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/Chemical 1.4.0-master/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/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/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 Chemical with version 1.4.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/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/Chemical 1.4.0-master/package.mo): time 0.07957/0.07958, allocations: 15.29 MB / 31.09 MB, free: 3.113 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001125/0.001125, allocations: 198.6 kB / 36.14 MB, free: 2.137 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.342/1.342, allocations: 222.9 MB / 264 MB, free: 4.805 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.000949/0.0009489, allocations: 103.1 kB / 318.4 MB, free: 3.438 MB / 250.7 MB
Notification: Performance of FrontEnd - loaded program: time 0.001007/0.001007, allocations: 54.02 kB / 382.7 MB, free: 48.76 MB / 298.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09356/0.09458, allocations: 53.62 MB / 436.3 MB, free: 1.031 MB / 298.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:4721:7-4721:66: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 1.4.0-master/package.mo:4721:7-4721:66: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 0.03333/0.128, allocations: 27.49 MB / 463.8 MB, free: 5.621 MB / 330.7 MB
Notification: Performance of NFInst.instExpressions: time 0.02821/0.1562, allocations: 25.81 MB / 489.6 MB, free: 11.71 MB / 362.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002206/0.1584, allocations: 43.69 kB / 489.7 MB, free: 11.67 MB / 362.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.001624/0.1601, allocations: 0.52 MB / 490.2 MB, free: 11.15 MB / 362.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.005803/0.1659, allocations: 1.812 MB / 492 MB, free: 9.324 MB / 362.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01083/0.1767, allocations: 3.089 MB / 495.1 MB, free: 6.219 MB / 362.7 MB
Notification: Performance of NFFlatten.flatten: time 0.008035/0.1848, allocations: 7.312 MB / 0.4906 GB, free: 14.88 MB / 378.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.005355/0.1902, allocations: 4.993 MB / 0.4955 GB, free: 9.809 MB / 378.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.006169/0.1964, allocations: 4.751 MB / 0.5002 GB, free: 5.043 MB / 378.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.006813/0.2032, allocations: 4.366 MB / 0.5044 GB, free: 0.6641 MB / 378.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.00161/0.2049, allocations: 488 kB / 0.5049 GB, free: 192 kB / 378.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.2032/0.4081, allocations: 3.044 MB / 0.5079 GB, free: 26.68 MB / 378.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.002546/0.4106, allocations: 1.541 MB / 0.5094 GB, free: 26.68 MB / 378.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.004638/0.4153, allocations: 3.092 MB / 0.5124 GB, free: 26.41 MB / 378.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.01893/0.4342, allocations: 10.4 MB / 0.5225 GB, free: 25.39 MB / 378.7 MB
Notification: Performance of FrontEnd - DAE generated: time 8.145e-06/0.4343, allocations: 3.375 kB / 0.5225 GB, free: 25.39 MB / 378.7 MB
Notification: Performance of FrontEnd: time 2.324e-06/0.4343, allocations: 0 / 0.5225 GB, free: 25.39 MB / 378.7 MB
Notification: Performance of Transformations before backend: time 0.0004813/0.4348, allocations: 0 / 0.5225 GB, free: 25.39 MB / 378.7 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 0.02511/0.4599, allocations: 7.426 MB / 0.5298 GB, free: 23.06 MB / 378.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.739e-05/0.46, allocations: 10.22 kB / 0.5298 GB, free: 23.06 MB / 378.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.005769/0.4657, allocations: 1.206 MB / 0.531 GB, free: 22.77 MB / 378.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.01015/0.4759, allocations: 3.14 MB / 0.534 GB, free: 22.11 MB / 378.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0009903/0.477, allocations: 0.6768 MB / 0.5347 GB, free: 21.75 MB / 378.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.003994/0.481, allocations: 0.4925 MB / 0.5352 GB, free: 21.74 MB / 378.