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 0.0009239/0.0009239, allocations: 80.94 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 0.0009578/0.0009578, allocations: 177 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 0.9829/0.9829, allocations: 177.1 MB / 203.8 MB, free: 5.496 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 0.08305/0.08305, allocations: 17.47 MB / 277.7 MB, free: 11.45 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 1.303e-06/1.303e-06, allocations: 0 / 300.8 MB, free: 1.73 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 8.827e-06/1.013e-05, allocations: 2.312 kB / 300.8 MB, free: 1.727 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 0.03118/0.03119, allocations: 38.72 MB / 339.5 MB, free: 13.63 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.03434/0.06553, allocations: 15.71 MB / 355.2 MB, free: 13.86 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001316/0.06684, allocations: 35.69 kB / 355.3 MB, free: 13.83 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.001027/0.06787, allocations: 448.1 kB / 355.7 MB, free: 13.39 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.009244/0.07711, allocations: 1.562 MB / 357.3 MB, free: 11.81 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01675/0.09386, allocations: 2.444 MB / 359.7 MB, free: 9.355 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.01502/0.1089, allocations: 7.632 MB / 367.3 MB, free: 1.691 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.003933/0.1128, allocations: 4.571 MB / 371.9 MB, free: 13.02 MB / 346.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.005426/0.1182, allocations: 6.28 MB / 378.2 MB, free: 6.73 MB / 346.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.004837/0.1231, allocations: 4.605 MB / 382.8 MB, free: 2.117 MB / 346.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.001083/0.1242, allocations: 0.6719 MB / 383.5 MB, free: 1.445 MB / 346.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.003962/0.1281, allocations: 2.138 MB / 385.6 MB, free: 15.3 MB / 362.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.001181/0.1293, allocations: 1.835 MB / 387.4 MB, free: 13.46 MB / 362.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.002417/0.1317, allocations: 2.546 MB / 390 MB, free: 10.91 MB / 362.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.00672/0.1384, allocations: 8.493 MB / 398.5 MB, free: 2.391 MB / 362.7 MB
Notification: Performance of FrontEnd - DAE generated: time 4.599e-06/0.1384, allocations: 0 / 398.5 MB, free: 2.391 MB / 362.7 MB
Notification: Performance of FrontEnd: time 1.392e-06/0.1384, allocations: 4 kB / 398.5 MB, free: 2.387 MB / 362.7 MB
Notification: Performance of Transformations before backend: time 4.508e-05/0.1385, allocations: 0 / 398.5 MB, free: 2.387 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 0.006772/0.1453, allocations: 6.14 MB / 404.6 MB, free: 12.18 MB / 378.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.181e-05/0.1453, allocations: 8.031 kB / 404.6 MB, free: 12.17 MB / 378.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.003362/0.1487, allocations: 1.95 MB / 406.6 MB, free: 10.21 MB / 378.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.002461/0.1511, allocations: 1.985 MB / 408.6 MB, free: 8.168 MB / 378.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0004029/0.1515, allocations: 0.999 MB / 409.6 MB, free: 7.02 MB / 378.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0006365/0.1522, allocations: 0.4962 MB / 410.1 MB, free: 6.523 MB / 378.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.004993/0.1571, allocations: 5.213 MB / 415.3 MB, free: 1.199 MB / 378.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 5.952e-05/0.1572, allocations: 4.125 kB / 415.3 MB, free: 1.195 MB / 378.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0004187/0.1576, allocations: 204.1 kB / 415.5 MB, free: 0.9961 MB / 378.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.503e-05/0.1577, allocations: 116 kB / 415.6 MB, free: 0.8828 MB / 378.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.005041/0.1627, allocations: 4.447 MB / 420 MB, free: 12.4 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 0.01801/0.1807, allocations: 13.67 MB / 433.7 MB, free: 14.54 MB / 410.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.1623/0.343, allocations: 29.96 MB / 463.7 MB, free: 101.4 MB / 410.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.002404/0.3454, allocations: 1.54 MB / 465.2 MB, free: 101.4 MB / 410.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.01133/0.3568, allocations: 7.785 MB / 473 MB, free: 100.7 MB / 410.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.504e-05/0.3568, allocations: 66.23 kB / 473 MB, free: 100.7 MB / 410.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.001974/0.3588, allocations: 1.148 MB / 474.2 MB, free: 100.1 MB / 410.7 MB
Notification: Performance of pre-optimization done (n=324): time 1.102e-05/0.3588, allocations: 2.656 kB / 474.2 MB, free: 100.1 MB / 410.7 MB
Notification: Performance of matching and sorting (n=376): time 0.03427/0.3931, allocations: 11.35 MB / 485.5 MB, free: 90.99 MB / 410.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.484e-05/0.3931, allocations: 90.36 kB / 485.6 MB, free: 90.89 MB / 410.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.001395/0.3945, allocations: 2.372 MB / 488 MB, free: 89.16 MB / 410.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.000215/0.3947, allocations: 88.39 kB / 488.1 MB, free: 89.11 MB / 410.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004805/0.3952, allocations: 1.881 MB / 490 MB, free: 87.75 MB / 410.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0005861/0.3958, allocations: 1.355 MB / 491.3 MB, free: 86.77 MB / 410.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0008694/0.3966, allocations: 0.8779 MB / 492.2 MB, free: 86.21 MB / 410.7 MB
