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) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001412/0.001412, allocations: 113.8 kB / 17.61 MB, free: 4.703 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001342/0.001342, allocations: 186 kB / 20.78 MB, free: 1.547 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.419/1.419, allocations: 225.6 MB / 249.4 MB, free: 3.176 MB / 190.1 MB
"
[Timeout remaining time 178]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.09424/0.09424, allocations: 15.54 MB / 320 MB, free: 13.13 MB / 254.1 MB
"
[Timeout remaining time 180]
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=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC")
translateModel(Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 0.001939/0.001939, allocations: 64.97 kB / 448.3 MB, free: 46.17 MB / 366.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1011/0.103, allocations: 56.56 MB / 0.493 GB, free: 19.05 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 0.0377/0.1407, allocations: 30.17 MB / 0.5224 GB, free: 7.051 MB / 382.1 MB
Notification: Performance of NFInst.instExpressions: time 0.03537/0.1761, allocations: 26.21 MB / 0.548 GB, free: 12.74 MB / 414.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001819/0.1779, allocations: 23.88 kB / 0.5481 GB, free: 12.71 MB / 414.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.002215/0.1801, allocations: 0.6009 MB / 0.5486 GB, free: 12.11 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.007752/0.1879, allocations: 2.161 MB / 0.5508 GB, free: 9.934 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01187/0.1997, allocations: 3.542 MB / 0.5542 GB, free: 6.371 MB / 414.1 MB
Notification: Performance of NFFlatten.flatten: time 0.01164/0.2114, allocations: 7.398 MB / 0.5614 GB, free: 14.95 MB / 430.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.007553/0.2189, allocations: 4.319 MB / 0.5657 GB, free: 10.55 MB / 430.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.008742/0.2277, allocations: 4.889 MB / 0.5704 GB, free: 5.652 MB / 430.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.009009/0.2367, allocations: 4.768 MB / 0.5751 GB, free: 0.8711 MB / 430.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.003141/0.2398, allocations: 0.6758 MB / 0.5758 GB, free: 200 kB / 430.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01261/0.2524, allocations: 3.366 MB / 0.579 GB, free: 12.82 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.003658/0.2561, allocations: 1.8 MB / 0.5808 GB, free: 11.02 MB / 446.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.007539/0.2636, allocations: 3.361 MB / 0.5841 GB, free: 7.645 MB / 446.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02778/0.2914, allocations: 11.2 MB / 0.595 GB, free: 12.41 MB / 462.1 MB
Notification: Performance of FrontEnd - DAE generated: time 8.316e-06/0.2914, allocations: 0 / 0.595 GB, free: 12.41 MB / 462.1 MB
Notification: Performance of FrontEnd: time 2.114e-06/0.2914, allocations: 0 / 0.595 GB, free: 12.41 MB / 462.1 MB
Notification: Performance of Transformations before backend: time 0.0004923/0.2919, allocations: 0 / 0.595 GB, free: 12.41 MB / 462.1 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 0.03431/0.3262, allocations: 7.32 MB / 0.6022 GB, free: 5 MB / 462.1 MB
Notification: Performance of prepare preOptimizeDAE: time 6.296e-05/0.3263, allocations: 8.031 kB / 0.6022 GB, free: 4.992 MB / 462.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.01135/0.3376, allocations: 1.238 MB / 0.6034 GB, free: 3.75 MB / 462.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.01113/0.3488, allocations: 3.256 MB / 0.6066 GB, free: 428 kB / 462.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.2967/0.6454, allocations: 0.6708 MB / 0.6072 GB, free: 91.61 MB / 462.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002503/0.6479, allocations: 0.4955 MB / 0.6077 GB, free: 91.61 MB / 462.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02328/0.6712, allocations: 9.449 MB / 0.6169 GB, free: 89.96 MB / 462.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001172/0.6713, allocations: 2.031 kB / 0.6169 GB, free: 89.96 MB / 462.