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02351/0.5045, allocations: 9.366 MB / 0.5443 GB, free: 20.18 MB / 378.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0002067/0.5047, allocations: 3.688 kB / 0.5443 GB, free: 20.18 MB / 378.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.002808/0.5076, allocations: 195 kB / 0.5445 GB, free: 20.18 MB / 378.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001331/0.5077, allocations: 115.9 kB / 0.5446 GB, free: 20.18 MB / 378.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02291/0.5306, allocations: 12.59 MB / 0.5569 GB, free: 11.25 MB / 378.7 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 0.07117/0.6018, allocations: 30.22 MB / 0.5864 GB, free: 12.9 MB / 410.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.05979/0.6617, allocations: 41.27 MB / 0.6267 GB, free: 1.133 MB / 442.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.01024/0.672, allocations: 5.075 MB / 0.6317 GB, free: 12.04 MB / 458.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.04836/0.7204, allocations: 20.92 MB / 0.6521 GB, free: 6.387 MB / 474.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.279e-05/0.7204, allocations: 68.58 kB / 0.6522 GB, free: 6.312 MB / 474.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004878/0.7253, allocations: 0.9507 MB / 0.6531 GB, free: 5.383 MB / 474.7 MB
Notification: Performance of pre-optimization done (n=324): time 2.152e-05/0.7254, allocations: 0 / 0.6531 GB, free: 5.383 MB / 474.7 MB
Notification: Performance of matching and sorting (n=376): time 0.1042/0.8296, allocations: 24.39 MB / 0.6769 GB, free: 13.08 MB / 0.4948 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.195e-05/0.8297, allocations: 90.36 kB / 0.677 GB, free: 12.98 MB / 0.4948 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.005089/0.8348, allocations: 2.961 MB / 0.6799 GB, free: 10.01 MB / 0.4948 GB
Notification: Performance of collectPreVariables (initialization): time 0.001197/0.836, allocations: 89.7 kB / 0.68 GB, free: 9.914 MB / 0.4948 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001441/0.8375, allocations: 2.164 MB / 0.6821 GB, free: 7.738 MB / 0.4948 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001906/0.8394, allocations: 1.294 MB / 0.6834 GB, free: 6.453 MB / 0.4948 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001585/0.841, allocations: 0.9793 MB / 0.6843 GB, free: 5.465 MB / 0.4948 GB
Notification: Performance of setup shared object (initialization): time 8.462e-05/0.8411, allocations: 306.4 kB / 0.6846 GB, free: 5.164 MB / 0.4948 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004582/0.8457, allocations: 2.959 MB / 0.6875 GB, free: 2.199 MB / 0.4948 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.2214/1.067, allocations: 4.481 MB / 0.6919 GB, free: 184.2 MB / 0.4948 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01492/1.082, allocations: 7.805 MB / 0.6995 GB, free: 182.3 MB / 0.4948 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.428e-05/1.082, allocations: 13.56 kB / 0.6995 GB, free: 182.3 MB / 0.4948 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05469/1.137, allocations: 13.82 MB / 0.713 GB, free: 179.2 MB / 0.4948 GB
Notification: Performance of prepare postOptimizeDAE: time 6.457e-05/1.137, allocations: 32.5 kB / 0.7131 GB, free: 179.2 MB / 0.4948 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.656e-05/1.137, allocations: 47.34 kB / 0.7131 GB, free: 179.2 MB / 0.4948 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008537/1.146, allocations: 3.475 MB / 0.7165 GB, free: 178.1 MB / 0.4948 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005895/1.151, allocations: 1.277 MB / 0.7177 GB, free: 177.8 MB / 0.4948 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02742/1.179, allocations: 16.61 MB / 0.734 GB, free: 163.4 MB / 0.4948 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.005601/1.185, allocations: 357 kB / 0.7343 GB, free: 163.1 MB / 0.4948 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001246/1.186, allocations: 287.3 kB / 0.7346 GB, free: 162.8 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 0.003444/1.189, allocations: 1.454 MB / 