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 0.001188/0.001187, allocations: 104.5 kB / 16.27 MB, free: 6.414 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001263/0.001263, allocations: 190.3 kB / 17.2 MB, free: 5.953 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.393/1.393, allocations: 222.9 MB / 240.9 MB, free: 15.26 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.07785/0.07785, allocations: 15.32 MB / 306.4 MB, free: 15.48 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001309/0.00131, allocations: 64.28 kB / 371 MB, free: 50.95 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1023/0.1037, allocations: 53.62 MB / 424.6 MB, free: 14.05 MB / 302.1 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 0.036/0.1397, allocations: 29.19 MB / 453.8 MB, free: 0.9688 MB / 318.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02956/0.1693, allocations: 26.08 MB / 479.9 MB, free: 6.785 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001975/0.1713, allocations: 23.88 kB / 479.9 MB, free: 6.762 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001687/0.173, allocations: 0.597 MB / 480.5 MB, free: 6.16 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.006614/0.1797, allocations: 2.141 MB / 482.6 MB, free: 4.004 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01002/0.1897, allocations: 3.515 MB / 486.1 MB, free: 480 kB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.007462/0.1972, allocations: 7.359 MB / 493.5 MB, free: 9.078 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006426/0.2036, allocations: 5.916 MB / 499.4 MB, free: 3.094 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.006568/0.2102, allocations: 4.854 MB / 0.4924 GB, free: 14.23 MB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.008407/0.2187, allocations: 4.627 MB / 0.497 GB, free: 9.59 MB / 382.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.00314/0.2218, allocations: 0.6718 MB / 0.4976 GB, free: 8.918 MB / 382.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0136/0.2355, allocations: 3.324 MB / 0.5009 GB, free: 5.59 MB / 382.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.003843/0.2394, allocations: 1.781 MB / 0.5026 GB, free: 3.805 MB / 382.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.007034/0.2464, allocations: 3.338 MB / 0.5059 GB, free: 464 kB / 382.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.2674/0.5138, allocations: 11 MB / 0.5166 GB, free: 31.32 MB / 382.1 MB
Notification: Performance of FrontEnd - DAE generated: time 1.091e-05/0.5139, allocations: 4.953 kB / 0.5166 GB, free: 31.32 MB / 382.1 MB
Notification: Performance of FrontEnd: time 2.645e-06/0.5139, allocations: 0 / 0.5166 GB, free: 31.32 MB / 382.1 MB
Notification: Performance of Transformations before backend: time 0.0003797/0.5143, allocations: 0 / 0.5166 GB, free: 31.32 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 0.03108/0.5454, allocations: 7.439 MB / 0.5239 GB, free: 28.99 MB / 382.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.873e-05/0.5454, allocations: 11.34 kB / 0.5239 GB, free: 28.99 MB / 382.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.008649/0.5541, allocations: 1.217 MB / 0.5251 GB, free: 28.7 MB / 382.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.009384/0.5635, allocations: 3.127 MB / 0.5281 GB, free: 28.04 MB / 382.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0006753/0.5642, allocations: 0.6742 MB / 0.5288 GB, free: 27.69 MB / 382.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.003857/0.5681, allocations: 0.4912 MB / 0.5293 GB, free: 27.68 MB / 382.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02441/0.5925, allocations: 9.37 MB / 0.5384 GB, free: 26.04 MB / 382.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001283/0.5927, allocations: 6.125 kB / 0.5384 GB, free: 26.04 MB / 382.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.001728/0.5944, allocations: 192.2 kB / 0.5386 GB, free: 25.89 MB / 382.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.253e-05/0.5945, allocations: 120.4 kB / 0.5387 GB, free: 25.89 MB / 382.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02414/0.6187, allocations: 12.59 MB / 0.551 GB, free: 17.11 MB / 382.1 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 0.07479/0.6935, allocations: 30.32 MB / 0.5806 GB, free: 2.746 MB / 398.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.06781/0.7614, allocations: 41.26 MB / 0.6209 GB, free: 6.992 MB / 446.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.01134/0.7727, allocations: 5.068 MB / 0.6259 GB, free: 1.898 MB / 446.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.05061/0.8234, allocations: 20.91 MB / 0.6463 GB, free: 12.3 MB / 478.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 8.272e-05/0.8235, allocations: 64.19 kB / 0.6463 GB, free: 12.23 MB / 478.1 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.005087/0.8286, allocations: 0.972 MB / 0.6473 GB, free: 11.28 MB / 478.1 MB
Notification: Performance of pre-optimization done (n=324): time 2.667e-05/0.8287, allocations: 6.25 kB / 0.6473 GB, free: 11.28 MB / 478.1 MB
Notification: Performance of matching and sorting (n=376): time 0.1121/0.9408, allocations: 24.39 MB / 0.6711 GB, free: 3 MB / 494.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 8.713e-05/0.9409, allocations: 90.36 kB / 0.6712 GB, free: 2.898 MB / 494.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.005543/0.9465, allocations: 2.959 MB / 0.6741 GB, free: 15.93 MB / 0.4981 GB
Notification: Performance of collectPreVariables (initialization): time 0.001369/0.9479, allocations: 85.7 kB / 0.6742 GB, free: 15.84 MB / 0.4981 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001783/0.9497, allocations: 2.169 MB / 0.6763 GB, free: 13.66 MB / 0.4981 GB
Notification: Performance of collectInitialBindings (initialization): time 0.002626/0.9523, allocations: 1.294 MB / 0.6776 GB, free: 12.38 MB / 0.4981 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.004356/0.9567, allocations: 0.9798 MB / 0.6785 GB, free: 11.39 MB / 0.4981 GB
