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 0.001399/0.001399, allocations: 92.42 kB / 19.7 MB, free: 2.137 MB / 14.72 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 0.00176/0.00176, allocations: 205.8 kB / 22.99 MB, free: 4.953 MB / 14.72 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 1.426/1.426, allocations: 230.6 MB / 256.8 MB, free: 7.805 MB / 206.1 MB
"
[Timeout remaining time 178]
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 0.1384/0.1384, allocations: 23.93 MB / 337.1 MB, free: 10.93 MB / 270.1 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: 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 0.002053/0.002053, allocations: 71.89 kB / 472.5 MB, free: 6.93 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3269/0.329, allocations: 59.88 MB / 0.5199 GB, free: 9.816 MB / 382.1 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 0.07502/0.404, allocations: 29.37 MB / 0.5485 GB, free: 10.47 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0317/0.4357, allocations: 23.04 MB / 0.571 GB, free: 5.324 MB / 414.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002012/0.4377, allocations: 35.69 kB / 0.5711 GB, free: 5.289 MB / 414.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.002078/0.4398, allocations: 0.5504 MB / 0.5716 GB, free: 4.734 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.007143/0.4469, allocations: 2.157 MB / 0.5737 GB, free: 2.562 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01027/0.4572, allocations: 3.581 MB / 0.5772 GB, free: 14.96 MB / 430.1 MB
Notification: Performance of NFFlatten.flatten: time 0.008728/0.4659, allocations: 7.398 MB / 0.5844 GB, free: 7.531 MB / 430.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.005828/0.4717, allocations: 4.343 MB / 0.5887 GB, free: 3.113 MB / 430.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.007493/0.4792, allocations: 4.967 MB / 0.5935 GB, free: 14.14 MB / 446.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.008393/0.4876, allocations: 4.764 MB / 0.5982 GB, free: 9.359 MB / 446.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.002631/0.4902, allocations: 0.6719 MB / 0.5988 GB, free: 8.688 MB / 446.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0108/0.501, allocations: 3.257 MB / 0.602 GB, free: 5.426 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.003376/0.5044, allocations: 1.808 MB / 0.6038 GB, free: 3.613 MB / 446.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.007104/0.5115, allocations: 2.896 MB / 0.6066 GB, free: 0.707 MB / 446.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02198/0.5335, allocations: 11.63 MB / 0.618 GB, free: 5.031 MB / 462.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.702e-06/0.5335, allocations: 4 kB / 0.618 GB, free: 5.027 MB / 462.1 MB
Notification: Performance of FrontEnd: time 2.195e-06/0.5335, allocations: 0 / 0.618 GB, free: 5.027 MB / 462.1 MB
Notification: Performance of Transformations before backend: time 0.0002869/0.5338, allocations: 3.938 kB / 0.618 GB, free: 5.023 MB / 462.1 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 0.02082/0.5546, allocations: 7.237 MB / 0.625 GB, free: 13.71 MB / 478.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.942e-05/0.5547, allocations: 8.031 kB / 0.625 GB, free: 13.71 MB / 478.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006942/0.5616, allocations: 1.238 MB / 0.6263 GB, free: 12.46 MB / 478.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.009314/0.5709, allocations: 3.317 MB / 0.6295 GB, free: 9.09 MB / 478.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0009623/0.5719, allocations: 1.007 MB / 0.6305 GB, free: 7.934 MB / 478.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002491/0.5744, allocations: 0.5041 MB / 0.631 GB, free: 7.43 MB / 478.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02182/0.5962, allocations: 9.466 MB / 0.6402 GB, free: 13.85 MB / 494.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001042/0.5963, allocations: 0 / 0.6402 GB, free: 13.85 MB / 494.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.001015/0.5973, allocations: 192 kB / 0.6404 GB, free: 13.66 MB / 494.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.821e-05/0.5974, allocations: 116 kB / 0.6405 GB, free: 13.55 MB / 494.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02464/0.6221, allocations: 12.66 MB / 0.6529 GB, free: 0.8672 MB / 494.1 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 0.06414/0.6862, allocations: 26.73 MB / 0.679 GB, free: 5.902 MB / 0.5137 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.05885/0.745, allocations: 26.13 MB / 0.7045 GB, free: 12.68 MB / 0.545 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.00886/0.7539, allocations: 4.712 MB / 0.7091 GB, free: 7.938 MB / 0.545 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.04088/0.7948, allocations: 16.9 MB / 0.7256 GB, free: 6.969 MB / 0.5606 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.188e-05/0.7949, allocations: 65.11 kB / 0.7257 GB, free: 6.895 MB / 0.5606 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004876/0.7997, allocations: 1.25 MB / 0.7269 GB, free: 5.641 MB / 0.5606 GB
Notification: Performance of pre-optimization done (n=324): time 1.473e-05/0.7997, allocations: 0 / 0.7269 GB, free: 5.641 MB / 0.5606 GB
Notification: Performance of matching and sorting (n=376): time 0.3346/1.134, allocations: 24.16 MB / 0.7505 GB, free: 169.8 MB / 0.5606 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.987e-05/1.134, allocations: 93.48 kB / 0.7506 GB, free: 169.8 MB / 0.5606 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003538/1.138, allocations: 2.837 MB / 0.7533 GB, free: 168.8 MB / 0.5606 GB
Notification: Performance of collectPreVariables (initialization): time 0.0009658/1.139, allocations: 86.52 kB / 0.7534 GB, free: 168.7 MB / 0.5606 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001082/1.14, allocations: 2.225 MB / 0.7556 GB, free: 167.3 MB / 0.5606 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001456/1.141, allocations: 1.358 MB / 0.7569 GB, free: 166.4 MB / 0.5606 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.00142/1.143, allocations: 0.9821 MB / 0.7579 GB, free: 166 MB / 0.5606 GB
