Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001358/0.001358, allocations: 117.8 kB / 17.13 MB, free: 5.758 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001472/0.001472, allocations: 194.1 kB / 20.08 MB, free: 2.848 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.393/1.393, allocations: 225.6 MB / 248.5 MB, free: 3.625 MB / 190.1 MB
"
[Timeout remaining time 178]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08183/0.08183, allocations: 15.54 MB / 318.9 MB, free: 13.66 MB / 254.1 MB
"
[Timeout remaining time 180]
Using package Chemical with version 1.4.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: translateModel(Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC")
translateModel(Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 0.001885/0.001885, allocations: 63.64 kB / 446.1 MB, free: 47.97 MB / 366.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.08911/0.09099, allocations: 56.55 MB / 0.4909 GB, free: 20.68 MB / 366.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:4740:7-4740:66: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 1.4.1-master/package.mo:4740:7-4740:66: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.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC): time 0.033/0.124, allocations: 30.22 MB / 0.5204 GB, free: 9.379 MB / 382.1 MB
Notification: Performance of NFInst.instExpressions: time 0.03182/0.1558, allocations: 26.16 MB / 0.5459 GB, free: 15.12 MB / 414.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001559/0.1574, allocations: 35.69 kB / 0.546 GB, free: 15.09 MB / 414.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001564/0.1589, allocations: 0.5971 MB / 0.5466 GB, free: 14.48 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.005809/0.1647, allocations: 2.153 MB / 0.5487 GB, free: 12.32 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.008966/0.1737, allocations: 3.542 MB / 0.5521 GB, free: 8.754 MB / 414.1 MB
Notification: Performance of NFFlatten.flatten: time 0.008554/0.1823, allocations: 7.398 MB / 0.5593 GB, free: 1.328 MB / 414.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006324/0.1886, allocations: 5.12 MB / 0.5643 GB, free: 12.13 MB / 430.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.006838/0.1954, allocations: 4.904 MB / 0.5691 GB, free: 7.219 MB / 430.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.008091/0.2035, allocations: 4.76 MB / 0.5738 GB, free: 2.445 MB / 430.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.002179/0.2057, allocations: 0.6719 MB / 0.5744 GB, free: 1.773 MB / 430.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01027/0.216, allocations: 3.367 MB / 0.5777 GB, free: 14.4 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.002936/0.2189, allocations: 1.804 MB / 0.5795 GB, free: 12.59 MB / 446.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.005741/0.2246, allocations: 3.354 MB / 0.5828 GB, free: 9.227 MB / 446.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0187/0.2433, allocations: 11.19 MB / 0.5937 GB, free: 14 MB / 462.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.129e-06/0.2434, allocations: 3.938 kB / 0.5937 GB, free: 13.99 MB / 462.1 MB
Notification: Performance of FrontEnd: time 1.262e-06/0.2434, allocations: 0 / 0.5937 GB, free: 13.99 MB / 462.1 MB
Notification: Performance of Transformations before backend: time 0.0002194/0.2436, allocations: 4 kB / 0.5937 GB, free: 13.99 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 0.01866/0.2622, allocations: 7.316 MB / 0.6008 GB, free: 6.582 MB / 462.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.776e-05/0.2623, allocations: 8.031 kB / 0.6009 GB, free: 6.574 MB / 462.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006379/0.2687, allocations: 1.241 MB / 0.6021 GB, free: 5.328 MB / 462.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.006937/0.2756, allocations: 3.256 MB / 0.6052 GB, free: 1.996 MB / 462.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0006499/0.2762, allocations: 0.6727 MB / 0.6059 GB, free: 1.254 MB / 462.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001884/0.2781, allocations: 0.4963 MB / 0.6064 GB, free: 0.7578 MB / 462.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.2455/0.5236, allocations: 9.446 MB / 0.6156 GB, free: 90.18 MB / 462.