Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.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 1.4.1-master/package.mo", uses=false)
Using package Chemical with version 1.4.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-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.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC")
translateModel(Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001585/0.001585, allocations: 100.1 kB / 15.88 MB, free: 12 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001908/0.001908, allocations: 196.4 kB / 16.79 MB, free: 6.809 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.37/1.37, allocations: 222.9 MB / 240.5 MB, free: 4.582 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2093/0.2093, allocations: 15.31 MB / 305.9 MB, free: 15.4 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001286/0.001286, allocations: 67.89 kB / 370.3 MB, free: 4.453 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.105/0.1063, allocations: 53.61 MB / 423.9 MB, free: 14.79 MB / 366.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:4740:7-4740:66: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 1.4.1-master/package.mo:4740:7-4740:66: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.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC): time 0.4006/0.5069, allocations: 29.97 MB / 453.9 MB, free: 38.59 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02861/0.5356, allocations: 26.03 MB / 479.9 MB, free: 25.55 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002666/0.5383, allocations: 43.44 kB / 480 MB, free: 25.54 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001813/0.5401, allocations: 0.5324 MB / 480.5 MB, free: 25.25 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.007518/0.5476, allocations: 1.869 MB / 482.4 MB, free: 24.12 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01171/0.5594, allocations: 3.081 MB / 485.4 MB, free: 22.31 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.008847/0.5683, allocations: 7.256 MB / 492.7 MB, free: 19.01 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006736/0.5751, allocations: 4.991 MB / 497.7 MB, free: 17.03 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.008124/0.5832, allocations: 4.728 MB / 0.4906 GB, free: 15.41 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.008444/0.5917, allocations: 4.386 MB / 0.4949 GB, free: 12.2 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.003007/0.5947, allocations: 484 kB / 0.4954 GB, free: 11.73 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01547/0.6102, allocations: 3.135 MB / 0.4984 GB, free: 8.887 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.00483/0.6151, allocations: 1.54 MB / 0.4999 GB, free: 7.703 MB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.008501/0.6236, allocations: 3.086 MB / 0.503 GB, free: 4.938 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.01291/0.6366, allocations: 8.364 MB / 0.5111 GB, free: 12.93 MB / 382.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.144e-06/0.6366, allocations: 4 kB / 0.5111 GB, free: 12.92 MB / 382.1 MB
Notification: Performance of FrontEnd: time 2.385e-06/0.6367, allocations: 0 / 0.5111 GB, free: 12.92 MB / 382.1 MB
Notification: Performance of Transformations before backend: time 0.0003663/0.637, allocations: 0 / 0.5111 GB, free: 12.92 MB / 382.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 1226
 * Number of variables: 1226
Notification: Performance of Generate backend data structure: time 0.02537/0.6624, allocations: 7.431 MB / 0.5184 GB, free: 5.406 MB / 382.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.855e-05/0.6625, allocations: 8.031 kB / 0.5184 GB, free: 5.398 MB / 382.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.007947/0.6704, allocations: 1.215 MB / 0.5196 GB, free: 4.18 MB / 382.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.008738/0.6792, allocations: 3.134 MB / 0.5226 GB, free: 0.9688 MB / 382.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0009143/0.6802, allocations: 0.6727 MB / 0.5233 GB, free: 232 kB / 382.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.003207/0.6834, allocations: 0.4962 MB / 0.5238 GB, free: 15.73 MB / 398.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02657/0.71, allocations: 9.366 MB / 0.5329 GB, free: 6.258 MB / 398.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001715/0.7102, allocations: 3.938 kB / 0.5329 GB, free: 6.254 MB / 398.