Notification: Performance of setup shared object (initialization): time 0.0001053/0.9568, allocations: 305.1 kB / 0.6788 GB, free: 11.09 MB / 0.4981 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.006223/0.9631, allocations: 2.959 MB / 0.6817 GB, free: 8.121 MB / 0.4981 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.008394/0.9715, allocations: 4.48 MB / 0.6861 GB, free: 3.02 MB / 0.4981 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.262/1.234, allocations: 7.802 MB / 0.6937 GB, free: 189.9 MB / 0.4981 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.651e-05/1.234, allocations: 13.97 kB / 0.6937 GB, free: 189.9 MB / 0.4981 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.0592/1.293, allocations: 13.83 MB / 0.7072 GB, free: 186.6 MB / 0.4981 GB
Notification: Performance of prepare postOptimizeDAE: time 5.114e-05/1.293, allocations: 27.78 kB / 0.7072 GB, free: 186.6 MB / 0.4981 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.679e-05/1.293, allocations: 50.28 kB / 0.7073 GB, free: 186.6 MB / 0.4981 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008453/1.301, allocations: 3.475 MB / 0.7107 GB, free: 185.4 MB / 0.4981 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005827/1.307, allocations: 1.271 MB / 0.7119 GB, free: 185 MB / 0.4981 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.03005/1.337, allocations: 18.48 MB / 0.73 GB, free: 167.8 MB / 0.4981 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.005283/1.343, allocations: 259.8 kB / 0.7302 GB, free: 167.5 MB / 0.4981 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.00111/1.344, allocations: 279.8 kB / 0.7305 GB, free: 167.3 MB / 0.4981 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 0.002995/1.347, allocations: 1.442 MB / 0.7319 GB, free: 165.8 MB / 0.4981 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001027/1.348, allocations: 354.3 kB / 0.7322 GB, free: 165.7 MB / 0.4981 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03566/1.384, allocations: 9.661 MB / 0.7417 GB, free: 156.1 MB / 0.4981 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.466e-05/1.384, allocations: 41.78 kB / 0.7417 GB, free: 156.1 MB / 0.4981 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.259e-05/1.384, allocations: 4 kB / 0.7417 GB, free: 156.1 MB / 0.4981 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001419/1.384, allocations: 22.61 kB / 0.7417 GB, free: 156.1 MB / 0.4981 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04417/1.428, allocations: 15.44 MB / 0.7568 GB, free: 140.7 MB / 0.4981 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.43e-05/1.428, allocations: 11.53 kB / 0.7568 GB, free: 140.7 MB / 0.4981 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00469/1.433, allocations: 0.8447 MB / 0.7576 GB, free: 139.9 MB / 0.4981 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005747/1.439, allocations: 2.134 MB / 0.7597 GB, free: 137.8 MB / 0.4981 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001054/1.44, allocations: 135.9 kB / 0.7599 GB, free: 137.7 MB / 0.4981 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.0205/1.46, allocations: 12.68 MB / 0.7722 GB, free: 124.6 MB / 0.4981 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 6.362e-06/1.46, allocations: 8.453 kB / 0.7722 GB, free: 124.6 MB / 0.4981 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03876/1.499, allocations: 12.97 MB / 0.7849 GB, free: 111.7 MB / 0.4981 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.002761/1.502, allocations: 0.9315 MB / 0.7858 GB, free: 110.8 MB / 0.4981 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0009538/1.503, allocations: 91.97 kB / 0.7859 GB, free: 110.7 MB / 0.4981 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.00264/1.505, allocations: 166.5 kB / 0.7861 GB, free: 110.5 MB / 0.4981 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001016/1.506, allocations: 458.4 kB / 0.7865 GB, free: 110.1 MB / 0.4981 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003059/1.507, allocations: 143.9 kB / 0.7866 GB, free: 109.9 MB / 0.4981 GB
Notification: Performance of sorting global known variables: time 0.00232/1.509, allocations: 1.991 MB / 0.7886 GB, free: 107.9 MB / 0.4981 GB
Notification: Performance of sort global known variables: time 2.2e-07/1.509, allocations: 0.5625 kB / 0.7886 GB, free: 107.9 MB / 0.4981 GB
Notification: Performance of remove unused functions: time 0.008386/1.517, allocations: 2.05 MB / 0.7906 GB, free: 106 MB / 0.4981 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 0.003743/1.521, allocations: 1.296 MB / 0.7919 GB, free: 105 MB / 0.4981 GB
Notification: Performance of simCode: created initialization part: time 0.03001/1.551, allocations: 14.97 MB / 0.8065 GB, free: 90.02 MB / 0.4981 GB
Notification: Performance of simCode: created event and clocks part: time 9.958e-06/1.551, allocations: 0 / 0.8065 GB, free: 90.02 MB / 0.4981 GB
Notification: Performance of simCode: created simulation system equations: time 0.007986/1.559, allocations: 4.092 MB / 0.8105 GB, free: 85.89 MB / 0.4981 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004563/1.564, allocations: 0.7763 MB / 0.8112 GB, free: 85.2 MB / 0.4981 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.02162/1.586, allocations: 10.86 MB / 0.8218 GB, free: 74.42 MB / 0.4981 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002237/1.588, allocations: 3.21 MB / 0.825 GB, free: 71.22 MB / 0.4981 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.002203/1.59, allocations: 0.49 MB / 0.8254 GB, free: 70.73 MB / 0.4981 GB
Notification: Performance of SimCode: time 6.71e-07/1.59, allocations: 0 / 0.8254 GB, free: 70.73 MB / 0.4981 GB
Notification: Performance of Templates: time 0.3674/1.958, allocations: 145.8 MB / 0.9678 GB, free: 108 MB / 0.4981 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)