Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.001339/0.001339, allocations: 88.72 kB / 19.44 MB, free: 356 kB / 13.93 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.001522/0.001522, allocations: 157.7 kB / 22.75 MB, free: 1.684 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 1.461/1.461, allocations: 177.1 MB / 203.1 MB, free: 5.605 MB / 186.7 MB
"
[Timeout remaining time 178]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo): time 0.1396/0.1396, allocations: 17.45 MB / 277 MB, free: 11.59 MB / 266.7 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo)
Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo)
Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo)
Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo)
Running command: translateModel(Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC")
translateModel(Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.563e-06/1.563e-06, allocations: 0 / 352.8 MB, free: 10.18 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.887e-05/3.044e-05, allocations: 5.125 kB / 352.8 MB, free: 10.18 MB / 282.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/Obsolete.mo:14335:7-14335:66: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 master/Obsolete.mo:14335:7-14335:66: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.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC): time 0.04683/0.04686, allocations: 29.91 MB / 382.8 MB, free: 12.4 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.03769/0.08456, allocations: 23.11 MB / 405.9 MB, free: 5.199 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002278/0.08683, allocations: 39.69 kB / 405.9 MB, free: 5.16 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.002305/0.08914, allocations: 0.5541 MB / 406.5 MB, free: 4.602 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.007693/0.09683, allocations: 2.241 MB / 408.7 MB, free: 2.344 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.1374/0.2342, allocations: 3.676 MB / 412.4 MB, free: 33.82 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.007294/0.2415, allocations: 7.639 MB / 420 MB, free: 32.19 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.005581/0.2471, allocations: 4.572 MB / 424.6 MB, free: 31.22 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.008781/0.2559, allocations: 6.331 MB / 430.9 MB, free: 29.27 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.007109/0.263, allocations: 4.608 MB / 435.5 MB, free: 27.96 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.001646/0.2646, allocations: 0.6784 MB / 436.2 MB, free: 27.96 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.007762/0.2724, allocations: 3.209 MB / 439.4 MB, free: 25.48 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.001773/0.2741, allocations: 1.829 MB / 441.2 MB, free: 23.8 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.003991/0.2781, allocations: 2.551 MB / 443.8 MB, free: 21.39 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.01456/0.2927, allocations: 12.32 MB / 456.1 MB, free: 9.777 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 6.082e-06/0.2927, allocations: 4 kB / 456.1 MB, free: 9.773 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.263e-06/0.2927, allocations: 0 / 456.1 MB, free: 9.773 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 0.0002186/0.2929, allocations: 0 / 456.1 MB, free: 9.773 MB / 330.7 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 0.01614/0.3091, allocations: 7.189 MB / 463.3 MB, free: 2.602 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.324e-05/0.3091, allocations: 12.03 kB / 463.3 MB, free: 2.59 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006718/0.3158, allocations: 2.047 MB / 465.4 MB, free: 0.5391 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.008332/0.3242, allocations: 3.377 MB / 468.7 MB, free: 13.28 MB / 346.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.001082/0.3252, allocations: 1.003 MB / 469.7 MB, free: 12.12 MB / 346.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002125/0.3274, allocations: 0.4885 MB / 470.2 MB, free: 11.64 MB / 346.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02076/0.3481, allocations: 9.462 MB / 479.7 MB, free: 2.074 MB / 346.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 8.717e-05/0.3482, allocations: 10.22 kB / 479.7 MB, free: 2.07 MB / 346.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0008563/0.3491, allocations: 192.4 kB / 479.9 MB, free: 1.883 MB / 346.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001212/0.3492, allocations: 120.6 kB / 480 MB, free: 1.766 MB / 346.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0252/0.3744, allocations: 12.66 MB / 492.7 MB, free: 5.102 MB / 362.7 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 0.06147/0.4359, allocations: 26.88 MB / 0.5074 GB, free: 10.52 MB / 394.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.06358/0.4994, allocations: 26.14 MB / 0.5329 GB, free: 1.355 MB / 410.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.01005/0.5095, allocations: 4.72 MB / 0.5375 GB, free: 12.61 MB / 426.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.03909/0.5486, allocations: 17.09 MB / 0.5542 GB, free: 11.66 MB / 442.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 7.535e-05/0.5487, allocations: 68.48 kB / 0.5543 GB, free: 11.59 MB / 442.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.005253/0.5539, allocations: 1.263 MB / 0.5555 GB, free: 10.39 MB / 442.7 MB
Notification: Performance of pre-optimization done (n=324): time 1.216e-05/0.5539, allocations: 0 / 0.5555 GB, free: 10.39 MB / 442.7 MB
Notification: Performance of matching and sorting (n=376): time 0.2345/0.7884, allocations: 24.28 MB / 0.5792 GB, free: 151.6 MB / 442.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.592e-05/0.7884, allocations: 89.86 kB / 0.5793 GB, free: 151.6 MB / 442.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003653/0.7921, allocations: 2.839 MB / 0.5821 GB, free: 150.6 MB / 442.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0008258/0.7929, allocations: 89.36 kB / 0.5821 GB, free: 150.5 MB / 442.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001167/0.7941, allocations: 2.21 MB / 0.5843 GB, free: 149.1 MB / 442.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001453/0.7955, allocations: 1.346 MB / 0.5856 GB, free: 148.2 MB / 442.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.002221/0.7978, allocations: 0.979 MB / 0.5866 GB, free: 147.7 MB / 442.7 MB
