allocations: 22.53 MB / 1.517 GB, free: 180.1 MB / 0.5763 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01897/5.37, allocations: 3.726 MB / 1.521 GB, free: 179.3 MB / 0.5763 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.2265/5.597, allocations: 93.74 MB / 1.612 GB, free: 87.66 MB / 0.5763 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02506/5.622, allocations: 1.151 MB / 1.613 GB, free: 86.55 MB / 0.5763 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.007666/5.63, allocations: 0.9312 MB / 1.614 GB, free: 85.62 MB / 0.5763 GB
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 677
 * 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 (1841):
 * Single equations (assignments): 1838
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 0
 * Torn equation systems: 3
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 2 {(1,100.0%) 3,(33,82.4%) 10}
 * Non-linear torn systems: 1 {1 3}
Notification: Performance of prepare postOptimizeDAE: time 0.02477/5.655, allocations: 5.38 MB / 1.619 GB, free: 80.47 MB / 0.5763 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.01078/5.665, allocations: 1.053 MB / 1.62 GB, free: 79.98 MB / 0.5763 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.6265/6.292, allocations: 48.51 MB / 1.668 GB, free: 194.9 MB / 0.5763 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0002703/6.292, allocations: 119.2 kB / 1.668 GB, free: 194.9 MB / 0.5763 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0002653/6.293, allocations: 18.22 kB / 1.668 GB, free: 194.9 MB / 0.5763 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0004681/6.293, allocations: 63.44 kB / 1.668 GB, free: 194.9 MB / 0.5763 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3876/6.681, allocations: 72.83 MB / 1.739 GB, free: 155 MB / 0.5763 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001615/6.681, allocations: 3.984 kB / 1.739 GB, free: 155 MB / 0.5763 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01529/6.696, allocations: 2.423 MB / 1.741 GB, free: 152.6 MB / 0.5763 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.03152/6.728, allocations: 11.75 MB / 1.753 GB, free: 140.9 MB / 0.5763 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.004894/6.733, allocations: 483.5 kB / 1.753 GB, free: 140.4 MB / 0.5763 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1049/6.838, allocations: 44.75 MB / 1.797 GB, free: 95.33 MB / 0.5763 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.44e-06/6.838, allocations: 7.938 kB / 1.797 GB, free: 95.32 MB / 0.5763 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.5851/7.423, allocations: 63.3 MB / 1.859 GB, free: 181.4 MB / 0.5763 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.01394/7.437, allocations: 3.282 MB / 1.862 GB, free: 181 MB / 0.5763 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.006038/7.443, allocations: 292.7 kB / 1.862 GB, free: 180.8 MB / 0.5763 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01615/7.459, allocations: 0.7927 MB / 1.863 GB, free: 180.6 MB / 0.5763 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.008268/7.467, allocations: 1.492 MB / 1.865 GB, free: 180.4 MB / 0.5763 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.005909/7.473, allocations: 472.9 kB / 1.865 GB, free: 180.4 MB / 0.5763 GB
Notification: Performance of sorting global known variables: time 0.01696/7.49, allocations: 6.889 MB / 1.872 GB, free: 178 MB / 0.5763 GB
Notification: Performance of sort global known variables: time 1.573e-06/7.49, allocations: 0 / 1.872 GB, free: 178 MB / 0.5763 GB
