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 0.0008562/0.0008562, allocations: 76.45 kB / 19.9 MB, free: 16 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 0.0007581/0.0007581, allocations: 165.9 kB / 23.18 MB, free: 1.383 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: 177.2 MB / 203.6 MB, free: 5.777 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 0.09782/0.09782, allocations: 17.38 MB / 277.4 MB, free: 11.89 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: Chemical requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed.
Notification: Performance of FrontEnd - loaded program: time 0.0008549/0.0008549, allocations: 67.89 kB / 412.8 MB, free: 15.88 MB / 394.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2615/0.2624, allocations: 59.84 MB / 472.7 MB, free: 29.79 MB / 410.7 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 0.02736/0.2898, allocations: 29.6 MB / 0.4905 GB, free: 17.29 MB / 410.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01681/0.3066, allocations: 23.04 MB / 0.513 GB, free: 12.8 MB / 426.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001113/0.3077, allocations: 31.75 kB / 0.513 GB, free: 12.77 MB / 426.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.001031/0.3087, allocations: 0.5538 MB / 0.5136 GB, free: 12.34 MB / 426.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.003942/0.3126, allocations: 2.164 MB / 0.5157 GB, free: 10.51 MB / 426.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.007124/0.3198, allocations: 3.593 MB / 0.5192 GB, free: 7.559 MB / 426.7 MB
Notification: Performance of NFFlatten.flatten: time 0.005347/0.3251, allocations: 7.397 MB / 0.5264 GB, free: 0.9414 MB / 426.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.003148/0.3283, allocations: 4.315 MB / 0.5306 GB, free: 12.55 MB / 442.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.004817/0.3331, allocations: 6.496 MB / 0.537 GB, free: 6.043 MB / 442.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.004804/0.3379, allocations: 4.951 MB / 0.5418 GB, free: 1.078 MB / 442.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0007975/0.3387, allocations: 0.6758 MB / 0.5425 GB, free: 412 kB / 442.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.007767/0.3464, allocations: 3.194 MB / 0.5456 GB, free: 13.2 MB / 458.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.001183/0.3476, allocations: 1.812 MB / 0.5474 GB, free: 11.39 MB / 458.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.003081/0.3507, allocations: 2.9 MB / 0.5502 GB, free: 8.477 MB / 458.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.01354/0.3643, allocations: 11.67 MB / 0.5616 GB, free: 12.77 MB / 474.7 MB
Notification: Performance of FrontEnd - DAE generated: time 6.643e-06/0.3643, allocations: 4 kB / 0.5616 GB, free: 12.77 MB / 474.7 MB
Notification: Performance of FrontEnd: time 2.084e-06/0.3643, allocations: 0 / 0.5616 GB, free: 12.77 MB / 474.7 MB
Notification: Performance of Transformations before backend: time 8.486e-05/0.3643, allocations: 3.938 kB / 0.5616 GB, free: 12.76 MB / 474.7 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 0.009154/0.3735, allocations: 7.241 MB / 0.5687 GB, free: 5.449 MB / 474.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.272e-05/0.3735, allocations: 8.031 kB / 0.5687 GB, free: 5.441 MB / 474.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.002975/0.3765, allocations: 1.243 MB / 0.5699 GB, free: 4.195 MB / 474.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.003746/0.3803, allocations: 3.317 MB / 0.5731 GB, free: 0.8203 MB / 474.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0004846/0.3808, allocations: 1.007 MB / 0.5741 GB, free: 15.66 MB / 490.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0006336/0.3814, allocations: 0.4924 MB / 0.5746 GB, free: 15.17 MB / 490.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.009747/0.3911, allocations: 9.466 MB / 0.5838 GB, free: 5.598 MB / 490.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 5.683e-05/0.3912, allocations: 7.984 kB / 0.5839 GB, free: 5.59 MB / 490.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0004373/0.3916, allocations: 192 kB / 0.584 GB, free: 5.402 MB / 490.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.444e-05/0.3917, allocations: 116 kB / 0.5841 GB, free: 5.289 MB / 490.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.01262/0.4043, allocations: 12.66 MB / 0.5965 GB, free: 8.605 MB / 0.4948 GB
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 0.02908/0.4334, allocations: 26.74 MB / 0.6226 GB, free: 13.62 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.2813/0.7147, allocations: 26.13 MB / 0.6481 GB, free: 128.7 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.007836/0.7225, allocations: 4.715 MB / 0.6527 GB, free: 127.6 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.03478/0.7573, allocations: 16.9 MB / 0.6693 GB, free: 121.6 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.875e-05/0.7574, allocations: 68.67 kB / 0.6693 GB, free: 121.5 MB / 0.5261 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.00303/0.7604, allocations: 1.261 MB / 0.6705 GB, free: 121.3 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=324): time 2.311e-05/0.7604, allocations: 0 / 0.6705 GB, free: 121.3 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=376): time 0.05459/0.815, allocations: 24.17 MB / 0.6942 GB, free: 107.2 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.515e-05/0.8151, allocations: 93.02 kB / 0.6942 GB, free: 107.1 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.002796/0.8179, allocations: 2.837 MB / 0.697 GB, free: 104.3 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 0.00101/0.8189, allocations: 85.7 kB / 0.6971 GB, free: 104.2 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0008564/0.8197, allocations: 2.225 MB / 0.6993 GB, free: 102.3 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001399/0.8211, allocations: 1.358 MB / 0.7006 GB, free: 101 