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 0.001216/0.00122, allocations: 108.2 kB / 16.41 MB, free: 6.504 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001209/0.001209, allocations: 187 kB / 17.34 MB, free: 5.742 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.251/1.251, allocations: 222.9 MB / 241 MB, free: 15.09 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.07882/0.07882, allocations: 15.3 MB / 306.5 MB, free: 15.39 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001165/0.001165, allocations: 68.09 kB / 425.9 MB, free: 11.43 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.08825/0.08943, allocations: 53.62 MB / 479.5 MB, free: 5.758 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 0.03477/0.1242, allocations: 29.19 MB / 0.4968 GB, free: 8.629 MB / 382.1 MB
Notification: Performance of NFInst.instExpressions: time 0.221/0.3453, allocations: 26.07 MB / 0.5222 GB, free: 15.06 MB / 382.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001439/0.3468, allocations: 25.34 kB / 0.5222 GB, free: 15.05 MB / 382.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001475/0.3482, allocations: 0.5943 MB / 0.5228 GB, free: 14.73 MB / 382.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.005798/0.3541, allocations: 2.144 MB / 0.5249 GB, free: 13.55 MB / 382.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.009385/0.3635, allocations: 3.518 MB / 0.5284 GB, free: 11.64 MB / 382.1 MB
Notification: Performance of NFFlatten.flatten: time 0.007155/0.3706, allocations: 7.387 MB / 0.5356 GB, free: 8.168 MB / 382.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.005845/0.3765, allocations: 5.928 MB / 0.5414 GB, free: 5.059 MB / 382.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.006268/0.3828, allocations: 4.874 MB / 0.5461 GB, free: 2.48 MB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.007056/0.3899, allocations: 4.63 MB / 0.5506 GB, free: 13.84 MB / 398.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.002415/0.3924, allocations: 0.668 MB / 0.5513 GB, free: 13.17 MB / 398.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01216/0.4045, allocations: 3.324 MB / 0.5545 GB, free: 9.844 MB / 398.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.003124/0.4077, allocations: 1.777 MB / 0.5563 GB, free: 8.062 MB / 398.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.005808/0.4135, allocations: 3.346 MB / 0.5595 GB, free: 4.703 MB / 398.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.01855/0.4321, allocations: 11.1 MB / 0.5704 GB, free: 9.566 MB / 414.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.823e-06/0.4321, allocations: 2.656 kB / 0.5704 GB, free: 9.566 MB / 414.1 MB
Notification: Performance of FrontEnd: time 1.543e-06/0.4321, allocations: 0 / 0.5704 GB, free: 9.566 MB / 414.1 MB
Notification: Performance of Transformations before backend: time 0.000243/0.4324, allocations: 0 / 0.5704 GB, free: 9.566 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 0.01815/0.4506, allocations: 7.426 MB / 0.5776 GB, free: 2.141 MB / 414.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.113e-05/0.4506, allocations: 8.031 kB / 0.5776 GB, free: 2.133 MB / 414.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006019/0.4566, allocations: 1.213 MB / 0.5788 GB, free: 0.918 MB / 414.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.006718/0.4634, allocations: 3.221 MB / 0.582 GB, free: 13.63 MB / 430.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0005801/0.464, allocations: 0.6805 MB / 0.5826 GB, free: 12.88 MB / 430.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.00193/0.4659, allocations: 0.4923 MB / 0.5831 GB, free: 12.39 MB / 430.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0175/0.4834, allocations: 9.362 MB / 0.5923 GB, free: 2.926 MB / 430.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 8.696e-05/0.4836, allocations: 10.62 kB / 0.5923 GB, free: 2.918 MB / 430.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0007188/0.4843, allocations: 192 kB / 0.5925 GB, free: 2.73 MB / 430.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.805e-05/0.4844, allocations: 120 kB / 0.5926 GB, free: 2.613 MB / 430.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02001/0.5044, allocations: 12.59 MB / 0.6049 GB, free: 6 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 0.05427/0.5587, allocations: 30.16 MB / 0.6343 GB, free: 7.18 MB / 478.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0557/0.6144, allocations: 41.27 MB / 0.6746 GB, free: 11.36 MB / 0.5137 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.007846/0.6223, allocations: 5.072 MB / 0.6796 GB, free: 6.262 MB / 0.5137 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.03438/0.6567, allocations: 20.89 MB / 0.7 GB, free: 444 kB / 0.5294 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.783e-05/0.6568, allocations: 69.11 kB / 0.7 GB, free: 364 kB / 0.5294 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.003176/0.66, allocations: 0.9669 MB / 0.701 GB, free: 15.39 MB / 0.545 GB
Notification: Performance of pre-optimization done (n=324): time 1.032e-05/0.66, allocations: 0 / 0.701 GB, free: 15.39 MB / 0.545 GB
Notification: Performance of matching and sorting (n=376): time 0.3097/0.9697, allocations: 24.39 MB / 0.7248 GB, free: 186.9 MB / 0.545 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.987e-05/0.9698, allocations: 89.86 kB / 0.7249 GB, free: 186.8 MB / 0.545 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003914/0.9737, allocations: 2.965 MB / 0.7278 GB, free: 185.8 MB / 0.545 GB
Notification: Performance of collectPreVariables (initialization): time 0.0008316/0.9746, allocations: 92.02 kB / 0.7279 GB, free: 185.7 MB / 0.545 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001143/0.9757, allocations: 2.156 MB / 0.73 GB, free: 184.1 MB / 0.545 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001549/0.9773, allocations: 1.295 MB / 0.7312 GB, free: 183.1 MB / 0.545 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001592/0.9789, allocations: 0.9799 MB / 0.7322 GB, free: 182.7 MB / 0.545 GB