Notification: Performance of setup shared object (initialization): time 3.117e-05/0.3967, allocations: 301.1 kB / 492.5 MB, free: 85.92 MB / 410.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0009432/0.3976, allocations: 0.8112 MB / 493.3 MB, free: 85.1 MB / 410.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001245/0.3989, allocations: 2.219 MB / 495.5 MB, free: 82.34 MB / 410.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0027/0.4016, allocations: 3.628 MB / 499.2 MB, free: 78.39 MB / 410.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.696e-05/0.4016, allocations: 12 kB / 499.2 MB, free: 78.38 MB / 410.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.02069/0.4223, allocations: 6.062 MB / 0.4934 GB, free: 72.74 MB / 410.7 MB
Notification: Performance of prepare postOptimizeDAE: time 3.452e-05/0.4223, allocations: 32.55 kB / 0.4934 GB, free: 72.71 MB / 410.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 3.799e-05/0.4223, allocations: 49.08 kB / 0.4935 GB, free: 72.67 MB / 410.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01193/0.4343, allocations: 5.618 MB / 0.499 GB, free: 67.21 MB / 410.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.002959/0.4372, allocations: 1.3 MB / 0.5002 GB, free: 65.99 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01118/0.4484, allocations: 6.039 MB / 0.5061 GB, free: 59.82 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.002535/0.4509, allocations: 154.7 kB / 0.5063 GB, free: 59.67 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0003841/0.4513, allocations: 223.8 kB / 0.5065 GB, free: 59.45 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 0.001227/0.4526, allocations: 422.5 kB / 0.5069 GB, free: 59.14 MB / 410.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000599/0.4532, allocations: 318.3 kB / 0.5072 GB, free: 58.83 MB / 410.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0165/0.4697, allocations: 4.422 MB / 0.5115 GB, free: 54.52 MB / 410.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.063e-05/0.4697, allocations: 42.69 kB / 0.5115 GB, free: 54.48 MB / 410.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 9.708e-06/0.4697, allocations: 4 kB / 0.5116 GB, free: 54.47 MB / 410.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 2.797e-05/0.4697, allocations: 19.92 kB / 0.5116 GB, free: 54.45 MB / 410.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01995/0.4897, allocations: 6.88 MB / 0.5183 GB, free: 48.16 MB / 410.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.116e-05/0.4897, allocations: 4 kB / 0.5183 GB, free: 48.16 MB / 410.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.002712/0.4924, allocations: 0.852 MB / 0.5191 GB, free: 47.35 MB / 410.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.008998/0.5014, allocations: 2.363 MB / 0.5214 GB, free: 45.06 MB / 410.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0003058/0.5017, allocations: 131.8 kB / 0.5216 GB, free: 44.93 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.008637/0.5103, allocations: 5.251 MB / 0.5267 GB, free: 39.52 MB / 410.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.826e-06/0.5103, allocations: 6.688 kB / 0.5267 GB, free: 39.51 MB / 410.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0126/0.5229, allocations: 5.266 MB / 0.5318 GB, free: 34.29 MB / 410.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0007367/0.5237, allocations: 443.6 kB / 0.5323 GB, free: 33.86 MB / 410.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0003162/0.524, allocations: 95.97 kB / 0.5324 GB, free: 33.77 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0009212/0.5249, allocations: 83.92 kB / 0.5324 GB, free: 33.69 MB / 410.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0005399/0.5255, allocations: 374.5 kB / 0.5328 GB, free: 33.32 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001794/0.5256, allocations: 107.9 kB / 0.5329 GB, free: 33.22 MB / 410.7 MB
Notification: Performance of sorting global known variables: time 0.0007173/0.5264, allocations: 1.144 MB / 0.534 GB, free: 32.18 MB / 410.7 MB
Notification: Performance of sort global known variables: time 9e-08/0.5264, allocations: 2.719 kB / 0.534 GB, free: 32.18 MB / 410.7 MB
Notification: Performance of remove unused functions: time 0.003405/0.5298, allocations: 1.776 MB / 0.5357 GB, free: 30.46 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 0.0009678/0.5307, allocations: 0.8756 MB / 0.5366 GB, free: 29.74 MB / 410.7 MB
Notification: Performance of simCode: created initialization part: time 0.003937/0.5347, allocations: 3.167 MB / 0.5397 GB, free: 26.78 MB / 410.7 MB
Notification: Performance of simCode: created event and clocks part: time 4.774e-05/0.5347, allocations: 39.84 kB / 0.5397 GB, free: 26.74 MB / 410.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.002096/0.5368, allocations: 1.803 MB / 0.5415 GB, free: 25.02 MB / 410.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001687/0.5385, allocations: 0.8055 MB / 0.5423 GB, free: 24.31 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 0.00972/0.5482, allocations: 8.365 MB / 0.5504 GB, free: 15.98 MB / 410.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0007533/0.549, allocations: 1.099 MB / 0.5515 GB, free: 14.85 MB / 410.7 MB
Notification: Performance of simCode: alias equations: time 0.001475/0.5504, allocations: 0.5951 MB / 0.5521 GB, free: 14.38 MB / 410.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001692/0.5521, allocations: 0.9441 MB / 0.553 GB, free: 13.43 MB / 410.7 MB
Notification: Performance of SimCode: time 1.052e-06/0.5521, allocations: 2.688 kB / 0.553 GB, free: 13.43 MB / 410.7 MB
Notification: Performance of Templates: time 0.1999/0.7521, allocations: 92.59 MB / 0.6435 GB, free: 106.6 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 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.35917535983026]