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 0.001499/0.001499, allocations: 111.3 kB / 15.23 MB, free: 0.6406 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001869/0.001869, allocations: 196.7 kB / 16.14 MB, free: 6.711 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.377/1.377, allocations: 222.9 MB / 239.8 MB, free: 4.609 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2389/0.2389, allocations: 15.31 MB / 305.3 MB, free: 15.38 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001269/0.001269, allocations: 60.09 kB / 369.7 MB, free: 4.445 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.12/0.1213, allocations: 53.62 MB / 423.3 MB, free: 14.78 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 0.4328/0.5542, allocations: 29.31 MB / 452.6 MB, free: 38.81 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02554/0.5797, allocations: 26.04 MB / 478.6 MB, free: 25.77 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002333/0.5821, allocations: 42.31 kB / 478.7 MB, free: 25.75 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.002/0.5841, allocations: 0.5308 MB / 479.2 MB, free: 25.47 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.006735/0.5909, allocations: 1.865 MB / 481.1 MB, free: 24.34 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0109/0.6018, allocations: 3.081 MB / 484.1 MB, free: 22.52 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.007718/0.6096, allocations: 7.265 MB / 491.4 MB, free: 19.21 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006105/0.6157, allocations: 4.987 MB / 496.4 MB, free: 17.25 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.007147/0.6229, allocations: 4.724 MB / 0.4894 GB, free: 15.63 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.007442/0.6304, allocations: 4.388 MB / 0.4936 GB, free: 12.87 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.00253/0.6329, allocations: 484 kB / 0.4941 GB, free: 12.4 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01148/0.6444, allocations: 3.139 MB / 0.4972 GB, free: 9.555 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.003478/0.648, allocations: 1.539 MB / 0.4987 GB, free: 8.371 MB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.007301/0.6553, allocations: 3.086 MB / 0.5017 GB, free: 5.605 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02095/0.6762, allocations: 10.49 MB / 0.5119 GB, free: 11.46 MB / 382.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.791e-06/0.6763, allocations: 0 / 0.5119 GB, free: 11.46 MB / 382.1 MB
Notification: Performance of FrontEnd: time 1.443e-06/0.6763, allocations: 4 kB / 0.5119 GB, free: 11.46 MB / 382.1 MB
Notification: Performance of Transformations before backend: time 0.0003122/0.6766, allocations: 0 / 0.5119 GB, free: 11.46 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 0.02118/0.6978, allocations: 7.435 MB / 0.5192 GB, free: 3.938 MB / 382.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.464e-05/0.6979, allocations: 12.03 kB / 0.5192 GB, free: 3.926 MB / 382.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006699/0.7046, allocations: 1.211 MB / 0.5204 GB, free: 2.711 MB / 382.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.007243/0.7119, allocations: 3.141 MB / 0.5235 GB, free: 15.49 MB / 398.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0006552/0.7125, allocations: 0.6727 MB / 0.5241 GB, free: 14.75 MB / 398.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002068/0.7146, allocations: 0.4923 MB / 0.5246 GB, free: 14.25 MB / 398.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02246/0.7371, allocations: 9.372 MB / 0.5338 GB, free: 4.773 MB / 398.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0002099/0.7374, allocations: 4 kB / 0.5338 GB, free: 4.77 MB / 398.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.001919/0.7393, allocations: 192 kB / 0.5339 GB, free: 4.582 MB / 398.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001038/0.7394, allocations: 116 kB / 0.534 GB, free: 4.469 MB / 398.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02582/0.7652, allocations: 12.59 MB / 0.5463 GB, free: 7.863 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 0.08451/0.8498, allocations: 30.23 MB / 0.5759 GB, free: 8.93 MB / 446.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.3202/1.17, allocations: 41.27 MB / 0.6162 GB, free: 106.9 MB / 462.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.008454/1.179, allocations: 5.074 MB / 0.6211 GB, free: 106.9 MB / 462.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.03971/1.218, allocations: 20.92 MB / 0.6416 GB, free: 96.98 MB / 462.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.659e-05/1.218, allocations: 64.11 kB / 0.6416 GB, free: 96.92 MB / 462.1 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004226/1.223, allocations: 0.9524 MB / 0.6425 GB, free: 96.63 MB / 462.1 MB
Notification: Performance of pre-optimization done (n=324): time 2.035e-05/1.223, allocations: 0 / 0.6425 GB, free: 96.63 MB / 462.1 MB
Notification: Performance of matching and sorting (n=376): time 0.1079/1.331, allocations: 24.39 MB / 0.6664 GB, free: 89.32 MB / 462.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.225e-05/1.331, allocations: 91.61 kB / 0.6665 GB, free: 89.25 MB / 462.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.005616/1.336, allocations: 2.957 MB / 0.6693 GB, free: 87.71 MB / 462.1 MB
Notification: Performance of collectPreVariables (initialization): time 0.001358/1.338, allocations: 90.42 kB / 0.6694 GB, free: 87.63 MB / 462.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001385/1.339, allocations: 2.158 MB / 0.6715 GB, free: 85.75 MB / 462.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.002406/1.342, allocations: 1.303 MB / 0.6728 GB, free: 84.62 MB / 462.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001702/1.343, allocations: 0.976 MB / 0.6738 GB, free: 84.08 MB / 462.1 MB