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0002627/0.5239, allocations: 3.219 kB / 0.6156 GB, free: 90.18 MB / 462.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.001931/0.5258, allocations: 192.2 kB / 0.6158 GB, free: 90.04 MB / 462.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001375/0.526, allocations: 118.4 kB / 0.6159 GB, free: 90.04 MB / 462.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02444/0.5504, allocations: 12.74 MB / 0.6284 GB, free: 84.97 MB / 462.1 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 0.05778/0.6082, allocations: 30.56 MB / 0.6582 GB, free: 56.84 MB / 462.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.05241/0.6606, allocations: 40.96 MB / 0.6982 GB, free: 13.36 MB / 462.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.007792/0.6684, allocations: 4.729 MB / 0.7028 GB, free: 8.609 MB / 462.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.04189/0.7103, allocations: 21.19 MB / 0.7235 GB, free: 2.758 MB / 478.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.645e-05/0.7103, allocations: 69.11 kB / 0.7236 GB, free: 2.68 MB / 478.1 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.005643/0.716, allocations: 1.278 MB / 0.7248 GB, free: 1.543 MB / 478.1 MB
Notification: Performance of pre-optimization done (n=324): time 1.739e-05/0.716, allocations: 0 / 0.7248 GB, free: 1.543 MB / 478.1 MB
Notification: Performance of matching and sorting (n=376): time 0.1078/0.8238, allocations: 24.42 MB / 0.7487 GB, free: 9.309 MB / 0.4981 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 8.69e-05/0.8239, allocations: 90.36 kB / 0.7488 GB, free: 9.207 MB / 0.4981 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.005047/0.8289, allocations: 2.963 MB / 0.7517 GB, free: 6.262 MB / 0.4981 GB
Notification: Performance of collectPreVariables (initialization): time 0.001055/0.83, allocations: 85.7 kB / 0.7517 GB, free: 6.172 MB / 0.4981 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001873/0.8318, allocations: 2.231 MB / 0.7539 GB, free: 4.141 MB / 0.4981 GB
Notification: Performance of collectInitialBindings (initialization): time 0.002308/0.8341, allocations: 1.361 MB / 0.7552 GB, free: 2.797 MB / 0.4981 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.00321/0.8373, allocations: 0.9807 MB / 0.7562 GB, free: 1.805 MB / 0.4981 GB
Notification: Performance of setup shared object (initialization): time 0.0001326/0.8375, allocations: 305.1 kB / 0.7565 GB, free: 1.504 MB / 0.4981 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.00567/0.8432, allocations: 2.962 MB / 0.7594 GB, free: 14.54 MB / 0.5138 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.007078/0.8502, allocations: 4.482 MB / 0.7638 GB, free: 9.406 MB / 0.5138 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01383/0.8641, allocations: 7.8 MB / 0.7714 GB, free: 1.02 MB / 0.5138 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.821e-05/0.8641, allocations: 16 kB / 0.7714 GB, free: 1.004 MB / 0.5138 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.06431/0.9284, allocations: 13.81 MB / 0.7849 GB, free: 3.332 MB / 0.5294 GB
Notification: Performance of prepare postOptimizeDAE: time 8.272e-05/0.9285, allocations: 24 kB / 0.7849 GB, free: 3.309 MB / 0.5294 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.685e-05/0.9286, allocations: 48 kB / 0.785 GB, free: 3.262 MB / 0.5294 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01104/0.9396, allocations: 3.486 MB / 0.7884 GB, free: 15.9 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.006064/0.9457, allocations: 1.265 MB / 0.7896 GB, free: 14.64 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.03614/0.9819, allocations: 18.44 MB / 0.8076 GB, free: 11.82 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004965/0.9868, allocations: 243.8 kB / 0.8078 GB, free: 11.58 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0009915/0.9878, allocations: 286.5 kB / 0.8081 GB, free: 11.3 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 0.003144/0.991, allocations: 1.441 MB / 0.8095 GB, free: 9.852 MB / 0.5606 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001036/0.992, allocations: 369.5 kB / 0.8099 