Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_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 0.0007582/0.0007582, allocations: 76.55 kB / 19.93 MB, free: 4.617 MB / 18.57 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 0.0007634/0.0007634, allocations: 177.9 kB / 23.22 MB, free: 1.332 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 0.8399/0.8399, allocations: 177.1 MB / 203.5 MB, free: 5.742 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo): time 0.07924/0.07924, allocations: 17.37 MB / 277.3 MB, free: 11.85 MB / 266.7 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/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_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_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.393e-06/1.393e-06, allocations: 0 / 412.7 MB, free: 15.91 MB / 394.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.818e-05/1.958e-05, allocations: 2.281 kB / 412.7 MB, free: 15.91 MB / 394.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/Obsolete.mo:14337:7-14337:66: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 2.0.0/Obsolete.mo:14337:7-14337:66: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 0.02633/0.02635, allocations: 29.69 MB / 442.4 MB, free: 2.27 MB / 410.7 MB
Notification: Performance of NFInst.instExpressions: time 0.1491/0.1755, allocations: 23.03 MB / 465.5 MB, free: 50.46 MB / 410.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0007204/0.1762, allocations: 31.81 kB / 465.5 MB, free: 50.45 MB / 410.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0007788/0.177, allocations: 0.5526 MB / 466 MB, free: 50.16 MB / 410.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.002607/0.1796, allocations: 2.242 MB / 468.3 MB, free: 48.78 MB / 410.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004034/0.1836, allocations: 3.688 MB / 472 MB, free: 46.62 MB / 410.7 MB
Notification: Performance of NFFlatten.flatten: time 0.002812/0.1864, allocations: 7.636 MB / 479.6 MB, free: 42.89 MB / 410.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.002194/0.1886, allocations: 4.331 MB / 483.9 MB, free: 41.07 MB / 410.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.003235/0.1919, allocations: 6.341 MB / 490.3 MB, free: 38.95 MB / 410.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.003696/0.1956, allocations: 4.604 MB / 494.9 MB, free: 37.55 MB / 410.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0007715/0.1963, allocations: 0.6777 MB / 495.6 MB, free: 37.55 MB / 410.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.00506/0.2014, allocations: 3.209 MB / 498.8 MB, free: 36.91 MB / 410.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.001034/0.2024, allocations: 1.83 MB / 0.4889 GB, free: 35.87 MB / 410.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.001955/0.2044, allocations: 2.549 MB / 0.4914 GB, free: 34.81 MB / 410.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.008411/0.2128, allocations: 12.3 MB / 0.5034 GB, free: 28.35 MB / 410.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.927e-06/0.2128, allocations: 0 / 0.5034 GB, free: 28.35 MB / 410.7 MB
Notification: Performance of FrontEnd: time 1.783e-06/0.2128, allocations: 0 / 0.5034 GB, free: 28.35 MB / 410.7 MB
Notification: Performance of Transformations before backend: time 5.223e-05/0.2129, allocations: 6.594 kB / 0.5034 GB, free: 28.35 MB / 410.7 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 0.007107/0.22, allocations: 7.191 MB / 0.5104 GB, free: 21.14 MB / 410.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.259e-05/0.22, allocations: 8.031 kB / 0.5104 GB, free: 21.14 MB / 410.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.002642/0.2226, allocations: 1.241 MB / 0.5116 GB, free: 19.9 MB / 410.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.00307/0.2257, allocations: 3.314 MB / 0.5148 GB, free: 16.53 MB / 410.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0002474/0.226, allocations: 1.003 MB / 0.5158 GB, free: 15.38 MB / 410.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0005877/0.2265, allocations: 0.49 MB / 0.5163 GB, free: 14.89 MB / 410.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.007482/0.234, allocations: 9.465 MB / 0.5256 GB, free: 5.32 MB / 410.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 6.306e-05/0.2341, allocations: 4.188 kB / 0.5256 GB, free: 5.316 MB / 410.