Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_master_Chemical.Obsolete.Examples.AcidBase.Phosphate.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 0.001184/0.001184, allocations: 80.94 kB / 19.94 MB, free: 4.543 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 0.001383/0.001383, allocations: 177 kB / 23.36 MB, free: 1.129 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 0.8536/0.8536, allocations: 177.1 MB / 203.8 MB, free: 5.496 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 0.09927/0.09927, allocations: 17.47 MB / 277.7 MB, free: 11.45 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.AcidBase.Phosphate,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.AcidBase.Phosphate")
translateModel(Chemical.Obsolete.Examples.AcidBase.Phosphate,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.AcidBase.Phosphate") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.032e-06/1.032e-06, allocations: 0 / 300.7 MB, free: 1.773 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 9.638e-06/1.067e-05, allocations: 6.828 kB / 300.7 MB, free: 1.77 MB / 266.7 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.AcidBase.Phosphate): time 0.02787/0.02788, allocations: 38.2 MB / 338.9 MB, free: 14.2 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01989/0.04778, allocations: 28.64 MB / 367.6 MB, free: 1.445 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0005509/0.04833, allocations: 31.75 kB / 367.6 MB, free: 1.414 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0008626/0.04919, allocations: 0.5387 MB / 368.2 MB, free: 0.8711 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.003953/0.05314, allocations: 2.672 MB / 370.8 MB, free: 14.18 MB / 346.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005609/0.05875, allocations: 3.719 MB / 374.5 MB, free: 10.44 MB / 346.7 MB
Notification: Performance of NFFlatten.flatten: time 0.00178/0.06053, allocations: 2.804 MB / 377.4 MB, free: 7.621 MB / 346.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0009621/0.06149, allocations: 1.427 MB / 378.8 MB, free: 6.145 MB / 346.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.00123/0.06272, allocations: 1.958 MB / 380.7 MB, free: 4.184 MB / 346.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001131/0.06386, allocations: 1.368 MB / 382.1 MB, free: 2.812 MB / 346.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002259/0.06408, allocations: 252 kB / 382.4 MB, free: 2.566 MB / 346.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.003567/0.06765, allocations: 3.018 MB / 385.4 MB, free: 15.54 MB / 362.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.000354/0.068, allocations: 0.6309 MB / 386 MB, free: 14.91 MB / 362.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0005818/0.06858, allocations: 0.9044 MB / 386.9 MB, free: 14 MB / 362.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.004185/0.07277, allocations: 5.607 MB / 392.5 MB, free: 8.375 MB / 362.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.045e-06/0.07277, allocations: 0 / 392.5 MB, free: 8.375 MB / 362.7 MB
Notification: Performance of FrontEnd: time 8.02e-07/0.07277, allocations: 0 / 392.5 MB, free: 8.375 MB / 362.7 MB
Notification: Performance of Transformations before backend: time 1.328e-05/0.07279, allocations: 0 / 392.5 MB, free: 8.375 MB / 362.7 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 466
 * Number of variables: 466
Notification: Performance of Generate backend data structure: time 0.002697/0.07548, allocations: 2.882 MB / 395.4 MB, free: 5.453 MB / 362.7 MB
Notification: Performance of prepare preOptimizeDAE: time 2.862e-05/0.07551, allocations: 8.031 kB / 395.4 MB, free: 5.445 MB / 362.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001129/0.07664, allocations: 0.7164 MB / 396.1 MB, free: 4.727 MB / 362.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0009143/0.07755, allocations: 0.8165 MB / 396.9 MB, free: 3.883 MB / 362.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001445/0.0777, allocations: 353.8 kB / 397.3 MB, free: 3.488 MB / 362.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002017/0.0779, allocations: 188.3 kB / 397.5 MB, free: 3.305 MB / 362.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001509/0.07941, allocations: 1.787 MB / 399.3 MB, free: 1.477 MB / 362.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.544e-05/0.07944, allocations: 4.188 kB / 399.3 MB, free: 1.473 MB / 362.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001259/0.07956, allocations: 72.12 kB / 399.3 MB, free: 1.402 MB / 362.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.124e-05/0.07958, allocations: 52 kB / 399.4 MB, free: 1.352 MB / 362.