Notification: Performance of setup shared object (initialization): time 4.431e-05/0.9789, allocations: 302.2 kB / 0.7325 GB, free: 182.4 MB / 0.545 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004233/0.9832, allocations: 2.962 MB / 0.7354 GB, free: 181.4 MB / 0.545 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.00466/0.9879, allocations: 4.477 MB / 0.7398 GB, free: 178.6 MB / 0.545 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.009299/0.9972, allocations: 7.803 MB / 0.7474 GB, free: 174 MB / 0.545 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.793e-05/0.9973, allocations: 16.91 kB / 0.7474 GB, free: 174 MB / 0.545 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05273/1.05, allocations: 13.82 MB / 0.7609 GB, free: 166.7 MB / 0.545 GB
Notification: Performance of prepare postOptimizeDAE: time 4.974e-05/1.05, allocations: 26.06 kB / 0.7609 GB, free: 166.7 MB / 0.545 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.71e-05/1.05, allocations: 48.28 kB / 0.761 GB, free: 166.7 MB / 0.545 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.007847/1.058, allocations: 3.475 MB / 0.7644 GB, free: 163.9 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.004938/1.063, allocations: 1.269 MB / 0.7656 GB, free: 162.6 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02739/1.09, allocations: 18.48 MB / 0.7836 GB, free: 143.7 MB / 0.545 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004362/1.095, allocations: 256.2 kB / 0.7839 GB, free: 143.5 MB / 0.545 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.000871/1.096, allocations: 287.7 kB / 0.7842 GB, free: 143.2 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 0.002505/1.098, allocations: 1.448 MB / 0.7856 GB, free: 141.8 MB / 0.545 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0008713/1.099, allocations: 342.3 kB / 0.7859 GB, free: 141.4 MB / 0.545 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03226/1.131, allocations: 9.664 MB / 0.7953 GB, free: 131.8 MB / 0.545 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.857e-05/1.131, allocations: 40 kB / 0.7954 GB, free: 131.8 MB / 0.545 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.6e-05/1.131, allocations: 4 kB / 0.7954 GB, free: 131.8 MB / 0.545 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.831e-05/1.132, allocations: 19.92 kB / 0.7954 GB, free: 131.8 MB / 0.545 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04173/1.173, allocations: 15.44 MB / 0.8105 GB, free: 116.4 MB / 0.545 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.576e-05/1.173, allocations: 4 kB / 0.8105 GB, free: 116.4 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004027/1.177, allocations: 0.8468 MB / 0.8113 GB, free: 115.5 MB / 0.545 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005581/1.183, allocations: 2.127 MB / 0.8134 GB, free: 113.4 MB / 0.545 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0008027/1.184, allocations: 135.8 kB / 0.8135 GB, free: 113.2 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.01974/1.204, allocations: 12.67 MB / 0.8259 GB, free: 100.2 MB / 0.545 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.236e-06/1.204, allocations: 7.016 kB / 0.8259 GB, free: 100.2 MB / 0.545 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03595/1.24, allocations: 12.97 MB / 0.8386 GB, free: 87.07 MB / 0.545 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.002763/1.242, allocations: 0.9297 MB / 0.8395 GB, free: 86.12 MB / 0.545 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.000856/1.243, allocations: 98.88 kB / 0.8396 GB, free: 86.02 MB / 0.545 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002496/1.246, allocations: 166.5 kB / 0.8397 GB, free: 85.86 MB / 0.545 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0009673/1.247, allocations: 458.4 kB / 0.8402 GB, free: 85.41 MB / 0.545 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002759/1.247, allocations: 147.9 kB / 0.8403 GB, free: 85.27 MB / 0.545 GB
Notification: Performance of sorting global known variables: time 0.002051/1.249, allocations: 1.989 MB / 0.8423 GB, free: 83.28 MB / 0.545 GB
Notification: Performance of sort global known variables: time 1.3e-07/1.249, allocations: 0 / 0.8423 GB, free: 83.28 MB / 0.545 GB
Notification: Performance of remove unused functions: time 0.006307/1.255, allocations: 2.05 MB / 0.8443 GB, free: 81.36 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 0.00225/1.258, allocations: 1.295 MB / 0.8455 GB, free: 80.34 MB / 0.545 GB
Notification: Performance of simCode: created initialization part: time 0.01381/1.271, allocations: 7.43 MB / 0.8528 GB, free: 72.88 MB / 0.545 GB
Notification: Performance of simCode: created event and clocks part: time 1.387e-05/1.272, allocations: 7.938 kB / 0.8528 GB, free: 72.87 MB / 0.545 GB
Notification: Performance of simCode: created simulation system equations: time 0.007685/1.279, allocations: 4.081 MB / 0.8568 GB, free: 68.75 MB / 0.545 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004315/1.284, allocations: 0.7887 MB / 0.8575 GB, free: 68.02 MB / 0.545 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01768/1.301, allocations: 10.75 MB / 0.868 GB, free: 57.21 MB / 0.545 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001994/1.303, allocations: 3.214 MB / 0.8712 GB, free: 53.96 MB / 0.545 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001936/1.305, allocations: 499.1 kB / 0.8717 GB, free: 53.47 MB / 0.545 GB
Notification: Performance of SimCode: time 8.81e-07/1.305, allocations: 0 / 0.8717 GB, free: 53.47 MB / 0.545 GB
Notification: Performance of Templates: time 0.363/1.668, allocations: 146.3 MB / 1.015 GB, free: 103.6 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)