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.00043/0.2345, allocations: 192.4 kB / 0.5257 GB, free: 5.129 MB / 410.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.388e-05/0.2346, allocations: 119.9 kB / 0.5259 GB, free: 5.012 MB / 410.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.01156/0.2461, allocations: 12.66 MB / 0.5382 GB, free: 8.324 MB / 426.7 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 0.02805/0.2742, allocations: 26.75 MB / 0.5643 GB, free: 13.44 MB / 458.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.03099/0.3052, allocations: 26.12 MB / 0.5899 GB, free: 4.254 MB / 474.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.004521/0.3097, allocations: 4.72 MB / 0.5945 GB, free: 15.51 MB / 490.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.01809/0.3278, allocations: 16.9 MB / 0.611 GB, free: 14.57 MB / 0.4948 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.387e-05/0.3278, allocations: 69.11 kB / 0.611 GB, free: 14.5 MB / 0.4948 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.002201/0.33, allocations: 1.245 MB / 0.6122 GB, free: 13.28 MB / 0.4948 GB
Notification: Performance of pre-optimization done (n=324): time 5.089e-06/0.33, allocations: 2.656 kB / 0.6122 GB, free: 13.28 MB / 0.4948 GB
Notification: Performance of matching and sorting (n=376): time 0.1913/0.5213, allocations: 24.17 MB / 0.6359 GB, free: 142.2 MB / 0.4948 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.508e-05/0.5213, allocations: 91.8 kB / 0.6359 GB, free: 142.1 MB / 0.4948 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.002414/0.5237, allocations: 2.843 MB / 0.6387 GB, free: 141.2 MB / 0.4948 GB
Notification: Performance of collectPreVariables (initialization): time 0.0005051/0.5242, allocations: 88.17 kB / 0.6388 GB, free: 141.1 MB / 0.4948 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0006674/0.5249, allocations: 2.209 MB / 0.641 GB, free: 139.7 MB / 0.4948 GB
Notification: Performance of collectInitialBindings (initialization): time 0.0006869/0.5256, allocations: 1.345 MB / 0.6423 GB, free: 138.8 MB / 0.4948 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0009127/0.5265, allocations: 0.9785 MB / 0.6432 GB, free: 138.4 MB / 0.4948 GB
Notification: Performance of setup shared object (initialization): time 2.73e-05/0.5265, allocations: 302.4 kB / 0.6435 GB, free: 138.1 MB / 0.4948 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.002541/0.5291, allocations: 2.971 MB / 0.6464 GB, free: 137.1 MB / 0.4948 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.002865/0.5319, allocations: 4.486 MB / 0.6508 GB, free: 134.3 MB / 0.4948 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005866/0.5378, allocations: 7.809 MB / 0.6584 GB, free: 130 MB / 0.4948 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.526e-05/0.5378, allocations: 17.75 kB / 0.6584 GB, free: 130 MB / 0.4948 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.02984/0.5677, allocations: 13.81 MB / 0.6719 GB, free: 126.6 MB / 0.4948 GB
Notification: Performance of prepare postOptimizeDAE: time 3.869e-05/0.5677, allocations: 26.16 kB / 0.672 GB, free: 126.6 MB / 0.4948 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.038e-05/0.5678, allocations: 47.19 kB / 0.672 GB, free: 126.6 MB / 0.4948 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.004695/0.5725, allocations: 3.475 MB / 0.6754 GB, free: 126.1 MB / 0.4948 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00253/0.575, allocations: 1.27 MB / 0.6766 GB, free: 126 MB / 0.4948 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01683/0.5918, allocations: 17.87 MB / 0.6941 GB, free: 114.6 MB / 0.4948 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.002127/0.594, allocations: 250.5 kB / 0.6943 GB, free: 114.4 MB / 0.4948 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0002812/0.5942, allocations: 282.2 kB / 0.6946 GB, free: 114.4 MB / 0.4948 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 0.001737/0.596, allocations: 1.449 MB / 0.696 GB, free: 113 MB / 0.4948 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0003907/0.5964, allocations: 345.8 kB / 0.6963 GB, free: 112.6 MB / 0.4948 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01724/0.6136, allocations: 9.619 MB / 0.7057 GB, free: 103.1 MB / 0.4948 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.379e-05/0.6136, allocations: 