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.002023/0.7123, allocations: 195.9 kB / 0.5331 GB, free: 6.062 MB / 398.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001087/0.7124, allocations: 116 kB / 0.5332 GB, free: 5.949 MB / 398.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0275/0.7399, allocations: 12.6 MB / 0.5455 GB, free: 9.332 MB / 414.1 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 0.06897/0.8089, allocations: 30.24 MB / 0.5751 GB, free: 10.39 MB / 446.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.2908/1.1, allocations: 41.27 MB / 0.6154 GB, free: 108.4 MB / 462.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.008451/1.108, allocations: 5.069 MB / 0.6203 GB, free: 108.4 MB / 462.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.03594/1.144, allocations: 20.92 MB / 0.6407 GB, free: 98.55 MB / 462.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.502e-05/1.144, allocations: 72.14 kB / 0.6408 GB, free: 98.48 MB / 462.1 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004103/1.148, allocations: 0.9466 MB / 0.6417 GB, free: 98.2 MB / 462.1 MB
Notification: Performance of pre-optimization done (n=324): time 1.567e-05/1.148, allocations: 0 / 0.6417 GB, free: 98.2 MB / 462.1 MB
Notification: Performance of matching and sorting (n=376): time 0.1027/1.251, allocations: 24.39 MB / 0.6656 GB, free: 90.96 MB / 462.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.212e-05/1.251, allocations: 96.33 kB / 0.6656 GB, free: 90.89 MB / 462.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004436/1.256, allocations: 2.958 MB / 0.6685 GB, free: 89.6 MB / 462.1 MB
Notification: Performance of collectPreVariables (initialization): time 0.001163/1.257, allocations: 85.39 kB / 0.6686 GB, free: 89.52 MB / 462.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.00125/1.258, allocations: 2.161 MB / 0.6707 GB, free: 87.63 MB / 462.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.00192/1.26, allocations: 1.3 MB / 0.672 GB, free: 86.51 MB / 462.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001774/1.262, allocations: 0.9775 MB / 0.673 GB, free: 85.97 MB / 462.1 MB
Notification: Performance of setup shared object (initialization): time 4.829e-05/1.262, allocations: 303.8 kB / 0.6732 GB, free: 85.67 MB / 462.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004271/1.266, allocations: 2.958 MB / 0.6761 GB, free: 84.14 MB / 462.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.005105/1.271, allocations: 4.478 MB / 0.6805 GB, free: 80.66 MB / 462.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01001/1.281, allocations: 7.808 MB / 0.6881 GB, free: 73.26 MB / 462.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.999e-05/1.282, allocations: 12 kB / 0.6881 GB, free: 73.25 MB / 462.1 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05369/1.335, allocations: 13.82 MB / 0.7016 GB, free: 59.8 MB / 462.1 MB
Notification: Performance of prepare postOptimizeDAE: time 5.434e-05/1.335, allocations: 28 kB / 0.7017 GB, free: 59.78 MB / 462.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.594e-05/1.335, allocations: 53.16 kB / 0.7017 GB, free: 59.73 MB / 462.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008258/1.344, allocations: 3.471 MB / 0.7051 GB, free: 56.41 MB / 462.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005156/1.349, allocations: 1.265 MB / 0.7063 GB, free: 55.14 MB / 462.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02778/1.377, allocations: 16.62 MB / 0.7226 GB, free: 38.17 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004843/1.382, allocations: 358 kB / 0.7229 GB, free: 37.83 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0009047/1.383, allocations: 279.8 kB / 0.7232 GB, free: 37.56 MB / 462.1 MB
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 218
 * 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 (599):
 * Single equations (assignments): 596
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 3
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 2 systems