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.001072/0.6724, allocations: 197.9 kB / 0.6171 GB, free: 89.81 MB / 462.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001383/0.6726, allocations: 116 kB / 0.6172 GB, free: 89.81 MB / 462.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02392/0.6965, allocations: 12.74 MB / 0.6297 GB, free: 84.39 MB / 462.1 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 0.05215/0.7486, allocations: 30.56 MB / 0.6595 GB, free: 55.04 MB / 462.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.04727/0.7959, allocations: 40.97 MB / 0.6995 GB, free: 11.55 MB / 462.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.008088/0.804, allocations: 4.721 MB / 0.7041 GB, free: 6.809 MB / 462.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.04226/0.8462, allocations: 21.22 MB / 0.7248 GB, free: 0.9375 MB / 478.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.796e-05/0.8463, allocations: 61.11 kB / 0.7249 GB, free: 0.8672 MB / 478.1 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004904/0.8512, allocations: 1.283 MB / 0.7262 GB, free: 15.73 MB / 494.1 MB
Notification: Performance of pre-optimization done (n=324): time 1.207e-05/0.8512, allocations: 0 / 0.7262 GB, free: 15.73 MB / 494.1 MB
Notification: Performance of matching and sorting (n=376): time 0.09793/0.9492, allocations: 24.4 MB / 0.75 GB, free: 7.5 MB / 0.4981 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 9.005e-05/0.9492, allocations: 86.36 kB / 0.7501 GB, free: 7.402 MB / 0.4981 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004667/0.9539, allocations: 2.968 MB / 0.753 GB, free: 4.453 MB / 0.4981 GB
Notification: Performance of collectPreVariables (initialization): time 0.001088/0.955, allocations: 85.7 kB / 0.753 GB, free: 4.363 MB / 0.4981 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001917/0.9569, allocations: 2.231 MB / 0.7552 GB, free: 2.32 MB / 0.4981 GB
Notification: Performance of collectInitialBindings (initialization): time 0.002162/0.9591, allocations: 1.36 MB / 0.7566 GB, free: 0.9805 MB / 0.4981 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001702/0.9608, allocations: 0.9808 MB / 0.7575 GB, free: 15.98 MB / 0.5137 GB
Notification: Performance of setup shared object (initialization): time 0.0001356/0.9609, allocations: 304.5 kB / 0.7578 GB, free: 15.69 MB / 0.5137 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004867/0.9658, allocations: 2.962 MB / 0.7607 GB, free: 12.72 MB / 0.5137 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.006623/0.9724, allocations: 4.477 MB / 0.7651 GB, free: 7.598 MB / 0.5137 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01457/0.987, allocations: 7.805 MB / 0.7727 GB, free: 15.21 MB / 0.5294 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.127e-05/0.987, allocations: 12 kB / 0.7727 GB, free: 15.2 MB / 0.5294 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.07764/1.065, allocations: 13.82 MB / 0.7862 GB, free: 1.516 MB / 0.5294 GB
Notification: Performance of prepare postOptimizeDAE: time 7.896e-05/1.065, allocations: 24 kB / 0.7862 GB, free: 1.492 MB / 0.5294 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0001271/1.065, allocations: 48 kB / 0.7863 GB, free: 1.445 MB / 0.5294 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01367/1.079, allocations: 3.47 MB / 0.7897 GB, free: 14.11 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005922/1.084, allocations: 1.269 MB / 0.7909 GB, free: 12.84 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.03698/1.121, allocations: 18.45 MB / 0.8089 GB, free: 10.02 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00568/1.127, allocations: 247.8 kB / 0.8091 GB, free: 9.773 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001378/1.129, allocations: 279.8 kB / 0.8094 GB, free: 9.5 MB / 0.5606 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 0.00411/1.133, allocations: 1.455 MB / 0.8108 GB, free: 8.035 MB / 0.5606 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001249/1.134, allocations: 365.6 kB / 0.8112 GB, free: 7.676 MB / 0.5606 