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 0.0007875/0.0007875, allocations: 72.5 kB / 19.93 MB, free: 4.633 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 0.0007517/0.0007517, allocations: 177.9 kB / 23.21 MB, free: 1.348 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 0.8264/0.8264, allocations: 177.2 MB / 203.5 MB, free: 5.73 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 0.09067/0.09067, allocations: 17.44 MB / 277.4 MB, free: 11.76 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 1.543e-06/1.543e-06, allocations: 0 / 412.9 MB, free: 15.74 MB / 394.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.783e-05/1.938e-05, allocations: 2.281 kB / 412.9 MB, free: 15.74 MB / 394.7 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 0.02173/0.02175, allocations: 29.69 MB / 442.6 MB, free: 2.102 MB / 410.7 MB
Notification: Performance of NFInst.instExpressions: time 0.1544/0.1761, allocations: 23.03 MB / 465.6 MB, free: 50.27 MB / 410.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0007284/0.1768, allocations: 35.53 kB / 465.7 MB, free: 50.25 MB / 410.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0007732/0.1776, allocations: 0.545 MB / 466.2 MB, free: 49.96 MB / 410.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.00261/0.1802, allocations: 2.247 MB / 468.4 MB, free: 48.59 MB / 410.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.00455/0.1848, allocations: 3.677 MB / 472.1 MB, free: 46.44 MB / 410.7 MB
Notification: Performance of NFFlatten.flatten: time 0.002996/0.1878, allocations: 7.638 MB / 479.8 MB, free: 42.71 MB / 410.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.002395/0.1902, allocations: 4.336 MB / 484.1 MB, free: 40.88 MB / 410.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.003628/0.1938, allocations: 6.339 MB / 490.4 MB, free: 38.76 MB / 410.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.00428/0.1981, allocations: 4.612 MB / 495.1 MB, free: 37.35 MB / 410.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0008817/0.199, allocations: 0.6735 MB / 495.7 MB, free: 37.35 MB / 410.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.005272/0.2042, allocations: 3.206 MB / 498.9 MB, free: 36.72 MB / 410.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.00108/0.2053, allocations: 1.836 MB / 0.489 GB, free: 35.67 MB / 410.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.002227/0.2075, allocations: 2.547 MB / 0.4915 GB, free: 34.61 MB / 410.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.01011/0.2176, allocations: 12.31 MB / 0.5035 GB, free: 28.09 MB / 410.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.817e-06/0.2176, allocations: 0 / 0.5035 GB, free: 28.09 MB / 410.7 MB
Notification: Performance of FrontEnd: time 1.202e-06/0.2177, allocations: 3.938 kB / 0.5035 GB, free: 28.09 MB / 410.7 MB
Notification: Performance of Transformations before backend: time 5.861e-05/0.2177, allocations: 2.656 kB / 0.5035 GB, free: 28.09 MB / 410.7 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 0.007222/0.2249, allocations: 7.183 MB / 0.5106 GB, free: 20.89 MB / 410.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.201e-05/0.225, allocations: 10.69 kB / 0.5106 GB, free: 20.88 MB / 410.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.002635/0.2276, allocations: 1.235 MB / 0.5118 GB, free: 19.65 MB / 410.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.003051/0.2306, allocations: 3.318 MB / 0.515 GB, free: 16.28 MB / 410.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0002412/0.2309, allocations: 1.007 MB / 0.516 GB, free: 15.12 MB / 410.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0005906/0.2315, allocations: 0.4885 MB / 0.5165 GB, free: 14.63 MB / 410.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.007377/0.2389, allocations: 9.461 MB / 0.5257 GB, free: 5.066 MB / 410.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 6.199e-05/0.2389, allocations: 8.125 kB / 0.5257 GB, free: 5.059 MB / 410.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.000437/0.2394, allocations: 192.4 kB / 0.5259 GB, free: 4.871 MB / 410.