Notification: Performance of setup shared object (initialization): time 6.141e-05/1.343, allocations: 307.7 kB / 0.6741 GB, free: 83.79 MB / 462.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004595/1.348, allocations: 2.951 MB / 0.6769 GB, free: 82.26 MB / 462.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.005759/1.354, allocations: 4.484 MB / 0.6813 GB, free: 78.78 MB / 462.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01099/1.365, allocations: 7.802 MB / 0.6889 GB, free: 71.74 MB / 462.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.151e-05/1.365, allocations: 12.5 kB / 0.6889 GB, free: 71.73 MB / 462.1 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05688/1.422, allocations: 13.83 MB / 0.7024 GB, free: 58.28 MB / 462.1 MB
Notification: Performance of prepare postOptimizeDAE: time 5.636e-05/1.422, allocations: 28 kB / 0.7025 GB, free: 58.25 MB / 462.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.995e-05/1.422, allocations: 48 kB / 0.7025 GB, free: 58.21 MB / 462.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008694/1.431, allocations: 3.477 MB / 0.7059 GB, free: 54.88 MB / 462.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005547/1.436, allocations: 1.266 MB / 0.7072 GB, free: 53.62 MB / 462.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02884/1.465, allocations: 16.61 MB / 0.7234 GB, free: 36.65 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.005692/1.471, allocations: 364.6 kB / 0.7237 GB, free: 36.3 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001274/1.472, allocations: 286.5 kB / 0.724 GB, free: 36.03 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 0.003552/1.476, allocations: 1.443 MB / 0.7254 GB, free: 34.57 MB / 462.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001158/1.477, allocations: 339.7 kB / 0.7257 GB, free: 34.24 MB / 462.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03555/1.513, allocations: 9.675 MB / 0.7352 GB, free: 24.65 MB / 462.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.796e-05/1.513, allocations: 40.75 kB / 0.7352 GB, free: 24.61 MB / 462.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.103e-05/1.513, allocations: 4 kB / 0.7352 GB, free: 24.61 MB / 462.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001241/1.513, allocations: 19.92 kB / 0.7352 GB, free: 24.59 MB / 462.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04449/1.557, allocations: 15.44 MB / 0.7503 GB, free: 9.164 MB / 462.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.624e-05/1.557, allocations: 4 kB / 0.7503 GB, free: 9.16 MB / 462.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00453/1.562, allocations: 0.8491 MB / 0.7511 GB, free: 8.312 MB / 462.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.00596/1.568, allocations: 2.127 MB / 0.7532 GB, free: 6.227 MB / 462.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001091/1.569, allocations: 135.9 kB / 0.7534 GB, free: 6.094 MB / 462.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02162/1.591, allocations: 11.44 MB / 0.7645 GB, free: 10.29 MB / 478.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.32e-06/1.591, allocations: 4 kB / 0.7645 GB, free: 10.28 MB / 478.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2663/1.857, allocations: 12.97 MB / 0.7772 GB, free: 133.3 MB / 478.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.002797/1.86, allocations: 0.9299 MB / 0.7781 GB, free: 133.2 MB / 478.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0009486/1.861, allocations: 92.42 kB / 0.7782 GB, free: 133.2 MB / 478.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.003018/1.864, allocations: 253 kB / 0.7784 GB, free: 133.2 MB / 478.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001215/1.865, allocations: 455 kB / 0.7789 GB, free: 133.2 MB / 478.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0004614/1.866, allocations: 144.9 kB / 0.779 GB, free: 133.2 MB / 478.1 MB
Notification: Performance of sorting global known variables: time 0.003049/1.869, allocations: 1.988 MB / 0.7809 GB, free: 133 MB / 478.1 MB
Notification: Performance of sort global known variables: time 3.31e-07/1.869, allocations: 0 / 0.7809 GB, free: 133 MB / 478.1 MB
Notification: Performance of remove unused functions: time 0.008313/1.877, allocations: 2.045 MB / 0.7829 GB, free: 133 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 0.003898/1.881, allocations: 1.296 MB / 0.7842 GB, free: 132.9 MB / 478.1 MB
Notification: Performance of simCode: created initialization part: time 0.01521/1.896, allocations: 7.405 MB / 0.7914 GB, free: 131.3 MB / 478.1 MB
Notification: Performance of simCode: created event and clocks part: time 8.146e-06/1.896, allocations: 0 / 0.7914 GB, free: 131.3 MB / 478.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.008657/1.905, allocations: 4.088 MB / 0.7954 GB, free: 129.8 MB / 478.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004706/1.91, allocations: 0.7244 MB / 0.7961 GB, free: 129.5 MB / 478.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.02342/1.933, allocations: 12.94 MB / 0.8088 GB, free: 123.3 MB / 478.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.004541/1.938, allocations: 3.3 MB / 0.812 GB, free: 122.3 MB / 478.1 MB
Notification: Performance of simCode: alias equations: time 0.008091/1.946, allocations: 1.6 MB / 0.8136 GB, free: 122.2 MB / 478.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.002112/1.948, allocations: 452.2 kB / 0.814 GB, free: 122.2 MB / 478.1 MB
Notification: Performance of SimCode: time 2.084e-06/1.948, allocations: 2.656 kB / 0.814 GB, free: 122.2 MB / 478.1 MB
Notification: Performance of Templates: time 0.1196/2.068, allocations: 88.17 MB / 0.9001 GB, free: 50.92 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)