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 0.00137/0.00137, allocations: 101.6 kB / 16.45 MB, free: 6.461 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 0.001622/0.001622, allocations: 199.8 kB / 19.41 MB, free: 3.645 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 1.565/1.565, allocations: 225.6 MB / 247.8 MB, free: 13.95 MB / 206.1 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 0.09398/0.09398, allocations: 15.53 MB / 318.2 MB, free: 10.22 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 0.002822/0.002822, allocations: 71.88 kB / 445.4 MB, free: 13.01 MB / 318.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1485/0.1513, allocations: 56.54 MB / 0.4902 GB, free: 4.355 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 0.5157/0.667, allocations: 30.12 MB / 0.5196 GB, free: 5.57 MB / 382.1 MB
Notification: Performance of NFInst.instExpressions: time 0.03054/0.6975, allocations: 26.15 MB / 0.5452 GB, free: 7.594 MB / 398.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001919/0.6995, allocations: 27.31 kB / 0.5452 GB, free: 7.582 MB / 398.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001933/0.7014, allocations: 0.5999 MB / 0.5458 GB, free: 7.238 MB / 398.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.008534/0.7099, allocations: 2.158 MB / 0.5479 GB, free: 5.902 MB / 398.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01226/0.7222, allocations: 3.547 MB / 0.5514 GB, free: 3.766 MB / 398.1 MB
Notification: Performance of NFFlatten.flatten: time 0.008963/0.7311, allocations: 7.394 MB / 0.5586 GB, free: 15.36 MB / 414.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006142/0.7373, allocations: 5.123 MB / 0.5636 GB, free: 12.2 MB / 414.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.006989/0.7443, allocations: 4.897 MB / 0.5684 GB, free: 9.988 MB / 414.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.00902/0.7533, allocations: 4.763 MB / 0.573 GB, free: 6.141 MB / 414.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0026/0.7559, allocations: 0.6719 MB / 0.5737 GB, free: 5.469 MB / 414.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01439/0.7703, allocations: 3.363 MB / 0.5769 GB, free: 2.102 MB / 414.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.003594/0.7739, allocations: 1.804 MB / 0.5787 GB, free: 300 kB / 414.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.006984/0.7809, allocations: 3.358 MB / 0.582 GB, free: 12.92 MB / 430.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02686/0.8077, allocations: 11.19 MB / 0.5929 GB, free: 1.691 MB / 430.1 MB
Notification: Performance of FrontEnd - DAE generated: time 8.636e-06/0.8077, allocations: 7.922 kB / 0.5929 GB, free: 1.684 MB / 430.1 MB
Notification: Performance of FrontEnd: time 1.864e-06/0.8077, allocations: 0 / 0.5929 GB, free: 1.684 MB / 430.1 MB
Notification: Performance of Transformations before backend: time 0.000338/0.8081, allocations: 0 / 0.5929 GB, free: 1.684 MB / 430.1 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 0.02481/0.8329, allocations: 7.328 MB / 0.6001 GB, free: 10.26 MB / 446.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.989e-05/0.8329, allocations: 8.031 kB / 0.6001 GB, free: 10.25 MB / 446.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.007768/0.8407, allocations: 1.241 MB / 0.6013 GB, free: 9.008 MB / 446.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.008154/0.8489, allocations: 3.249 MB / 0.6045 GB, free: 5.684 MB / 446.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0008522/0.8497, allocations: 0.6805 MB / 0.6051 GB, free: 4.934 MB / 446.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002703/0.8524, allocations: 0.4924 MB / 0.6056 GB, free: 4.441 MB / 446.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02382/0.8762, allocations: 9.45 MB / 0.6149 GB, free: 10.88 MB / 462.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001098/0.8763, allocations: 0 / 0.6149 GB, free: 10.88 MB / 462.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.001335/0.8777, allocations: 192 kB / 0.615 GB, free: 10.69 MB / 462.