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 0.001771/0.001771, allocations: 106.7 kB / 15.98 MB, free: 6.355 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001889/0.001889, allocations: 192.6 kB / 16.91 MB, free: 6.188 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.384/1.384, allocations: 222.9 MB / 240.6 MB, free: 13.72 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.0839/0.0839, allocations: 15.3 MB / 306 MB, free: 15.45 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001935/0.001935, allocations: 66.27 kB / 370.5 MB, free: 50.41 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1011/0.103, allocations: 53.62 MB / 424.1 MB, free: 14.36 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 0.03972/0.1428, allocations: 30.89 MB / 455 MB, free: 15.57 MB / 334.1 MB
Notification: Performance of NFInst.instExpressions: time 0.03427/0.1771, allocations: 25.75 MB / 480.7 MB, free: 5.715 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002393/0.1795, allocations: 43.69 kB / 480.8 MB, free: 5.672 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.002201/0.1817, allocations: 0.5278 MB / 481.3 MB, free: 5.141 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.007498/0.1892, allocations: 1.925 MB / 483.2 MB, free: 3.203 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01084/0.2001, allocations: 3.14 MB / 486.4 MB, free: 48 kB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.01012/0.2103, allocations: 7.39 MB / 493.8 MB, free: 8.625 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.008448/0.2188, allocations: 5.9 MB / 499.7 MB, free: 2.656 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.008758/0.2276, allocations: 5.247 MB / 0.4931 GB, free: 13.39 MB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.008594/0.2362, allocations: 4.713 MB / 0.4977 GB, free: 8.668 MB / 382.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.002498/0.2387, allocations: 0.668 MB / 0.4983 GB, free: 8 MB / 382.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0132/0.252, allocations: 3.397 MB / 0.5017 GB, free: 4.586 MB / 382.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.003549/0.2555, allocations: 1.823 MB / 0.5034 GB, free: 2.758 MB / 382.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.2207/0.4763, allocations: 3.365 MB / 0.5067 GB, free: 32.13 MB / 382.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.01318/0.4895, allocations: 8.495 MB / 0.515 GB, free: 31.73 MB / 382.1 MB
Notification: Performance of FrontEnd - DAE generated: time 1.002e-05/0.4896, allocations: 0 / 0.515 GB, free: 31.73 MB / 382.1 MB
Notification: Performance of FrontEnd: time 3.376e-06/0.4896, allocations: 0 / 0.515 GB, free: 31.73 MB / 382.1 MB
Notification: Performance of Transformations before backend: time 0.000479/0.4901, allocations: 0 / 0.515 GB, free: 31.73 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 0.03092/0.521, allocations: 7.434 MB / 0.5223 GB, free: 29.4 MB / 382.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.52e-05/0.5211, allocations: 13.75 kB / 0.5223 GB, free: 29.4 MB / 382.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.008935/0.53, allocations: 1.21 MB / 0.5235 GB, free: 29.11 MB / 382.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.009343/0.5394, allocations: 3.14 MB / 0.5265 GB, free: 28.45 MB / 382.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0007183/0.5402, allocations: 0.6783 MB / 0.5272 GB, free: 28.1 MB / 382.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.004046/0.5442, allocations: 0.4905 MB / 0.5277 GB, free: 28.09 MB / 382.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02579/0.57, allocations: 9.366 MB / 0.5368 GB, free: 27.23 MB / 382.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0002855/0.5704, allocations: 3.562 kB / 0.5368 GB, free: 27.23 MB / 382.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.003038/0.5734, allocations: 197.2 kB / 0.537 GB, free: 27.21 MB / 382.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001089/0.5736, allocations: 114.1 kB / 0.5371 GB, free: 27.21 MB / 382.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02265/0.5962, allocations: 12.59 MB / 0.5494 GB, free: 18.77 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 0.06764/0.6639, allocations: 30.24 MB / 0.5789 GB, free: 4.477 MB / 398.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.06904/0.733, allocations: 41.26 MB / 0.6192 GB, free: 8.723 MB / 446.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.01055/0.7436, allocations: 5.077 MB / 0.6242 GB, free: 3.625 MB / 446.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.04138/0.785, allocations: 20.93 MB / 0.6446 GB, free: 14.01 MB / 478.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.229e-05/0.7851, allocations: 65.11 kB / 0.6447 GB, free: 13.93 MB / 478.1 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.00424/0.7894, allocations: 0.9669 MB / 0.6456 GB, free: 12.98 MB / 478.1 MB
Notification: Performance of pre-optimization done (n=324): time 1.234e-05/0.7894, allocations: 4 kB / 0.6456 GB, free: 12.98 MB / 478.1 MB
Notification: Performance of matching and sorting (n=376): time 0.103/0.8924, allocations: 24.39 MB / 0.6695 GB, free: 4.699 MB / 494.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 8.06e-05/0.8925, allocations: 90.36 kB / 0.6696 GB, free: 4.598 MB / 494.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004387/0.8969, allocations: 2.958 MB / 0.6724 GB, free: 1.625 MB / 494.1 MB
Notification: Performance of collectPreVariables (initialization): time 0.001055/0.8979, allocations: 89.7 kB / 0.6725 GB, free: 1.531 MB / 494.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.00187/0.8998, allocations: 2.169 MB / 0.6746 GB, free: 15.35 MB / 0.4981 GB
Notification: Performance of collectInitialBindings (initialization): time 0.002055/0.9019, allocations: 1.301 MB / 0.6759 GB, free: 14.06 MB / 0.4981 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001856/0.9037, allocations: 0.9765 MB / 0.6769 GB, free: 13.07 MB / 0.4981 GB
