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 0.0008293/0.0008293, allocations: 80.75 kB / 19.94 MB, free: 4.547 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 0.0009161/0.0009161, allocations: 181 kB / 23.36 MB, free: 1.133 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 0.8881/0.8881, allocations: 177.1 MB / 203.8 MB, free: 5.461 MB / 186.7 MB
"
[Timeout remaining time 179]
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 0.08014/0.08014, allocations: 17.46 MB / 277.7 MB, free: 11.42 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 1.683e-06/1.683e-06, allocations: 0 / 300.8 MB, free: 1.75 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.183e-05/1.352e-05, allocations: 3.406 kB / 300.8 MB, free: 1.746 MB / 266.7 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 0.0426/0.04261, allocations: 38.67 MB / 339.4 MB, free: 13.67 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01389/0.0565, allocations: 15.7 MB / 355.1 MB, free: 13.91 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001624/0.05812, allocations: 31.75 kB / 355.2 MB, free: 13.88 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009585/0.05908, allocations: 456 kB / 355.6 MB, free: 13.43 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.003284/0.06237, allocations: 1.586 MB / 357.2 MB, free: 11.83 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.00445/0.06682, allocations: 2.482 MB / 359.7 MB, free: 9.336 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.005888/0.07271, allocations: 7.617 MB / 367.3 MB, free: 1.688 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.004445/0.07715, allocations: 4.603 MB / 371.9 MB, free: 12.98 MB / 346.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.007005/0.08415, allocations: 6.308 MB / 378.2 MB, free: 6.668 MB / 346.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.006009/0.09016, allocations: 4.605 MB / 382.8 MB, free: 2.055 MB / 346.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.001539/0.0917, allocations: 0.6719 MB / 383.5 MB, free: 1.383 MB / 346.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004457/0.09616, allocations: 2.079 MB / 385.6 MB, free: 15.3 MB / 362.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.001412/0.09757, allocations: 1.835 MB / 387.4 MB, free: 13.46 MB / 362.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.003154/0.1007, allocations: 2.554 MB / 389.9 MB, free: 10.9 MB / 362.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.01021/0.1109, allocations: 8.489 MB / 398.4 MB, free: 2.383 MB / 362.7 MB
Notification: Performance of FrontEnd - DAE generated: time 5.03e-06/0.1109, allocations: 0 / 398.4 MB, free: 2.383 MB / 362.7 MB
Notification: Performance of FrontEnd: time 1.433e-06/0.1109, allocations: 4 kB / 398.4 MB, free: 2.379 MB / 362.7 MB
Notification: Performance of Transformations before backend: time 0.0001898/0.1111, allocations: 0 / 398.4 MB, free: 2.379 MB / 362.7 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 0.00951/0.1206, allocations: 6.136 MB / 404.6 MB, free: 12.18 MB / 378.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.648e-05/0.1207, allocations: 8.031 kB / 404.6 MB, free: 12.17 MB / 378.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.003962/0.1246, allocations: 1.95 MB / 406.5 MB, free: 10.21 MB / 378.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.003485/0.1281, allocations: 1.985 MB / 408.5 MB, free: 8.164 MB / 378.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0004569/0.1286, allocations: 1.003 MB / 409.5 MB, free: 7.012 MB / 378.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0008793/0.1295, allocations: 0.4924 MB / 410 MB, free: 6.52 MB / 378.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.006238/0.1357, allocations: 5.209 MB / 415.2 MB, free: 1.199 MB / 378.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 6.521e-05/0.1358, allocations: 12.12 kB / 415.2 MB, free: 1.188 MB / 378.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.000451/0.1362, allocations: 200.1 kB / 415.4 MB, free: 0.9922 MB / 378.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.574e-05/0.1363, allocations: 116 kB / 415.5 MB, free: 0.8789 MB / 378.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.005536/0.1418, allocations: 4.451 MB / 420 MB, free: 12.39 MB / 394.7 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 0.02132/0.1631, allocations: 13.67 MB / 433.7 MB, free: 14.53 MB / 410.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.1716/0.3347, allocations: 29.96 MB / 463.6 MB, free: 103 MB / 410.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.002383/0.3371, allocations: 1.533 MB / 465.2 MB, free: 102.9 MB / 410.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.0114/0.3485, allocations: 7.788 MB / 472.9 MB, free: 102.5 MB / 410.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.341e-05/0.3485, allocations: 63.7 kB / 473 MB, free: 102.5 MB / 410.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.002037/0.3506, allocations: 1.154 MB / 474.2 MB, free: 102 MB / 410.7 MB
Notification: Performance of pre-optimization done (n=324): time 9.688e-06/0.3506, allocations: 0 / 474.2 MB, free: 102 MB / 410.7 MB
Notification: Performance of matching and sorting (n=376): time 0.03275/0.3833, allocations: 11.35 MB / 485.5 MB, free: 93.08 MB / 410.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.589e-05/0.3834, allocations: 90.36 kB / 485.6 MB, free: 92.98 MB / 410.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.001687/0.385, allocations: 2.37 MB / 488 MB, free: 91.25 MB / 410.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0006153/0.3857, allocations: 88.02 kB / 488.1 MB, free: 91.21 MB / 410.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0005313/0.3862, allocations: 1.877 MB / 489.9 MB, free: 89.65 MB / 410.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0007893/0.387, allocations: 1.359 MB / 491.3 MB, free: 88.37 MB / 410.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0008057/0.3878, allocations: 0.8728 MB / 492.2 MB, free: 87.58 MB / 410.7 MB