   {(9,4,100.0%), (1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of prepare postOptimizeDAE: time 0.002926/1.385, allocations: 1.447 MB / 0.7246 GB, free: 36.1 MB / 462.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0009244/1.386, allocations: 339.7 kB / 0.7249 GB, free: 35.77 MB / 462.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03438/1.421, allocations: 9.677 MB / 0.7344 GB, free: 26.18 MB / 462.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.184e-05/1.421, allocations: 40 kB / 0.7344 GB, free: 26.14 MB / 462.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.923e-05/1.421, allocations: 4 kB / 0.7344 GB, free: 26.13 MB / 462.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001277/1.421, allocations: 19.92 kB / 0.7344 GB, free: 26.11 MB / 462.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04357/1.465, allocations: 15.45 MB / 0.7495 GB, free: 10.68 MB / 462.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.949e-05/1.465, allocations: 2.578 kB / 0.7495 GB, free: 10.68 MB / 462.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004388/1.469, allocations: 0.8507 MB / 0.7503 GB, free: 9.832 MB / 462.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.006262/1.475, allocations: 2.12 MB / 0.7524 GB, free: 7.75 MB / 462.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0009883/1.476, allocations: 139.9 kB / 0.7526 GB, free: 7.613 MB / 462.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02136/1.498, allocations: 11.44 MB / 0.7637 GB, free: 11.81 MB / 478.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.119e-06/1.498, allocations: 7.188 kB / 0.7637 GB, free: 11.8 MB / 478.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2981/1.796, allocations: 12.97 MB / 0.7764 GB, free: 131.9 MB / 478.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.00344/1.799, allocations: 0.9266 MB / 0.7773 GB, free: 131.8 MB / 478.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001049/1.8, allocations: 98.81 kB / 0.7774 GB, free: 131.8 MB / 478.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.003284/1.804, allocations: 254.5 kB / 0.7776 GB, free: 131.8 MB / 478.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001217/1.805, allocations: 453.4 kB / 0.7781 GB, free: 131.8 MB / 478.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003819/1.805, allocations: 146.7 kB / 0.7782 GB, free: 131.8 MB / 478.1 MB
Notification: Performance of sorting global known variables: time 0.002788/1.808, allocations: 1.987 MB / 0.7801 GB, free: 131.6 MB / 478.1 MB
Notification: Performance of sort global known variables: time 1.6e-07/1.808, allocations: 0 / 0.7801 GB, free: 131.6 MB / 478.1 MB
Notification: Performance of remove unused functions: time 0.00907/1.817, allocations: 2.048 MB / 0.7821 GB, free: 131.6 MB / 478.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 15
 * Number of states: 19 (solution.temperature,OxyRHm[1].logn,OxyRHm[2].logn,OxyRHm[3].logn,OxyRHm[4].logn,DeoxyRHm[1].logn,DeoxyRHm[2].logn,DeoxyRHm[3].logn,DeoxyRHm[4].logn,OxyTHm[1].logn,OxyTHm[2].logn,OxyTHm[3].logn,OxyTHm[4].logn,DeoxyTHm[1].logn,DeoxyTHm[2].logn,DeoxyTHm[3].logn,DeoxyTHm[4].logn,oxygen_unbound.logn,H2O.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 (408):
 * Single equations (assignments): 405
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 3
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 2 systems
   {(1,3,100.0%), (9,4,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of Backend phase and start with SimCode phase: time 0.003283/1.821, allocations: 1.288 MB / 0.7834 GB, free: 131.5 MB / 478.1 MB
Notification: Performance of simCode: created initialization part: time 0.01484/1.835, allocations: 7.398 MB / 0.7906 GB, free: 130.5 MB / 478.1 MB
Notification: Performance of simCode: created event and clocks part: time 1.177e-05/1.835, allocations: 0 / 0.7906 GB, free: 130.5 MB / 478.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.009432/1.845, allocations: 4.089 MB / 0.7946 GB, free: 129 MB / 478.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004701/1.85, allocations: 0.722 MB / 0.7953 GB, free: 128.8 MB / 478.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.02438/1.874, allocations: 12.89 MB / 0.8079 GB, free: 122.6 MB / 478.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.003897/1.878, allocations: 3.212 MB / 0.811 GB, free: 121.6 MB / 478.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.002518/1.881, allocations: 496.5 kB / 0.8115 GB, free: 121.5 MB / 478.1 MB
Notification: Performance of SimCode: time 1.242e-06/1.881, allocations: 0 / 0.8115 GB, free: 121.5 MB / 478.1 MB
Notification: Performance of Templates: time 0.3565/2.237, allocations: 146.2 MB / 0.9543 GB, free: 131 MB / 478.1 MB
make -j1 -f Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.makefile
(rm -f Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.sim & ./Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1)