GB, free: 9.488 MB / 0.5606 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.3113/1.303, allocations: 9.625 MB / 0.8193 GB, free: 187.6 MB / 0.5606 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.736e-05/1.303, allocations: 41.81 kB / 0.8193 GB, free: 187.6 MB / 0.5606 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.071e-05/1.303, allocations: 5.25 kB / 0.8193 GB, free: 187.6 MB / 0.5606 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001323/1.303, allocations: 20 kB / 0.8193 GB, free: 187.6 MB / 0.5606 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.05208/1.356, allocations: 15.42 MB / 0.8344 GB, free: 184 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.46e-05/1.356, allocations: 7.875 kB / 0.8344 GB, free: 184 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004796/1.36, allocations: 0.8508 MB / 0.8352 GB, free: 183.9 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.006041/1.366, allocations: 2.124 MB / 0.8373 GB, free: 183.6 MB / 0.5606 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0009907/1.367, allocations: 133.9 kB / 0.8374 GB, free: 183.6 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02144/1.389, allocations: 12.64 MB / 0.8498 GB, free: 177 MB / 0.5606 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.579e-06/1.389, allocations: 3.344 kB / 0.8498 GB, free: 177 MB / 0.5606 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03953/1.428, allocations: 12.96 MB / 0.8624 GB, free: 170.4 MB / 0.5606 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.002456/1.431, allocations: 0.9546 MB / 0.8634 GB, free: 170 MB / 0.5606 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0007889/1.432, allocations: 95.75 kB / 0.8634 GB, free: 169.9 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002729/1.434, allocations: 165.4 kB / 0.8636 GB, free: 169.8 MB / 0.5606 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001022/1.435, allocations: 457.5 kB / 0.864 GB, free: 169.6 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003015/1.436, allocations: 147.3 kB / 0.8642 GB, free: 169.5 MB / 0.5606 GB
Notification: Performance of sorting global known variables: time 0.002243/1.438, allocations: 1.988 MB / 0.8661 GB, free: 168.5 MB / 0.5606 GB
Notification: Performance of sort global known variables: time 1.1e-07/1.438, allocations: 0 / 0.8661 GB, free: 168.5 MB / 0.5606 GB
Notification: Performance of remove unused functions: time 0.007403/1.445, allocations: 2.058 MB / 0.8681 GB, free: 166.7 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 0.002695/1.448, allocations: 1.322 MB / 0.8694 GB, free: 165.7 MB / 0.5606 GB
Notification: Performance of simCode: created initialization part: time 0.01302/1.461, allocations: 7.058 MB / 0.8763 GB, free: 158.7 MB / 0.5606 GB
Notification: Performance of simCode: created event and clocks part: time 6.823e-06/1.461, allocations: 2.812 kB / 0.8763 GB, free: 158.7 MB / 0.5606 GB
Notification: Performance of simCode: created simulation system equations: time 0.007156/1.468, allocations: 3.779 MB / 0.88 GB, free: 154.9 MB / 0.5606 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003817/1.472, allocations: 0.7724 MB / 0.8808 GB, free: 154.2 MB / 0.5606 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01752/1.49, allocations: 10.9 MB / 0.8914 GB, free: 143.3 MB / 0.5606 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002078/1.492, allocations: 3.208 MB / 0.8945 GB, free: 140.1 MB / 0.5606 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.002057/1.494, allocations: 0.49 MB / 0.895 GB, free: 139.6 MB / 0.5606 GB
Notification: Performance of SimCode: time 1.323e-06/1.494, allocations: 0 / 0.895 GB, free: 139.6 MB / 0.5606 GB
Notification: Performance of Templates: time 0.374/1.868, allocations: 146.7 MB / 1.038 GB, free: 174.8 MB / 0.5606 GB
"
[Timeout remaining time 658]
make -j1 -f Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.makefile [Timeout 660]
(rm -f Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.sim & ./Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 14.092061608098447]
Failed to read output from testmodel.py, exit status != 0:
2.04196907998994 1.885582687 1.639752387
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7f43b3fd6050>