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.365e-05/0.2394, allocations: 119.9 kB / 0.526 GB, free: 4.754 MB / 410.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.01136/0.2508, allocations: 12.66 MB / 0.5384 GB, free: 8.066 MB / 426.7 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 0.02765/0.2784, allocations: 26.76 MB / 0.5645 GB, free: 13.18 MB / 458.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.03204/0.3104, allocations: 26.12 MB / 0.59 GB, free: 3.992 MB / 474.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.00545/0.3159, allocations: 4.72 MB / 0.5946 GB, free: 15.24 MB / 490.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.01916/0.3351, allocations: 16.89 MB / 0.6111 GB, free: 14.32 MB / 0.4948 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.771e-05/0.3351, allocations: 67.92 kB / 0.6112 GB, free: 14.25 MB / 0.4948 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.002384/0.3375, allocations: 1.257 MB / 0.6124 GB, free: 13.02 MB / 0.4948 GB
Notification: Performance of pre-optimization done (n=324): time 5.27e-06/0.3375, allocations: 2.656 kB / 0.6124 GB, free: 13.02 MB / 0.4948 GB
Notification: Performance of matching and sorting (n=376): time 0.2009/0.5384, allocations: 24.17 MB / 0.636 GB, free: 142.1 MB / 0.4948 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.614e-05/0.5384, allocations: 93.14 kB / 0.6361 GB, free: 142 MB / 0.4948 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.002309/0.5407, allocations: 2.836 MB / 0.6389 GB, free: 141 MB / 0.4948 GB
Notification: Performance of collectPreVariables (initialization): time 0.0004724/0.5412, allocations: 90.08 kB / 0.639 GB, free: 140.9 MB / 0.4948 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0006428/0.5419, allocations: 2.21 MB / 0.6411 GB, free: 139.5 MB / 0.4948 GB
Notification: Performance of collectInitialBindings (initialization): time 0.0007193/0.5426, allocations: 1.347 MB / 0.6424 GB, free: 138.6 MB / 0.4948 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0009118/0.5435, allocations: 0.9732 MB / 0.6434 GB, free: 138.2 MB / 0.4948 GB
Notification: Performance of setup shared object (initialization): time 2.669e-05/0.5435, allocations: 310.6 kB / 0.6437 GB, free: 137.9 MB / 0.4948 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.002577/0.5461, allocations: 2.961 MB / 0.6466 GB, free: 137 MB / 0.4948 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.002872/0.549, allocations: 4.486 MB / 0.651 GB, free: 134.1 MB / 0.4948 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005882/0.5548, allocations: 7.81 MB / 0.6586 GB, free: 129.9 MB / 0.4948 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.109e-05/0.5549, allocations: 18.97 kB / 0.6586 GB, free: 129.9 MB / 0.4948 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.03062/0.5855, allocations: 13.81 MB / 0.6721 GB, free: 126.4 MB / 0.4948 GB
Notification: Performance of prepare postOptimizeDAE: time 5.322e-05/0.5855, allocations: 26.59 kB / 0.6721 GB, free: 126.4 MB / 0.4948 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.16e-05/0.5856, allocations: 51.05 kB / 0.6722 GB, free: 126.4 MB / 0.4948 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.005021/0.5906, allocations: 3.468 MB / 0.6756 GB, free: 125.9 MB / 0.4948 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.003224/0.5939, allocations: 1.268 MB / 0.6768 GB, free: 125.8 MB / 0.4948 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01765/0.6115, allocations: 17.87 MB / 0.6943 GB, free: 114.4 MB / 0.4948 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.002966/0.6145, allocations: 256.1 kB / 0.6945 GB, free: 114.2 MB / 0.4948 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0003026/0.6148, allocations: 278.5 kB / 0.6948 GB, free: 114 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 0.002143/0.6169, allocations: 1.454 MB / 0.6962 GB, free: 112.6 MB / 0.4948 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0004198/0.6173, allocations: 345.8 kB / 0.6965 GB, free: 112.2 MB / 0.4948 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01745/0.6348, allocations: 