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 0.00159/0.00159, allocations: 109.5 kB / 16.41 MB, free: 6.492 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001373/0.001373, allocations: 187 kB / 17.34 MB, free: 5.762 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.32/1.32, allocations: 222.9 MB / 241 MB, free: 15.15 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.07612/0.07612, allocations: 15.3 MB / 306.5 MB, free: 15.41 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001266/0.001266, allocations: 64.12 kB / 425.9 MB, free: 11.55 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.08934/0.09061, allocations: 53.61 MB / 479.5 MB, free: 5.891 MB / 350.1 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 0.03736/0.128, allocations: 29.2 MB / 0.4968 GB, free: 8.758 MB / 382.1 MB
Notification: Performance of NFInst.instExpressions: time 0.2346/0.3626, allocations: 26.06 MB / 0.5222 GB, free: 15.16 MB / 382.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001571/0.3642, allocations: 27.38 kB / 0.5222 GB, free: 15.16 MB / 382.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001546/0.3658, allocations: 0.5955 MB / 0.5228 GB, free: 14.83 MB / 382.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.005922/0.3717, allocations: 2.148 MB / 0.5249 GB, free: 13.65 MB / 382.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01008/0.3818, allocations: 3.519 MB / 0.5284 GB, free: 11.68 MB / 382.1 MB
Notification: Performance of NFFlatten.flatten: time 0.008081/0.3899, allocations: 7.396 MB / 0.5356 GB, free: 8.199 MB / 382.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006245/0.3962, allocations: 5.93 MB / 0.5414 GB, free: 5.109 MB / 382.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.007638/0.4039, allocations: 4.871 MB / 0.5461 GB, free: 2.582 MB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.007818/0.4118, allocations: 4.622 MB / 0.5506 GB, free: 13.95 MB / 398.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.002561/0.4144, allocations: 0.668 MB / 0.5513 GB, free: 13.28 MB / 398.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01456/0.4289, allocations: 3.32 MB / 0.5545 GB, free: 9.957 MB / 398.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.003716/0.4327, allocations: 1.788 MB / 0.5563 GB, free: 8.164 MB / 398.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.00729/0.44, allocations: 3.342 MB / 0.5595 GB, free: 4.809 MB / 398.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02255/0.4626, allocations: 11.11 MB / 0.5704 GB, free: 9.668 MB / 414.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.173e-06/0.4626, allocations: 0 / 0.5704 GB, free: 9.668 MB / 414.1 MB
Notification: Performance of FrontEnd: time 2.113e-06/0.4627, allocations: 2.656 kB / 0.5704 GB, free: 9.668 MB / 414.1 MB
Notification: Performance of Transformations before backend: time 0.0003078/0.463, allocations: 0 / 0.5704 GB, free: 9.668 MB / 414.1 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 0.02151/0.4845, allocations: 7.421 MB / 0.5776 GB, free: 2.246 MB / 414.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.616e-05/0.4846, allocations: 10.72 kB / 0.5776 GB, free: 2.238 MB / 414.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.007169/0.4917, allocations: 1.21 MB / 0.5788 GB, free: 1.023 MB / 414.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.007602/0.4994, allocations: 3.221 MB / 0.582 GB, free: 13.73 MB / 430.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0007559/0.5002, allocations: 0.6766 MB / 0.5826 GB, free: 12.99 MB / 430.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002167/0.5023, allocations: 0.4948 MB / 0.5831 GB, free: 12.5 MB / 430.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0213/0.5237, allocations: 9.362 MB / 0.5923 GB, free: 3.035 MB / 430.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001228/0.5238, allocations: 7.938 kB / 0.5923 GB, free: 3.027 MB / 430.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.001158/0.525, allocations: 196 kB / 0.5925 GB, free: 2.836 MB / 430.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.184e-05/0.5251, allocations: 116 kB / 0.5926 GB, free: 2.723 MB / 430.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02287/0.548, allocations: 12.59 MB / 0.6049 GB, free: 6.113 MB / 446.1 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 0.0626/0.6106, allocations: 30.17 MB / 0.6343 GB, free: 7.285 MB / 478.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.06198/0.6727, allocations: 41.26 MB / 0.6746 GB, free: 11.48 MB / 0.5137 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.009122/0.6818, allocations: 5.068 MB / 0.6796 GB, free: 6.379 MB / 0.5137 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.04095/0.7228, allocations: 20.9 MB / 0.7 GB, free: 0.5391 MB / 0.5294 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.16e-05/0.7229, allocations: 65.11 kB / 0.7 GB, free: 476 kB / 0.5294 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004086/0.727, allocations: 0.963 MB / 0.701 GB, free: 15.5 MB / 0.545 GB
Notification: Performance of pre-optimization done (n=324): time 2.265e-05/0.7271, allocations: 0 / 0.701 GB, free: 15.5 MB / 0.545 GB
Notification: Performance of matching and sorting (n=376): time 0.3543/1.081, allocations: 24.4 MB / 0.7248 GB, free: 186.9 MB / 0.545 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 8.611e-05/1.081, allocations: 92.64 kB / 0.7249 GB, free: 186.8 MB / 0.545 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004564/1.086, allocations: 2.958 MB / 0.7278 GB, free: 185.8 MB / 0.545 GB
Notification: Performance of collectPreVariables (initialization): time 0.001056/1.087, allocations: 89.67 kB / 0.7279 GB, free: 185.7 MB / 0.545 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001277/1.088, allocations: 2.158 MB / 0.73 GB, free: 184.1 MB / 0.545 GB