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001433/0.8226, allocations: 0.9846 MB / 0.7016 GB, free: 99.99 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 3.554e-05/0.8226, allocations: 301.1 kB / 0.7018 GB, free: 99.69 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.00331/0.8259, allocations: 2.967 MB / 0.7047 GB, free: 96.72 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.003587/0.8295, allocations: 4.487 MB / 0.7091 GB, free: 91.55 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.007764/0.8373, allocations: 7.81 MB / 0.7167 GB, free: 83.11 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.941e-05/0.8373, allocations: 15.28 kB / 0.7168 GB, free: 83.1 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.03248/0.8698, allocations: 13.81 MB / 0.7302 GB, free: 69.42 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 5.045e-05/0.8699, allocations: 27.98 kB / 0.7303 GB, free: 69.39 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.058e-05/0.8699, allocations: 48 kB / 0.7303 GB, free: 69.35 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.004925/0.8748, allocations: 3.475 MB / 0.7337 GB, free: 66.03 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.003644/0.8785, allocations: 1.268 MB / 0.735 GB, free: 64.76 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02003/0.8985, allocations: 17.87 MB / 0.7524 GB, free: 46.62 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.003874/0.9024, allocations: 247.8 kB / 0.7526 GB, free: 46.38 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001278/0.9037, allocations: 282.5 kB / 0.7529 GB, free: 46.1 MB / 0.5261 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 0.003589/0.9072, allocations: 1.461 MB / 0.7543 GB, free: 44.63 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.00112/0.9084, allocations: 345.7 kB / 0.7547 GB, free: 44.29 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.02182/0.9302, allocations: 9.624 MB / 0.7641 GB, free: 34.74 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.687e-05/0.9302, allocations: 40 kB / 0.7641 GB, free: 34.7 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.743e-05/0.9303, allocations: 6.656 kB / 0.7641 GB, free: 34.7 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001516/0.9304, allocations: 23.86 kB / 0.7641 GB, free: 34.68 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.03106/0.9615, allocations: 14.36 MB / 0.7782 GB, free: 20.35 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.558e-05/0.9615, allocations: 7.984 kB / 0.7782 GB, free: 20.34 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.002911/0.9644, allocations: 0.8451 MB / 0.779 GB, free: 19.5 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.003417/0.9678, allocations: 2.123 MB / 0.7811 GB, free: 17.4 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0008296/0.9687, allocations: 138.6 kB / 0.7812 GB, free: 17.27 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.01326/0.9819, allocations: 12.11 MB / 0.793 GB, free: 4.883 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.057e-06/0.9819, allocations: 4 kB / 0.793 GB, free: 4.879 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.02857/1.01, allocations: 12.94 MB / 0.8057 GB, free: 7.875 MB / 0.5417 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.00283/1.013, allocations: 0.8996 MB / 0.8065 GB, free: 6.973 MB / 0.5417 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0009621/1.014, allocations: 95.97 kB / 0.8066 GB, free: 6.879 MB / 0.5417 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002131/1.016, allocations: 163.8 kB / 0.8068 GB, free: 6.719 MB / 0.5417 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0009538/1.017, allocations: 476.8 kB / 0.8072 GB, free: 6.254 MB / 0.5417 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003686/1.018, allocations: 147.9 kB / 0.8074 GB, free: 6.109 MB / 0.5417 GB
Notification: Performance of sorting global known variables: time 0.002433/1.02, allocations: 1.847 MB / 0.8092 GB, free: 4.258 MB / 0.5417 GB
Notification: Performance of sort global known variables: time 2.41e-07/1.02, allocations: 0 / 0.8092 GB, free: 4.258 MB / 0.5417 GB
Notification: Performance of remove unused functions: time 0.007526/1.028, allocations: 2.056 MB / 0.8112 GB, free: 2.199 MB / 0.5417 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 0.003096/1.031, allocations: 1.321 MB / 0.8125 GB, free: 1.066 MB / 0.5417 GB
Notification: Performance of simCode: created initialization part: time 0.01314/1.044, allocations: 7.074 MB / 0.8194 GB, free: 9.973 MB / 0.5573 GB
Notification: Performance of simCode: created event and clocks part: time 8.556e-06/1.044, allocations: 0 / 0.8194 GB, free: 9.973 MB / 0.5573 GB
Notification: Performance of simCode: created simulation system equations: time 0.00785/1.052, allocations: 3.774 MB / 0.8231 GB, free: 6.164 MB / 0.5573 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004961/1.057, allocations: 0.7645 MB / 0.8238 GB, free: 5.477 MB / 0.5573 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.02283/1.08, allocations: 10.97 MB / 0.8345 GB, free: 10.47 MB / 0.573 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.004444/1.084, allocations: 2.782 MB / 0.8373 GB, free: 7.695 MB / 0.573 GB
Notification: Performance of simCode: alias equations: time 0.004625/1.089, allocations: 1.567 MB / 0.8388 GB, free: 6.156 MB / 0.573 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.00145/1.09, allocations: 456.2 kB / 0.8392 GB, free: 5.711 MB / 0.573 GB
Notification: Performance of SimCode: time 3.246e-06/1.09, allocations: 0 / 0.8392 GB, free: 5.711 MB / 0.573 GB
Notification: Performance of Templates: time 0.4476/1.538, allocations: 92 MB / 0.9291 GB, free: 152.5 MB / 0.5886 GB
"
[Timeout remaining time 658]
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 -s cvode -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 6.360261181020178]
Failed to read output from testmodel.py, exit status != 0:
1.545248616952449 1.552996519 1.187195534
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7869a86ad3a0>