9.608 MB / 0.7059 GB, free: 102.7 MB / 0.4948 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.619e-05/0.6348, allocations: 44.69 kB / 0.7059 GB, free: 102.7 MB / 0.4948 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.243e-05/0.6348, allocations: 7.984 kB / 0.7059 GB, free: 102.7 MB / 0.4948 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 2.833e-05/0.6348, allocations: 23.75 kB / 0.706 GB, free: 102.6 MB / 0.4948 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02167/0.6565, allocations: 14.34 MB / 0.72 GB, free: 88.39 MB / 0.4948 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 9.087e-06/0.6565, allocations: 4 kB / 0.72 GB, free: 88.39 MB / 0.4948 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001913/0.6584, allocations: 0.8515 MB / 0.7208 GB, free: 87.54 MB / 0.4948 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.00284/0.6613, allocations: 2.133 MB / 0.7229 GB, free: 85.43 MB / 0.4948 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.000248/0.6615, allocations: 135.9 kB / 0.723 GB, free: 85.3 MB / 0.4948 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.01178/0.6733, allocations: 12.1 MB / 0.7348 GB, free: 72.91 MB / 0.4948 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.567e-06/0.6733, allocations: 11.92 kB / 0.7348 GB, free: 72.9 MB / 0.4948 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01991/0.6932, allocations: 12.93 MB / 0.7475 GB, free: 59.91 MB / 0.4948 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.001827/0.695, allocations: 0.9016 MB / 0.7484 GB, free: 59.02 MB / 0.4948 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.00034/0.6954, allocations: 94.67 kB / 0.7484 GB, free: 58.93 MB / 0.4948 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001135/0.6965, allocations: 163.8 kB / 0.7486 GB, free: 58.77 MB / 0.4948 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0006182/0.6971, allocations: 470.3 kB / 0.749 GB, free: 58.3 MB / 0.4948 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001939/0.6973, allocations: 143.9 kB / 0.7492 GB, free: 58.16 MB / 0.4948 GB
Notification: Performance of sorting global known variables: time 0.001617/0.6989, allocations: 1.847 MB / 0.751 GB, free: 56.31 MB / 0.4948 GB
Notification: Performance of sort global known variables: time 2.71e-07/0.6989, allocations: 0 / 0.751 GB, free: 56.31 MB / 0.4948 GB
Notification: Performance of remove unused functions: time 0.004821/0.7038, allocations: 2.064 MB / 0.753 GB, free: 54.37 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 0.001671/0.7054, allocations: 1.37 MB / 0.7543 GB, free: 53.17 MB / 0.4948 GB
Notification: Performance of simCode: created initialization part: time 0.007133/0.7126, allocations: 7.076 MB / 0.7613 GB, free: 46.07 MB / 0.4948 GB
Notification: Performance of simCode: created event and clocks part: time 3.677e-06/0.7126, allocations: 448 / 0.7613 GB, free: 46.07 MB / 0.4948 GB
Notification: Performance of simCode: created simulation system equations: time 0.003596/0.7162, allocations: 3.76 MB / 0.7649 GB, free: 42.27 MB / 0.4948 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001759/0.7179, allocations: 0.7639 MB / 0.7657 GB, free: 41.56 MB / 0.4948 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.009355/0.7273, allocations: 10.76 MB / 0.7762 GB, free: 30.73 MB / 0.4948 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001212/0.7285, allocations: 2.692 MB / 0.7788 GB, free: 27.98 MB / 0.4948 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0009236/0.7294, allocations: 499 kB / 0.7793 GB, free: 27.5 MB / 0.4948 GB
Notification: Performance of SimCode: time 6.61e-07/0.7294, allocations: 0 / 0.7793 GB, free: 27.5 MB / 0.4948 GB
Notification: Performance of Templates: time 0.2513/0.9807, allocations: 149.1 MB / 0.9249 GB, free: 88.16 MB / 0.5105 GB
"
[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=480 -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 8.577608831226826]
Failed to read output from testmodel.py, exit status != 0:
0.9860768672078848 0.991898211 0.772959031
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7fc379892150>