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.3647/1.499, allocations: 9.633 MB / 0.8206 GB, free: 187.2 MB / 0.5606 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001125/1.499, allocations: 39.56 kB / 0.8206 GB, free: 187.2 MB / 0.5606 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.011e-05/1.499, allocations: 4.344 kB / 0.8206 GB, free: 187.2 MB / 0.5606 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001606/1.499, allocations: 18.55 kB / 0.8206 GB, free: 187.2 MB / 0.5606 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.05356/1.552, allocations: 15.41 MB / 0.8357 GB, free: 184.5 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.576e-05/1.552, allocations: 3.969 kB / 0.8357 GB, free: 184.5 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00473/1.557, allocations: 0.8495 MB / 0.8365 GB, free: 184.5 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.006291/1.563, allocations: 2.121 MB / 0.8386 GB, free: 184.2 MB / 0.5606 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001605/1.565, allocations: 137.8 kB / 0.8387 GB, free: 184.1 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02189/1.587, allocations: 12.63 MB / 0.8511 GB, free: 176.3 MB / 0.5606 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 6.002e-06/1.587, allocations: 7.812 kB / 0.8511 GB, free: 176.3 MB / 0.5606 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0391/1.626, allocations: 12.96 MB / 0.8637 GB, free: 169.5 MB / 0.5606 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.003281/1.629, allocations: 0.955 MB / 0.8647 GB, free: 168.9 MB / 0.5606 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001076/1.63, allocations: 91.97 kB / 0.8648 GB, free: 168.8 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.003006/1.633, allocations: 159.8 kB / 0.8649 GB, free: 168.7 MB / 0.5606 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001163/1.635, allocations: 457.1 kB / 0.8653 GB, free: 168.2 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003252/1.635, allocations: 147.9 kB / 0.8655 GB, free: 168.1 MB / 0.5606 GB
Notification: Performance of sorting global known variables: time 0.002577/1.638, allocations: 1.985 MB / 0.8674 GB, free: 166.1 MB / 0.5606 GB
Notification: Performance of sort global known variables: time 9e-08/1.638, allocations: 0 / 0.8674 GB, free: 166.1 MB / 0.5606 GB
Notification: Performance of remove unused functions: time 0.008294/1.646, allocations: 2.066 MB / 0.8694 GB, free: 164.2 MB / 0.5606 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 0.003477/1.649, allocations: 1.315 MB / 0.8707 GB, free: 163.3 MB / 0.5606 GB
Notification: Performance of simCode: created initialization part: time 0.01422/1.664, allocations: 7.072 MB / 0.8776 GB, free: 156.2 MB / 0.5606 GB
Notification: Performance of simCode: created event and clocks part: time 9.718e-06/1.664, allocations: 0 / 0.8776 GB, free: 156.2 MB / 0.5606 GB
Notification: Performance of simCode: created simulation system equations: time 0.00818/1.672, allocations: 3.78 MB / 0.8813 GB, free: 152.4 MB / 0.5606 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.005714/1.677, allocations: 0.7851 MB / 0.8821 GB, free: 151.7 MB / 0.5606 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01901/1.696, allocations: 10.99 MB / 0.8928 GB, free: 140.7 MB / 0.5606 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.00253/1.699, allocations: 3.302 MB / 0.896 GB, free: 137.5 MB / 0.5606 GB
Notification: Performance of simCode: alias equations: time 0.004188/1.703, allocations: 1.587 MB / 0.8976 GB, free: 136 MB / 0.5606 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.00135/1.704, allocations: 457.8 kB / 0.898 GB, free: 135.6 MB / 0.5606 GB
Notification: Performance of SimCode: time 1.944e-06/1.704, allocations: 0 / 0.898 GB, free: 135.6 MB / 0.5606 GB
Notification: Performance of Templates: time 0.1262/1.831, allocations: 94.05 MB / 0.9899 GB, free: 42.33 MB / 0.5606 GB
"
[Timeout remaining time 658]
make -j1 -f Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.makefile [Timeout 660]
(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) [Timeout 480]
[Calling os._exit(0), Time elapsed: 9.681923725642264]