Notification: Performance of collectInitialBindings (initialization): time 0.00161/1.09, allocations: 1.302 MB / 0.7312 GB, free: 183.1 MB / 0.545 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001577/1.092, allocations: 0.973 MB / 0.7322 GB, free: 182.7 MB / 0.545 GB
Notification: Performance of setup shared object (initialization): time 4.385e-05/1.092, allocations: 308.8 kB / 0.7325 GB, free: 182.4 MB / 0.545 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.00453/1.096, allocations: 2.953 MB / 0.7354 GB, free: 181.5 MB / 0.545 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.005555/1.102, allocations: 4.485 MB / 0.7398 GB, free: 178.6 MB / 0.545 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0105/1.112, allocations: 7.808 MB / 0.7474 GB, free: 174.1 MB / 0.545 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0001049/1.112, allocations: 19.03 kB / 0.7474 GB, free: 174.1 MB / 0.545 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05444/1.167, allocations: 13.82 MB / 0.7609 GB, free: 166.8 MB / 0.545 GB
Notification: Performance of prepare postOptimizeDAE: time 5.816e-05/1.167, allocations: 25.72 kB / 0.7609 GB, free: 166.8 MB / 0.545 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.464e-05/1.167, allocations: 48.97 kB / 0.761 GB, free: 166.8 MB / 0.545 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008072/1.175, allocations: 3.472 MB / 0.7644 GB, free: 163.9 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005169/1.18, allocations: 1.27 MB / 0.7656 GB, free: 162.7 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02928/1.21, allocations: 18.48 MB / 0.7836 GB, free: 143.8 MB / 0.545 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004835/1.215, allocations: 255.8 kB / 0.7839 GB, free: 143.6 MB / 0.545 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001124/1.216, allocations: 286.3 kB / 0.7842 GB, free: 143.3 MB / 0.545 GB
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 0.003102/1.219, allocations: 1.451 MB / 0.7856 GB, free: 141.8 MB / 0.545 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0009826/1.22, allocations: 342 kB / 0.7859 GB, free: 141.5 MB / 0.545 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03432/1.254, allocations: 9.666 MB / 0.7953 GB, free: 131.9 MB / 0.545 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.74e-05/1.254, allocations: 40 kB / 0.7954 GB, free: 131.9 MB / 0.545 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.208e-05/1.254, allocations: 4 kB / 0.7954 GB, free: 131.9 MB / 0.545 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001301/1.254, allocations: 19.92 kB / 0.7954 GB, free: 131.8 MB / 0.545 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04404/1.299, allocations: 15.44 MB / 0.8105 GB, free: 116.4 MB / 0.545 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.367e-05/1.299, allocations: 4 kB / 0.8105 GB, free: 116.4 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004524/1.303, allocations: 0.8464 MB / 0.8113 GB, free: 115.6 MB / 0.545 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005797/1.309, allocations: 2.119 MB / 0.8134 GB, free: 113.4 MB / 0.545 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0009169/1.31, allocations: 143.8 kB / 0.8135 GB, free: 113.3 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02075/1.331, allocations: 12.67 MB / 0.8259 GB, free: 100.2 MB / 0.545 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.429e-06/1.331, allocations: 4.875 kB / 0.8259 GB, free: 100.2 MB / 0.545 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03873/1.369, allocations: 12.97 MB / 0.8386 GB, free: 87.14 MB / 0.545 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.002726/1.372, allocations: 0.9375 MB / 0.8395 GB, free: 86.18 MB / 0.545 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0009433/1.373, allocations: 90.61 kB / 0.8396 GB, free: 86.09 MB / 0.545 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002675/1.376, allocations: 171.8 kB / 0.8397 GB, free: 85.93 MB / 0.545 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0009529/1.377, allocations: 454.5 kB / 0.8402 GB, free: 85.48 MB / 0.545 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002966/1.377, allocations: 143.9 kB / 0.8403 GB, free: 85.34 MB / 0.545 GB
Notification: Performance of sorting global known variables: time 0.002178/1.379, allocations: 1.994 MB / 0.8422 GB, free: 83.35 MB / 0.545 GB
Notification: Performance of sort global known variables: time 1.3e-07/1.379, allocations: 0 / 0.8422 GB, free: 83.35 MB / 0.545 GB
Notification: Performance of remove unused functions: time 0.006723/1.386, allocations: 2.053 MB / 0.8443 GB, free: 81.42 MB / 0.545 GB
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 0.002541/1.389, allocations: 1.306 MB / 0.8455 GB, free: 80.39 MB / 0.545 GB
Notification: Performance of simCode: created initialization part: time 0.01298/1.402, allocations: 7.429 MB / 0.8528 GB, free: 72.93 MB / 0.545 GB
Notification: Performance of simCode: created event and clocks part: time 1.186e-05/1.402, allocations: 4 kB / 0.8528 GB, free: 72.93 MB / 0.545 GB
Notification: Performance of simCode: created simulation system equations: time 0.007635/1.409, allocations: 4.09 MB / 0.8568 GB, free: 68.8 MB / 0.545 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003713/1.413, allocations: 0.7757 MB / 0.8575 GB, free: 68.08 MB / 0.545 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01748/1.431, allocations: 10.74 MB / 0.868 GB, free: 57.29 MB / 0.545 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002111/1.433, allocations: 3.222 MB / 0.8712 GB, free: 54.03 MB / 0.545 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001899/1.435, allocations: 497.8 kB / 0.8716 GB, free: 53.54 MB / 0.545 GB
Notification: Performance of SimCode: time 7.31e-07/1.435, allocations: 0 / 0.8716 GB, free: 53.54 MB / 0.545 GB
Notification: Performance of Templates: time 0.3638/1.799, allocations: 147 MB / 1.015 GB, free: 103.2 MB / 0.545 GB
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)