Notification: Performance of setup shared object (initialization): time 3.576e-05/1.143, allocations: 306.2 kB / 0.7582 GB, free: 165.7 MB / 0.5606 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004115/1.147, allocations: 2.963 MB / 0.7611 GB, free: 164.3 MB / 0.5606 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004664/1.152, allocations: 4.487 MB / 0.7655 GB, free: 160.8 MB / 0.5606 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.008926/1.161, allocations: 7.814 MB / 0.7731 GB, free: 155.6 MB / 0.5606 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.341e-05/1.161, allocations: 15.28 kB / 0.7731 GB, free: 155.6 MB / 0.5606 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05161/1.212, allocations: 13.81 MB / 0.7866 GB, free: 145.3 MB / 0.5606 GB
Notification: Performance of prepare postOptimizeDAE: time 4.852e-05/1.212, allocations: 30.59 kB / 0.7866 GB, free: 145.3 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.37e-05/1.212, allocations: 48 kB / 0.7867 GB, free: 145.2 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.007779/1.22, allocations: 3.474 MB / 0.79 GB, free: 141.9 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005233/1.225, allocations: 1.258 MB / 0.7913 GB, free: 140.6 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02766/1.253, allocations: 17.9 MB / 0.8088 GB, free: 122.5 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004562/1.258, allocations: 247.8 kB / 0.809 GB, free: 122.2 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0008836/1.259, allocations: 279.8 kB / 0.8093 GB, free: 122 MB / 0.5606 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 0.002706/1.261, allocations: 1.45 MB / 0.8107 GB, free: 120.5 MB / 0.5606 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0008944/1.262, allocations: 345.7 kB / 0.811 GB, free: 120.2 MB / 0.5606 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03152/1.294, allocations: 9.617 MB / 0.8204 GB, free: 110.7 MB / 0.5606 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.059e-05/1.294, allocations: 40 kB / 0.8204 GB, free: 110.6 MB / 0.5606 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.674e-05/1.294, allocations: 4 kB / 0.8204 GB, free: 110.6 MB / 0.5606 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001125/1.294, allocations: 19.92 kB / 0.8205 GB, free: 110.6 MB / 0.5606 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04009/1.334, allocations: 14.36 MB / 0.8345 GB, free: 96.29 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.88e-05/1.334, allocations: 4 kB / 0.8345 GB, free: 96.29 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004261/1.338, allocations: 0.8515 MB / 0.8353 GB, free: 95.44 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005297/1.344, allocations: 2.128 MB / 0.8374 GB, free: 93.34 MB / 0.5606 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0006716/1.344, allocations: 139.9 kB / 0.8375 GB, free: 93.21 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.0192/1.363, allocations: 12.1 MB / 0.8493 GB, free: 80.82 MB / 0.5606 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.157e-06/1.363, allocations: 7.938 kB / 0.8494 GB, free: 80.82 MB / 0.5606 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03623/1.4, allocations: 12.93 MB / 0.862 GB, free: 67.81 MB / 0.5606 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.002943/1.403, allocations: 0.9027 MB / 0.8629 GB, free: 66.91 MB / 0.5606 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0008073/1.403, allocations: 95.97 kB / 0.863 GB, free: 66.82 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002279/1.406, allocations: 166.6 kB / 0.8631 GB, free: 66.66 MB / 0.5606 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0008928/1.407, allocations: 466.2 kB / 0.8636 GB, free: 66.2 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002956/1.407, allocations: 147.9 kB / 0.8637 GB, free: 66.06 MB / 0.5606 GB
Notification: Performance of sorting global known variables: time 0.001919/1.409, allocations: 1.847 MB / 0.8655 GB, free: 64.21 MB / 0.5606 GB
Notification: Performance of sort global known variables: time 7.1e-08/1.409, allocations: 2.656 kB / 0.8655 GB, free: 64.21 MB / 0.5606 GB
Notification: Performance of remove unused functions: time 0.008204/1.417, allocations: 2.062 MB / 0.8675 GB, free: 62.2 MB / 0.5606 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 0.002914/1.42, allocations: 1.322 MB / 0.8688 GB, free: 61.07 MB / 0.5606 GB
Notification: Performance of simCode: created initialization part: time 0.01246/1.432, allocations: 7.072 MB / 0.8757 GB, free: 53.98 MB / 0.5606 GB
Notification: Performance of simCode: created event and clocks part: time 8.966e-06/1.432, allocations: 0 / 0.8757 GB, free: 53.98 MB / 0.5606 GB
Notification: Performance of simCode: created simulation system equations: time 0.007105/1.439, allocations: 3.758 MB / 0.8794 GB, free: 50.19 MB / 0.5606 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003922/1.443, allocations: 0.777 MB / 0.8802 GB, free: 49.49 MB / 0.5606 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01741/1.461, allocations: 10.94 MB / 0.8908 GB, free: 38.51 MB / 0.5606 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001983/1.463, allocations: 2.692 MB / 0.8935 GB, free: 35.83 MB / 0.5606 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001972/1.465, allocations: 498 kB / 0.8939 GB, free: 35.35 MB / 0.5606 GB
Notification: Performance of SimCode: time 1.242e-06/1.465, allocations: 0 / 0.8939 GB, free: 35.35 MB / 0.5606 GB
Notification: Performance of Templates: time 0.3994/1.864, allocations: 148.8 MB / 1.039 GB, free: 142.7 MB / 0.5919 GB
"
[Timeout remaining time 658]
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=480 -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 14.588227533968166]
Failed to read output from testmodel.py, exit status != 0:
1.8744472789694555 1.883195522 1.347209159
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7f9336c9af50>