Notification: Performance of setup shared object (initialization): time 0.0001473/0.9039, allocations: 309.1 kB / 0.6772 GB, free: 12.77 MB / 0.4981 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.005232/0.9091, allocations: 2.951 MB / 0.68 GB, free: 9.812 MB / 0.4981 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.006856/0.916, allocations: 4.485 MB / 0.6844 GB, free: 4.707 MB / 0.4981 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.201/1.117, allocations: 7.801 MB / 0.692 GB, free: 190.6 MB / 0.4981 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.139e-05/1.117, allocations: 14.28 kB / 0.6921 GB, free: 190.6 MB / 0.4981 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05658/1.174, allocations: 13.82 MB / 0.7056 GB, free: 187.5 MB / 0.4981 GB
Notification: Performance of prepare postOptimizeDAE: time 5.297e-05/1.174, allocations: 30.22 kB / 0.7056 GB, free: 187.5 MB / 0.4981 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.831e-05/1.174, allocations: 51.47 kB / 0.7056 GB, free: 187.5 MB / 0.4981 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008355/1.182, allocations: 3.471 MB / 0.709 GB, free: 186.2 MB / 0.4981 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005443/1.188, allocations: 1.272 MB / 0.7103 GB, free: 185.9 MB / 0.4981 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02978/1.218, allocations: 18.48 MB / 0.7283 GB, free: 169.6 MB / 0.4981 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.005471/1.223, allocations: 360.7 kB / 0.7287 GB, free: 169.3 MB / 0.4981 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0009458/1.224, allocations: 279.8 kB / 0.7289 GB, free: 169 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 0.002733/1.227, allocations: 1.443 MB / 0.7303 GB, free: 167.6 MB / 0.4981 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0009031/1.228, allocations: 350.9 kB / 0.7307 GB, free: 167.4 MB / 0.4981 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03386/1.262, allocations: 9.665 MB / 0.7401 GB, free: 157.8 MB / 0.4981 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.27e-05/1.262, allocations: 40 kB / 0.7401 GB, free: 157.8 MB / 0.4981 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.518e-05/1.262, allocations: 6.656 kB / 0.7402 GB, free: 157.8 MB / 0.4981 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001292/1.262, allocations: 19.92 kB / 0.7402 GB, free: 157.8 MB / 0.4981 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0418/1.304, allocations: 15.44 MB / 0.7552 GB, free: 142.4 MB / 0.4981 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.696e-05/1.304, allocations: 7.938 kB / 0.7553 GB, free: 142.4 MB / 0.4981 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004484/1.308, allocations: 0.849 MB / 0.7561 GB, free: 141.6 MB / 0.4981 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005531/1.314, allocations: 2.133 MB / 0.7582 GB, free: 139.5 MB / 0.4981 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0009403/1.315, allocations: 144.7 kB / 0.7583 GB, free: 139.4 MB / 0.4981 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02005/1.335, allocations: 12.68 MB / 0.7707 GB, free: 126.4 MB / 0.4981 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.8e-06/1.335, allocations: 11.92 kB / 0.7707 GB, free: 126.4 MB / 0.4981 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03837/1.373, allocations: 12.96 MB / 0.7834 GB, free: 113.4 MB / 0.4981 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.002784/1.376, allocations: 0.9311 MB / 0.7843 GB, free: 112.5 MB / 0.4981 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0008304/1.377, allocations: 95.97 kB / 0.7844 GB, free: 112.4 MB / 0.4981 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002758/1.38, allocations: 258.6 kB / 0.7846 GB, free: 112.2 MB / 0.4981 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001041/1.381, allocations: 461.1 kB / 0.785 GB, free: 111.7 MB / 0.4981 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003036/1.381, allocations: 143.9 kB / 0.7852 GB, free: 111.6 MB / 0.4981 GB
Notification: Performance of sorting global known variables: time 0.002178/1.383, allocations: 1.989 MB / 0.7871 GB, free: 109.6 MB / 0.4981 GB
Notification: Performance of sort global known variables: time 1.51e-07/1.383, allocations: 0 / 0.7871 GB, free: 109.6 MB / 0.4981 GB
Notification: Performance of remove unused functions: time 0.00703/1.39, allocations: 2.045 MB / 0.7891 GB, free: 107.7 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 0.002935/1.393, allocations: 1.289 MB / 0.7904 GB, free: 106.6 MB / 0.4981 GB
Notification: Performance of simCode: created initialization part: time 0.02935/1.423, allocations: 14.97 MB / 0.805 GB, free: 91.65 MB / 0.4981 GB
Notification: Performance of simCode: created event and clocks part: time 7.655e-06/1.423, allocations: 2.719 kB / 0.805 GB, free: 91.65 MB / 0.4981 GB
Notification: Performance of simCode: created simulation system equations: time 0.007427/1.43, allocations: 4.088 MB / 0.809 GB, free: 87.53 MB / 0.4981 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003948/1.434, allocations: 0.7764 MB / 0.8097 GB, free: 86.83 MB / 0.4981 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.018/1.452, allocations: 12.89 MB / 0.8223 GB, free: 74.03 MB / 0.4981 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002009/1.454, allocations: 3.207 MB / 0.8255 GB, free: 70.84 MB / 0.4981 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.002103/1.456, allocations: 0.4979 MB / 0.826 GB, free: 70.34 MB / 0.4981 GB
Notification: Performance of SimCode: time 1.072e-06/1.456, allocations: 0 / 0.826 GB, free: 70.34 MB / 0.4981 GB
Notification: Performance of Templates: time 0.3158/1.772, allocations: 146.2 MB / 0.9687 GB, free: 108.1 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)