Notification: Performance of remove unused functions: time 0.03671/7.527, allocations: 6.591 MB / 1.878 GB, free: 177.3 MB / 0.5763 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 15
 * Number of states: 60 (solution.temperature,O2_free.logn,H2O.logn,relaxed.OxyHm[1].logn,relaxed.OxyHm[2].logn,relaxed.OxyHm[3].logn,relaxed.OxyHm[4].logn,relaxed.DeoxyHm[1].logn,relaxed.DeoxyHm[2].logn,relaxed.DeoxyHm[3].logn,relaxed.DeoxyHm[4].logn,relaxed.HmAH[1].logn,relaxed.HmAH[2].logn,relaxed.HmAH[3].logn,relaxed.HmAH[4].logn,relaxed.HmA[1].logn,relaxed.HmA[2].logn,relaxed.HmA[3].logn,relaxed.HmA[4].logn,relaxed.HmNH3[1].logn,relaxed.HmNH3[2].logn,relaxed.HmNH3[3].logn,relaxed.HmNH3[4].logn,relaxed.HmNH2[1].logn,relaxed.HmNH2[2].logn,relaxed.HmNH2[3].logn,relaxed.HmNH2[4].logn,relaxed.HmNHCOO[1].logn,relaxed.HmNHCOO[2].logn,relaxed.HmNHCOO[3].logn,relaxed.HmNHCOO[4].logn,tensed.OxyHm[1].logn,tensed.OxyHm[2].logn,tensed.OxyHm[3].logn,tensed.OxyHm[4].logn,tensed.DeoxyHm[1].logn,tensed.DeoxyHm[2].logn,tensed.DeoxyHm[3].logn,tensed.DeoxyHm[4].logn,tensed.HmAH[1].logn,tensed.HmAH[2].logn,tensed.HmAH[3].logn,tensed.HmAH[4].logn,tensed.HmA[1].logn,tensed.HmA[2].logn,tensed.HmA[3].logn,tensed.HmA[4].logn,tensed.HmNH3[1].logn,tensed.HmNH3[2].logn,tensed.HmNH3[3].logn,tensed.HmNH3[4].logn,tensed.HmNH2[1].logn,tensed.HmNH2[2].logn,tensed.HmNH2[3].logn,tensed.HmNH2[4].logn,tensed.HmNHCOO[1].logn,tensed.HmNHCOO[2].logn,tensed.HmNHCOO[3].logn,tensed.HmNHCOO[4].logn,CO2_free.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 (1234):
 * Single equations (assignments): 1231
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 0
 * Torn equation systems: 3
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 2 {(1,100.0%) 3,(33,82.4%) 10}
 * Non-linear torn systems: 1 {1 3}
Notification: Performance of Backend phase and start with SimCode phase: time 0.01206/7.539, allocations: 3.441 MB / 1.882 GB, free: 176.6 MB / 0.5763 GB
Notification: Performance of simCode: created initialization part: time 0.07288/7.612, allocations: 27.63 MB / 1.909 GB, free: 166.3 MB / 0.5763 GB
Notification: Performance of simCode: created event and clocks part: time 1.647e-05/7.612, allocations: 3.844 kB / 1.909 GB, free: 166.3 MB / 0.5763 GB
Notification: Performance of simCode: created simulation system equations: time 0.04309/7.655, allocations: 14.83 MB / 1.923 GB, free: 156 MB / 0.5763 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.01587/7.671, allocations: 2.175 MB / 1.925 GB, free: 154.3 MB / 0.5763 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.1053/7.776, allocations: 43.18 MB / 1.967 GB, free: 115.4 MB / 0.5763 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01589/7.792, allocations: 10.22 MB / 1.977 GB, free: 105.1 MB / 0.5763 GB
Notification: Performance of simCode: alias equations: time 0.0204/7.813, allocations: 5.29 MB / 1.983 GB, free: 99.88 MB / 0.5763 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.009606/7.822, allocations: 1.428 MB / 1.984 GB, free: 98.45 MB / 0.5763 GB
Notification: Performance of SimCode: time 1.233e-06/7.822, allocations: 0 / 1.984 GB, free: 98.45 MB / 0.5763 GB
Notification: Performance of Templates: time 0.9967/8.819, allocations: 300.5 MB / 2.277 GB, free: 179 MB / 0.5763 GB
make -j1 -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.makefile
Environment - environmentSimulation:
(rm -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.sim & ./Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe 2>&1)
Environment - environmentSimulation: