Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_master_Chemical.Obsolete.Examples.SimpleReaction2.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 0.001046/0.001046, allocations: 93.06 kB / 19.65 MB, free: 272 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 0.001179/0.001179, allocations: 169 kB / 23.02 MB, free: 1.543 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 1.016/1.016, allocations: 177.1 MB / 203.4 MB, free: 5.629 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 0.1112/0.1112, allocations: 17.45 MB / 277.4 MB, free: 11.55 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.SimpleReaction2,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.SimpleReaction2")
translateModel(Chemical.Obsolete.Examples.SimpleReaction2,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.SimpleReaction2") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.825e-06/2.825e-06, allocations: 4 kB / 353.5 MB, free: 9.855 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.72e-05/2.003e-05, allocations: 8.781 kB / 353.5 MB, free: 9.848 MB / 282.7 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.SimpleReaction2): time 0.02773/0.02775, allocations: 28.83 MB / 382.4 MB, free: 13.14 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01082/0.03857, allocations: 11.76 MB / 394.1 MB, free: 1.34 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0006436/0.03921, allocations: 15.88 kB / 394.1 MB, free: 1.324 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.00061/0.03982, allocations: 242 kB / 394.4 MB, free: 1.086 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.002332/0.04215, allocations: 1.035 MB / 395.4 MB, free: 44 kB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.003164/0.04532, allocations: 1.58 MB / 397 MB, free: 14.45 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001239/0.04656, allocations: 1.294 MB / 398.3 MB, free: 13.15 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006595/0.04722, allocations: 0.5812 MB / 398.9 MB, free: 12.55 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0007204/0.04794, allocations: 0.8501 MB / 399.7 MB, free: 11.7 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000643/0.04858, allocations: 0.569 MB / 400.3 MB, free: 11.13 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001457/0.04873, allocations: 108 kB / 400.4 MB, free: 11.02 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.002476/0.0512, allocations: 1.228 MB / 401.6 MB, free: 9.793 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002066/0.05141, allocations: 275.1 kB / 401.9 MB, free: 9.523 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0006148/0.05202, allocations: 399.2 kB / 402.3 MB, free: 9.133 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.002972/0.05499, allocations: 2.354 MB / 404.6 MB, free: 6.77 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 4.319e-06/0.055, allocations: 0 / 404.6 MB, free: 6.77 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.102e-06/0.055, allocations: 0 / 404.6 MB, free: 6.77 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 1.871e-05/0.05502, allocations: 0 / 404.6 MB, free: 6.77 MB / 330.7 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 222
 * Number of variables: 222
Notification: Performance of Generate backend data structure: time 0.001917/0.05694, allocations: 1.553 MB / 406.2 MB, free: 5.176 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.847e-05/0.05697, allocations: 16.03 kB / 406.2 MB, free: 5.16 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0007117/0.05769, allocations: 347.1 kB / 406.5 MB, free: 4.82 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0006091/0.0583, allocations: 0.5291 MB / 407.1 MB, free: 4.262 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001047/0.0584, allocations: 122 kB / 407.2 MB, free: 4.129 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001065/0.05851, allocations: 96.31 kB / 407.3 MB, free: 4.035 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0009665/0.05947, allocations: 0.8466 MB / 408.1 MB, free: 3.164 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.776e-05/0.05949, allocations: 4.125 kB / 408.1 MB, free: 3.16 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.132e-05/0.05955, allocations: 40.12 kB / 408.2 MB, free: 3.121 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.08e-05/0.05957, allocations: 20 kB / 408.2 MB, free: 3.102 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001025/0.0606, allocations: 0.8469 MB / 409 MB, free: 2.254 MB / 330.7 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 0.1743/0.2349, allocations: 2.709 MB / 411.8 MB, free: 46.85 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.001565/0.2365, allocations: 1.314 MB / 413.1 MB, free: 46.8 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003399/0.2368, allocations: 268.3 kB / 413.3 MB, free: 46.78 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.002552/0.2394, allocations: 2.088 MB / 415.4 MB, free: 46.43 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.906e-05/0.2394, allocations: 44.58 kB / 415.5 MB, free: 46.39 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=56): time 1.843e-06/0.2394, allocations: 1.281 kB / 415.5 MB, free: 46.39 MB / 330.7 MB
Notification: Performance of matching and sorting (n=63): time 0.00178/0.2412, allocations: 1.324 MB / 416.8 MB, free: 46.1 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.243e-05/0.2412, allocations: 59.09 kB / 416.8 MB, free: 46.04 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003911/0.2416, allocations: 0.5382 MB / 417.4 MB, free: 45.84 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 2.406e-05/0.2416, allocations: 37.08 kB / 417.4 MB, free: 45.8 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001851/0.2418, allocations: 0.515 MB / 417.9 MB, free: 45.52 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001042/0.2419, allocations: 229.7 kB / 418.2 MB, free: 45.41 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001453/0.2421, allocations: 182.5 kB / 418.3 MB, free: 45.37 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 9.559e-05/0.2422, allocations: 0.5508 MB / 418.9 MB, free: 44.88 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001875/0.2423, allocations: 127.1 kB / 419 MB, free: 44.88 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003013/0.2426, allocations: 0.5865 MB / 419.6 MB, free: 44.29 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005566/0.2432, allocations: 0.7929 MB / 420.4 MB, free: 43.7 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.21e-06/0.2432, allocations: 3.125 kB / 420.4 MB, free: 43.7 MB / 330.7 MB
Notification: Performance of matching and sorting (n=115) (initialization): time 0.0008153/0.244, allocations: 0.744 MB / 421.1 MB, free: 43.62 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.95e-05/0.244, allocations: 9 kB / 421.1 MB, free: 43.62 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.257e-05/0.2441, allocations: 11.22 kB / 421.2 MB, free: 43.62 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.247e-05/0.2441, allocations: 18.52 kB / 421.2 MB, free: 43.62 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005316/0.2446, allocations: 260.1 kB / 421.4 MB, free: 43.62 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.875e-05/0.2446, allocations: 25.02 kB / 421.5 MB, free: 43.62 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002124/0.2448, allocations: 30.98 kB / 421.5 MB, free: 43.62 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.146e-05/0.2449, allocations: 48.83 kB / 421.5 MB, free: 43.62 MB / 330.7 MB
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 49
 * 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 (115):
 * Single equations (assignments): 115
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0001346/0.245, allocations: 224 kB / 421.8 MB, free: 43.46 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 7.992e-05/0.2451, allocations: 85 kB / 421.8 MB, free: 43.42 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0006801/0.2458, allocations: 0.5652 MB / 422.4 MB, free: 43.36 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.299e-06/0.2458, allocations: 6.344 kB / 422.4 MB, free: 43.36 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.397e-06/0.2458, allocations: 0 / 422.4 MB, free: 43.36 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.234e-06/0.2458, allocations: 3.562 kB / 422.4 MB, free: 43.36 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004935/0.2463, allocations: 0.572 MB / 423 MB, free: 43.14 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.886e-06/0.2463, allocations: 3.094 kB / 423 MB, free: 43.14 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0003642/0.2467, allocations: 168.6 kB / 423.2 MB, free: 43.14 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.157e-06/0.2467, allocations: 5.906 kB / 423.2 MB, free: 43.14 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.671e-05/0.2467, allocations: 26.33 kB / 423.2 MB, free: 43.14 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.845e-06/0.2467, allocations: 3.156 kB / 423.2 MB, free: 43.14 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.126e-06/0.2467, allocations: 4.688 kB / 423.2 MB, free: 43.14 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000659/0.2474, allocations: 0.7889 MB / 424 MB, free: 42.84 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001253/0.2475, allocations: 109.3 kB / 424.1 MB, free: 42.8 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.113e-05/0.2475, allocations: 13.91 kB / 424.1 MB, free: 42.8 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001263/0.2477, allocations: 12.72 kB / 424.1 MB, free: 42.8 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.072e-05/0.2477, allocations: 55.48 kB / 424.2 MB, free: 42.8 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.491e-05/0.2478, allocations: 28.06 kB / 424.2 MB, free: 42.8 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.000172/0.2479, allocations: 320.1 kB / 424.5 MB, free: 42.68 MB / 330.7 MB
Notification: Performance of sort global known variables: time 8e-08/0.2479, allocations: 0 / 424.5 MB, free: 42.68 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.0008749/0.2488, allocations: 487.1 kB / 425 MB, free: 42.68 MB / 330.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 5
 * Number of states: 4 (solution.temperature,A.logn,B.logn,C.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 (71):
 * Single equations (assignments): 71
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.0006696/0.2495, allocations: 0.6296 MB / 425.6 MB, free: 42.51 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.0004878/0.25, allocations: 481 kB / 426.1 MB, free: 42.48 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.325e-06/0.25, allocations: 0 / 426.1 MB, free: 42.48 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001846/0.2501, allocations: 226.8 kB / 426.3 MB, free: 42.46 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004694/0.2506, allocations: 172.8 kB / 426.5 MB, free: 42.46 MB / 330.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0018/0.2524, allocations: 1.392 MB / 427.9 MB, free: 41.73 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001016/0.2525, allocations: 164 kB / 428 MB, free: 41.65 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 0.0003259/0.2528, allocations: 163.4 kB / 428.2 MB, free: 41.64 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001275/0.253, allocations: 101.3 kB / 428.3 MB, free: 41.62 MB / 330.7 MB
Notification: Performance of SimCode: time 8.01e-07/0.253, allocations: 0 / 428.3 MB, free: 41.62 MB / 330.7 MB
Notification: Performance of Templates: time 0.01367/0.2666, allocations: 16.15 MB / 444.4 MB, free: 30.69 MB / 330.7 MB
"
[Timeout remaining time 660]
make -j1 -f Chemical_master_Chemical.Obsolete.Examples.SimpleReaction2.makefile [Timeout 660]
(rm -f Chemical_master_Chemical.Obsolete.Examples.SimpleReaction2.pipe ; mkfifo Chemical_master_Chemical.Obsolete.Examples.SimpleReaction2.pipe ; head -c 1048576 < Chemical_master_Chemical.Obsolete.Examples.SimpleReaction2.pipe >> ../files/Chemical_master_Chemical.Obsolete.Examples.SimpleReaction2.sim & ./Chemical_master_Chemical.Obsolete.Examples.SimpleReaction2 -abortSlowSimulation -alarm=240  -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.SimpleReaction2.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 3.678078204393387]