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001152/0.8778, allocations: 116 kB / 0.6151 GB, free: 10.58 MB / 462.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02912/0.9069, allocations: 12.73 MB / 0.6276 GB, free: 13.82 MB / 478.1 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 0.0735/0.9804, allocations: 30.57 MB / 0.6574 GB, free: 14.54 MB / 0.4982 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.07351/1.054, allocations: 40.96 MB / 0.6974 GB, free: 3.02 MB / 0.5294 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.01125/1.065, allocations: 4.721 MB / 0.702 GB, free: 14.27 MB / 0.5451 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.3008/1.366, allocations: 21.2 MB / 0.7227 GB, free: 175 MB / 0.5451 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.779e-05/1.366, allocations: 69.77 kB / 0.7228 GB, free: 174.9 MB / 0.5451 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004873/1.371, allocations: 1.278 MB / 0.724 GB, free: 174.9 MB / 0.5451 GB
Notification: Performance of pre-optimization done (n=324): time 1.302e-05/1.371, allocations: 3.219 kB / 0.7241 GB, free: 174.9 MB / 0.5451 GB
Notification: Performance of matching and sorting (n=376): time 0.09444/1.465, allocations: 24.42 MB / 0.7479 GB, free: 167.1 MB / 0.5451 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.322e-05/1.465, allocations: 89.36 kB / 0.748 GB, free: 167 MB / 0.5451 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.00372/1.469, allocations: 2.963 MB / 0.7509 GB, free: 165.5 MB / 0.5451 GB
Notification: Performance of collectPreVariables (initialization): time 0.001234/1.47, allocations: 84.86 kB / 0.751 GB, free: 165.4 MB / 0.5451 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001261/1.472, allocations: 2.221 MB / 0.7531 GB, free: 163.7 MB / 0.5451 GB
Notification: Performance of collectInitialBindings (initialization): time 0.00173/1.473, allocations: 1.362 MB / 0.7545 GB, free: 162.7 MB / 0.5451 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.00149/1.475, allocations: 0.9838 MB / 0.7554 GB, free: 162.2 MB / 0.5451 GB
Notification: Performance of setup shared object (initialization): time 5.717e-05/1.475, allocations: 301.1 kB / 0.7557 GB, free: 161.9 MB / 0.5451 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004253/1.479, allocations: 2.96 MB / 0.7586 GB, free: 160.3 MB / 0.5451 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004701/1.484, allocations: 4.478 MB / 0.763 GB, free: 155.8 MB / 0.5451 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.009167/1.493, allocations: 7.804 MB / 0.7706 GB, free: 147.5 MB / 0.5451 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.598e-05/1.493, allocations: 14.62 kB / 0.7706 GB, free: 147.5 MB / 0.5451 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.0543/1.547, allocations: 13.82 MB / 0.7841 GB, free: 133.8 MB / 0.5451 GB
Notification: Performance of prepare postOptimizeDAE: time 6.875e-05/1.547, allocations: 31.44 kB / 0.7841 GB, free: 133.8 MB / 0.5451 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.777e-05/1.548, allocations: 48 kB / 0.7842 GB, free: 133.7 MB / 0.5451 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008243/1.556, allocations: 3.475 MB / 0.7876 GB, free: 130.4 MB / 0.5451 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005851/1.562, allocations: 1.269 MB / 0.7888 GB, free: 129.1 MB / 0.5451 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02926/1.591, allocations: 18.44 MB / 0.8068 GB, free: 110.3 MB / 0.5451 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004979/1.596, allocations: 254.4 kB / 0.8071 GB, free: 110.1 MB / 0.5451 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0009584/1.597, allocations: 275.8 kB / 0.8073 GB, free: 109.8 MB / 0.5451 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 0.002658/1.599, allocations: 1.456 MB / 0.8087 GB, free: 108.4 MB / 0.5451 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.00101/1.6, allocations: 361.6 kB / 0.8091 GB, free: 108 MB / 0.5451 