Notification: Performance of setup shared object (initialization): time 4.1e-05/0.7978, allocations: 301.1 kB / 0.5869 GB, free: 147.4 MB / 442.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004335/0.8021, allocations: 2.967 MB / 0.5898 GB, free: 145.9 MB / 442.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004761/0.8069, allocations: 4.484 MB / 0.5941 GB, free: 142.4 MB / 442.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.009479/0.8164, allocations: 7.808 MB / 0.6018 GB, free: 136.3 MB / 442.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.773e-05/0.8164, allocations: 19.94 kB / 0.6018 GB, free: 136.3 MB / 442.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05516/0.8716, allocations: 14.04 MB / 0.6155 GB, free: 122.4 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 5.703e-05/0.8716, allocations: 24 kB / 0.6155 GB, free: 122.3 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.011e-05/0.8717, allocations: 48 kB / 0.6156 GB, free: 122.3 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.02656/0.8983, allocations: 7.671 MB / 0.6231 GB, free: 114.8 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005348/0.9036, allocations: 1.27 MB / 0.6243 GB, free: 113.5 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.0299/0.9335, allocations: 17.89 MB / 0.6418 GB, free: 95.35 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004353/0.9379, allocations: 255.7 kB / 0.642 GB, free: 95.1 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0009918/0.9389, allocations: 279.8 kB / 0.6423 GB, free: 94.83 MB / 442.7 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 0.003086/0.942, allocations: 1.453 MB / 0.6437 GB, free: 93.4 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.00189/0.9438, allocations: 461.8 kB / 0.6441 GB, free: 92.95 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03534/0.9792, allocations: 9.616 MB / 0.6535 GB, free: 83.42 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.428e-05/0.9792, allocations: 43.94 kB / 0.6536 GB, free: 83.38 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.214e-05/0.9793, allocations: 4 kB / 0.6536 GB, free: 83.38 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001213/0.9794, allocations: 22.61 kB / 0.6536 GB, free: 83.36 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.048/1.027, allocations: 14.35 MB / 0.6676 GB, free: 69.07 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.012e-05/1.027, allocations: 4 kB / 0.6676 GB, free: 69.07 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004477/1.032, allocations: 0.8479 MB / 0.6684 GB, free: 68.23 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.01624/1.048, allocations: 3.374 MB / 0.6717 GB, free: 64.91 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001089/1.049, allocations: 139.9 kB / 0.6719 GB, free: 64.77 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02148/1.071, allocations: 12.12 MB / 0.6837 GB, free: 52.36 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.829e-06/1.071, allocations: 4 kB / 0.6837 GB, free: 52.36 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.04072/1.111, allocations: 13.06 MB / 0.6965 GB, free: 39.23 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.002715/1.114, allocations: 0.912 MB / 0.6974 GB, free: 38.33 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001271/1.115, allocations: 87.98 kB / 0.6974 GB, free: 38.25 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.003099/1.119, allocations: 167.8 kB / 0.6976 GB, free: 38.08 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001366/1.12, allocations: 466.3 kB / 0.698 GB, free: 37.62 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0005455/1.12, allocations: 147.9 kB / 0.6982 GB, free: 37.48 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.002582/1.123, allocations: 1.847 MB / 0.7 GB, free: 35.63 MB / 442.7 MB
Notification: Performance of sort global known variables: time 8e-08/1.123, allocations: 2.656 kB / 0.7 GB, free: 35.63 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.006565/1.13, allocations: 2.06 MB / 0.702 GB, free: 33.75 MB / 442.7 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 0.002852/1.132, allocations: 1.372 MB / 0.7033 GB, free: 32.73 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.0131/1.146, allocations: 7.082 MB / 0.7103 GB, free: 25.63 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 9.097e-06/1.146, allocations: 6.688 kB / 0.7103 GB, free: 25.62 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.007576/1.153, allocations: 3.766 MB / 0.7139 GB, free: 21.82 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004774/1.158, allocations: 0.847 MB / 0.7148 GB, free: 21.06 MB / 442.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01879/1.177, allocations: 10.94 MB / 0.7255 GB, free: 10.05 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002789/1.179, allocations: 2.787 MB / 0.7282 GB, free: 7.266 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.004414/1.184, allocations: 1.561 MB / 0.7297 GB, free: 5.727 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001773/1.186, allocations: 463 kB / 0.7301 GB, free: 5.277 MB / 442.7 MB
Notification: Performance of SimCode: time 1.843e-06/1.186, allocations: 0 / 0.7301 GB, free: 5.277 MB / 442.7 MB
Notification: Performance of Templates: time 0.2572/1.443, allocations: 92.11 MB / 0.8201 GB, free: 78.27 MB / 442.7 MB
"
[Timeout remaining time 659]
make -j1 -f Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.makefile [Timeout 660]
(rm -f Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; mkfifo Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; head -c 1048576 < Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe >> ../files/Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.sim & ./Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 480]
[Calling os._exit(0), Time elapsed: 9.189534058910795]