43.94 kB / 0.7058 GB, free: 103.1 MB / 0.4948 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.887e-06/0.6136, allocations: 4 kB / 0.7058 GB, free: 103.1 MB / 0.4948 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 2.144e-05/0.6136, allocations: 19.92 kB / 0.7058 GB, free: 103 MB / 0.4948 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02088/0.6345, allocations: 14.36 MB / 0.7198 GB, free: 88.79 MB / 0.4948 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 8.606e-06/0.6345, allocations: 4 kB / 0.7198 GB, free: 88.79 MB / 0.4948 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001857/0.6364, allocations: 0.849 MB / 0.7207 GB, free: 87.94 MB / 0.4948 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.002858/0.6392, allocations: 2.124 MB / 0.7227 GB, free: 85.84 MB / 0.4948 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.000188/0.6394, allocations: 139.9 kB / 0.7229 GB, free: 85.7 MB / 0.4948 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.01141/0.6509, allocations: 12.1 MB / 0.7347 GB, free: 73.32 MB / 0.4948 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.775e-06/0.6509, allocations: 7.984 kB / 0.7347 GB, free: 73.31 MB / 0.4948 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01925/0.6701, allocations: 12.94 MB / 0.7473 GB, free: 60.32 MB / 0.4948 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.001383/0.6715, allocations: 0.9021 MB / 0.7482 GB, free: 59.42 MB / 0.4948 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.000309/0.6718, allocations: 94.62 kB / 0.7483 GB, free: 59.33 MB / 0.4948 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001117/0.6729, allocations: 167.8 kB / 0.7484 GB, free: 59.16 MB / 0.4948 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0005801/0.6735, allocations: 470.3 kB / 0.7489 GB, free: 58.7 MB / 0.4948 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001861/0.6737, allocations: 143.9 kB / 0.749 GB, free: 58.56 MB / 0.4948 GB
Notification: Performance of sorting global known variables: time 0.001469/0.6751, allocations: 1.847 MB / 0.7508 GB, free: 56.71 MB / 0.4948 GB
Notification: Performance of sort global known variables: time 7e-08/0.6751, allocations: 0 / 0.7508 GB, free: 56.71 MB / 0.4948 GB
Notification: Performance of remove unused functions: time 0.004265/0.6794, allocations: 2.062 MB / 0.7529 GB, free: 54.76 MB / 0.4948 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 0.001599/0.681, allocations: 1.372 MB / 0.7542 GB, free: 53.57 MB / 0.4948 GB
Notification: Performance of simCode: created initialization part: time 0.007031/0.688, allocations: 7.069 MB / 0.7611 GB, free: 46.47 MB / 0.4948 GB
Notification: Performance of simCode: created event and clocks part: time 2.995e-06/0.688, allocations: 5.5 kB / 0.7611 GB, free: 46.46 MB / 0.4948 GB
Notification: Performance of simCode: created simulation system equations: time 0.003531/0.6916, allocations: 3.765 MB / 0.7648 GB, free: 42.66 MB / 0.4948 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001728/0.6933, allocations: 0.7579 MB / 0.7655 GB, free: 41.96 MB / 0.4948 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.009431/0.7027, allocations: 10.75 MB / 0.776 GB, free: 31.13 MB / 0.4948 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001221/0.704, allocations: 2.696 MB / 0.7786 GB, free: 28.39 MB / 0.4948 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0009237/0.7049, allocations: 499.2 kB / 0.7791 GB, free: 27.9 MB / 0.4948 GB
Notification: Performance of SimCode: time 6.11e-07/0.7049, allocations: 4 kB / 0.7791 GB, free: 27.9 MB / 0.4948 GB
Notification: Performance of Templates: time 0.2236/0.9285, allocations: 149.1 MB / 0.9248 GB, free: 88.73 MB / 0.5105 GB
"
[Timeout remaining time 659]
make -j1 -f Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.makefile [Timeout 660]
(rm -f Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; mkfifo Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; head -c 1048576 < Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe >> ../files/Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.sim & ./Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 8.503428694792092]
Failed to read output from testmodel.py, exit status != 0:
0.9345334256067872 0.939705821 0.725433415
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7bc69afc52b0>