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03273/1.633, allocations: 9.633 MB / 0.8185 GB, free: 98.48 MB / 0.5451 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.003e-05/1.633, allocations: 40 kB / 0.8185 GB, free: 98.44 MB / 0.5451 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.232e-05/1.633, allocations: 9.031 kB / 0.8185 GB, free: 98.43 MB / 0.5451 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001299/1.633, allocations: 22.55 kB / 0.8186 GB, free: 98.41 MB / 0.5451 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04357/1.677, allocations: 15.42 MB / 0.8336 GB, free: 83 MB / 0.5451 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.104e-05/1.677, allocations: 4.688 kB / 0.8336 GB, free: 83 MB / 0.5451 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00472/1.682, allocations: 0.8455 MB / 0.8344 GB, free: 82.16 MB / 0.5451 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.00571/1.687, allocations: 2.134 MB / 0.8365 GB, free: 80.05 MB / 0.5451 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0009424/1.688, allocations: 139.9 kB / 0.8367 GB, free: 79.91 MB / 0.5451 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02116/1.71, allocations: 12.63 MB / 0.849 GB, free: 66.89 MB / 0.5451 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.971e-06/1.71, allocations: 7.844 kB / 0.849 GB, free: 66.88 MB / 0.5451 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.04172/1.751, allocations: 12.94 MB / 0.8617 GB, free: 53.88 MB / 0.5451 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.004058/1.755, allocations: 0.9642 MB / 0.8626 GB, free: 52.91 MB / 0.5451 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001136/1.756, allocations: 91.97 kB / 0.8627 GB, free: 52.82 MB / 0.5451 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002832/1.759, allocations: 163.8 kB / 0.8628 GB, free: 52.66 MB / 0.5451 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001094/1.76, allocations: 450.4 kB / 0.8633 GB, free: 52.21 MB / 0.5451 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003214/1.761, allocations: 147.9 kB / 0.8634 GB, free: 52.07 MB / 0.5451 GB
Notification: Performance of sorting global known variables: time 0.002303/1.763, allocations: 1.992 MB / 0.8654 GB, free: 50.08 MB / 0.5451 GB
Notification: Performance of sort global known variables: time 1.11e-07/1.763, allocations: 0 / 0.8654 GB, free: 50.08 MB / 0.5451 GB
Notification: Performance of remove unused functions: time 0.006892/1.77, allocations: 2.062 MB / 0.8674 GB, free: 48.03 MB / 0.5451 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 0.002786/1.773, allocations: 1.324 MB / 0.8687 GB, free: 46.89 MB / 0.5451 GB
Notification: Performance of simCode: created initialization part: time 0.01381/1.787, allocations: 7.065 MB / 0.8756 GB, free: 39.81 MB / 0.5451 GB
Notification: Performance of simCode: created event and clocks part: time 1.329e-05/1.787, allocations: 7.938 kB / 0.8756 GB, free: 39.8 MB / 0.5451 GB
Notification: Performance of simCode: created simulation system equations: time 0.008027/1.795, allocations: 3.77 MB / 0.8792 GB, free: 36 MB / 0.5451 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004607/1.799, allocations: 0.7752 MB / 0.88 GB, free: 35.28 MB / 0.5451 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01913/1.818, allocations: 10.94 MB / 0.8907 GB, free: 24.26 MB / 0.5451 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002263/1.821, allocations: 3.304 MB / 0.8939 GB, free: 20.92 MB / 0.5451 GB
Notification: Performance of simCode: alias equations: time 0.004045/1.825, allocations: 1.582 MB / 0.8955 GB, free: 19.36 MB / 0.5451 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.00136/1.826, allocations: 465.9 kB / 0.8959 GB, free: 18.91 MB / 0.5451 GB
Notification: Performance of SimCode: time 1.092e-06/1.826, allocations: 0 / 0.8959 GB, free: 18.91 MB / 0.5451 GB
Notification: Performance of Templates: time 0.4508/2.277, allocations: 92.01 MB / 0.9858 GB, free: 146 MB / 0.5607 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: 9.98570460267365]