0.736 GB, free: 161.4 MB / 0.4948 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001015/1.19, allocations: 342.3 kB / 0.7363 GB, free: 161.2 MB / 0.4948 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03351/1.224, allocations: 9.659 MB / 0.7458 GB, free: 151.7 MB / 0.4948 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.351e-05/1.224, allocations: 43.72 kB / 0.7458 GB, free: 151.7 MB / 0.4948 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.935e-05/1.224, allocations: 4 kB / 0.7458 GB, free: 151.6 MB / 0.4948 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.000132/1.224, allocations: 23.86 kB / 0.7458 GB, free: 151.6 MB / 0.4948 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04307/1.267, allocations: 15.44 MB / 0.7609 GB, free: 136.3 MB / 0.4948 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.723e-05/1.267, allocations: 7.281 kB / 0.7609 GB, free: 136.3 MB / 0.4948 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004492/1.272, allocations: 0.8468 MB / 0.7617 GB, free: 135.4 MB / 0.4948 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005692/1.277, allocations: 2.127 MB / 0.7638 GB, free: 133.4 MB / 0.4948 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001097/1.279, allocations: 136.9 kB / 0.7639 GB, free: 133.2 MB / 0.4948 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.01978/1.298, allocations: 11.43 MB / 0.7751 GB, free: 121.5 MB / 0.4948 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.29e-06/1.298, allocations: 10.59 kB / 0.7751 GB, free: 121.5 MB / 0.4948 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.09284/1.391, allocations: 38.93 MB / 0.8131 GB, free: 82.43 MB / 0.4948 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.003145/1.394, allocations: 0.9318 MB / 0.814 GB, free: 81.48 MB / 0.4948 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.00132/1.396, allocations: 99.91 kB / 0.8141 GB, free: 81.38 MB / 0.4948 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.003453/1.399, allocations: 254.9 kB / 0.8144 GB, free: 81.15 MB / 0.4948 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001201/1.401, allocations: 450.4 kB / 0.8148 GB, free: 80.71 MB / 0.4948 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003245/1.401, allocations: 150.6 kB / 0.815 GB, free: 80.56 MB / 0.4948 GB
Notification: Performance of sorting global known variables: time 0.002504/1.403, allocations: 1.985 MB / 0.8169 GB, free: 78.58 MB / 0.4948 GB
Notification: Performance of sort global known variables: time 2.21e-07/1.403, allocations: 7.938 kB / 0.8169 GB, free: 78.57 MB / 0.4948 GB
Notification: Performance of remove unused functions: time 0.01099/1.414, allocations: 2.508 MB / 0.8193 GB, free: 76.18 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 0.003223/1.418, allocations: 1.267 MB / 0.8206 GB, free: 75.14 MB / 0.4948 GB
Notification: Performance of simCode: created initialization part: time 0.01326/1.431, allocations: 7.402 MB / 0.8278 GB, free: 67.7 MB / 0.4948 GB
Notification: Performance of simCode: created event and clocks part: time 7.775e-06/1.431, allocations: 2 kB / 0.8278 GB, free: 67.7 MB / 0.4948 GB
Notification: Performance of simCode: created simulation system equations: time 0.007337/1.438, allocations: 4.087 MB / 0.8318 GB, free: 63.57 MB / 0.4948 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004104/1.442, allocations: 0.7251 MB / 0.8325 GB, free: 62.86 MB / 0.4948 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.02155/1.464, allocations: 15.47 MB / 0.8476 GB, free: 47.29 MB / 0.4948 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002617/1.467, allocations: 3.403 MB / 0.8509 GB, free: 43.85 MB / 0.4948 GB
Notification: Performance of simCode: alias equations: time 0.005024/1.472, allocations: 1.674 MB / 0.8526 GB, free: 42.2 MB / 0.4948 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001531/1.473, allocations: 490 kB / 0.853 GB, free: 41.72 MB / 0.4948 GB
Notification: Performance of SimCode: time 1.022e-06/1.473, allocations: 0 / 0.853 GB, free: 41.72 MB / 0.4948 GB
Notification: Performance of Templates: time 0.358/1.831, allocations: 100.5 MB / 0.9511 GB, free: 121.2 MB / 0.4948 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)