Notification: Performance of setup shared object (initialization): time 3.511e-05/0.3878, allocations: 304.2 kB / 492.5 MB, free: 87.28 MB / 410.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0009404/0.3888, allocations: 0.8113 MB / 493.3 MB, free: 86.46 MB / 410.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001136/0.3899, allocations: 2.221 MB / 495.5 MB, free: 83.7 MB / 410.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.002574/0.3925, allocations: 3.622 MB / 499.1 MB, free: 79.75 MB / 410.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.17e-05/0.3925, allocations: 17.97 kB / 499.1 MB, free: 79.74 MB / 410.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.02007/0.4126, allocations: 6.063 MB / 0.4934 GB, free: 74.1 MB / 410.7 MB
Notification: Performance of prepare postOptimizeDAE: time 4.116e-05/0.4126, allocations: 24 kB / 0.4934 GB, free: 74.08 MB / 410.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.51e-05/0.4127, allocations: 52.95 kB / 0.4934 GB, free: 74.03 MB / 410.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01201/0.4247, allocations: 5.626 MB / 0.4989 GB, free: 68.57 MB / 410.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.002814/0.4275, allocations: 1.171 MB / 0.5001 GB, free: 67.48 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.009934/0.4374, allocations: 6.009 MB / 0.5059 GB, free: 61.34 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.002459/0.4399, allocations: 156 kB / 0.5061 GB, free: 61.19 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0004241/0.4403, allocations: 215.8 kB / 0.5063 GB, free: 60.98 MB / 410.7 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 0.001238/0.4415, allocations: 423.2 kB / 0.5067 GB, free: 60.63 MB / 410.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0006152/0.4421, allocations: 315.7 kB / 0.507 GB, free: 60.32 MB / 410.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01223/0.4544, allocations: 4.431 MB / 0.5113 GB, free: 56 MB / 410.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.55e-05/0.4544, allocations: 40 kB / 0.5114 GB, free: 55.96 MB / 410.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.054e-05/0.4544, allocations: 4 kB / 0.5114 GB, free: 55.96 MB / 410.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.029e-05/0.4545, allocations: 19.92 kB / 0.5114 GB, free: 55.94 MB / 410.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01623/0.4707, allocations: 6.875 MB / 0.5181 GB, free: 49.64 MB / 410.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.051e-05/0.4707, allocations: 8.656 kB / 0.5181 GB, free: 49.64 MB / 410.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.002199/0.4729, allocations: 0.7645 MB / 0.5189 GB, free: 48.92 MB / 410.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.006822/0.4797, allocations: 2.372 MB / 0.5212 GB, free: 46.62 MB / 410.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0005632/0.4803, allocations: 127.8 kB / 0.5213 GB, free: 46.5 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.007172/0.4875, allocations: 5.234 MB / 0.5264 GB, free: 41.09 MB / 410.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.356e-06/0.4875, allocations: 7.984 kB / 0.5264 GB, free: 41.09 MB / 410.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01461/0.5021, allocations: 5.261 MB / 0.5315 GB, free: 35.87 MB / 410.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001321/0.5034, allocations: 441.5 kB / 0.532 GB, free: 35.43 MB / 410.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0004442/0.5039, allocations: 87.97 kB / 0.5321 GB, free: 35.35 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001095/0.505, allocations: 91.92 kB / 0.5321 GB, free: 35.26 MB / 410.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0005412/0.5055, allocations: 370 kB / 0.5325 GB, free: 34.9 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001896/0.5057, allocations: 107.9 kB / 0.5326 GB, free: 34.79 MB / 410.7 MB
Notification: Performance of sorting global known variables: time 0.0008312/0.5065, allocations: 1.143 MB / 0.5337 GB, free: 33.75 MB / 410.7 MB
Notification: Performance of sort global known variables: time 1.8e-07/0.5065, allocations: 0 / 0.5337 GB, free: 33.75 MB / 410.7 MB
Notification: Performance of remove unused functions: time 0.003459/0.51, allocations: 1.783 MB / 0.5355 GB, free: 31.97 MB / 410.7 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 0.001092/0.5111, allocations: 0.8692 MB / 0.5363 GB, free: 31.25 MB / 410.7 MB
Notification: Performance of simCode: created initialization part: time 0.004443/0.5155, allocations: 3.154 MB / 0.5394 GB, free: 28.29 MB / 410.7 MB
Notification: Performance of simCode: created event and clocks part: time 5.906e-05/0.5156, allocations: 47.84 kB / 0.5394 GB, free: 28.25 MB / 410.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.002294/0.5179, allocations: 1.808 MB / 0.5412 GB, free: 26.53 MB / 410.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.002046/0.5199, allocations: 0.8166 MB / 0.542 GB, free: 25.82 MB / 410.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.009697/0.5296, allocations: 8.357 MB / 0.5502 GB, free: 17.48 MB / 410.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0007799/0.5304, allocations: 1.091 MB / 0.5512 GB, free: 16.37 MB / 410.7 MB
Notification: Performance of simCode: alias equations: time 0.001769/0.5322, allocations: 0.6066 MB / 0.5518 GB, free: 15.89 MB / 410.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001638/0.5338, allocations: 0.9441 MB / 0.5527 GB, free: 14.93 MB / 410.7 MB
Notification: Performance of SimCode: time 1.693e-06/0.5338, allocations: 4.922 kB / 0.5527 GB, free: 14.93 MB / 410.7 MB
Notification: Performance of Templates: time 0.2117/0.7455, allocations: 92.58 MB / 0.6431 GB, free: 111.2 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=240  -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.084478374104947]