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001515/0.0811, allocations: 1.542 MB / 400.9 MB, free: 15.8 MB / 378.7 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 0.005543/0.08664, allocations: 4.799 MB / 405.7 MB, free: 10.92 MB / 378.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.004821/0.09146, allocations: 5.082 MB / 410.8 MB, free: 5.805 MB / 378.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0005076/0.09197, allocations: 0.5306 MB / 411.3 MB, free: 5.27 MB / 378.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.005402/0.09737, allocations: 4.552 MB / 415.9 MB, free: 0.6953 MB / 378.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.877e-05/0.0974, allocations: 51.81 kB / 415.9 MB, free: 0.6328 MB / 378.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0005715/0.09797, allocations: 290.8 kB / 416.2 MB, free: 356 kB / 378.7 MB
Notification: Performance of pre-optimization done (n=158): time 2.635e-06/0.09797, allocations: 0 / 416.2 MB, free: 356 kB / 378.7 MB
Notification: Performance of matching and sorting (n=187): time 0.01099/0.109, allocations: 4.854 MB / 421.1 MB, free: 11.45 MB / 394.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.389e-05/0.109, allocations: 73.41 kB / 421.1 MB, free: 11.37 MB / 394.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004402/0.1094, allocations: 0.7854 MB / 421.9 MB, free: 10.57 MB / 394.7 MB
Notification: Performance of collectPreVariables (initialization): time 7.991e-05/0.1095, allocations: 57.7 kB / 422 MB, free: 10.5 MB / 394.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002593/0.1098, allocations: 0.7209 MB / 422.7 MB, free: 9.77 MB / 394.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003127/0.1101, allocations: 0.6661 MB / 423.4 MB, free: 9.098 MB / 394.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003431/0.1104, allocations: 407.7 kB / 423.8 MB, free: 8.691 MB / 394.7 MB
Notification: Performance of setup shared object (initialization): time 5.954e-05/0.1105, allocations: 305.1 kB / 424.1 MB, free: 8.391 MB / 394.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003596/0.1109, allocations: 307.3 kB / 424.4 MB, free: 8.086 MB / 394.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005974/0.1115, allocations: 0.8871 MB / 425.3 MB, free: 6.938 MB / 394.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001109/0.1126, allocations: 1.456 MB / 426.7 MB, free: 5.23 MB / 394.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.131e-06/0.1126, allocations: 8 kB / 426.7 MB, free: 5.223 MB / 394.7 MB
Notification: Performance of matching and sorting (n=277) (initialization): time 0.00406/0.1166, allocations: 1.865 MB / 428.6 MB, free: 3.34 MB / 394.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.918e-05/0.1166, allocations: 12.22 kB / 428.6 MB, free: 3.328 MB / 394.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.414e-05/0.1167, allocations: 20 kB / 428.6 MB, free: 3.309 MB / 394.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001798/0.1185, allocations: 0.6579 MB / 429.3 MB, free: 2.641 MB / 394.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0008803/0.1193, allocations: 0.507 MB / 429.8 MB, free: 2.133 MB / 394.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.00223/0.1216, allocations: 3.006 MB / 432.8 MB, free: 14.96 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0005341/0.1221, allocations: 75.98 kB / 432.9 MB, free: 14.88 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001113/0.1222, allocations: 95.95 kB / 433 MB, free: 14.79 MB / 410.7 MB
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 82
 * 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 (268):
 * Single equations (assignments): 265
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 1
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Equation system details (not torn):
 * Constant Jacobian (size): 0 systems
 * Linear Jacobian (size,density): 1 system
   {(4,100.0%)}
 * Non-linear Jacobian (size): 0 systems
 * Without analytic Jacobian (size): 0 systems
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 1 system
   {(1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of prepare postOptimizeDAE: time 0.0003159/0.1225, allocations: 252 kB / 433.2 MB, free: 14.53 MB / 410.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001792/0.1227, allocations: 147.9 kB / 433.3 MB, free: 14.39 MB / 410.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.00432/0.127, allocations: 1.901 MB / 435.2 MB, free: 12.46 MB / 410.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.029e-05/0.127, allocations: 23.94 kB / 435.3 MB, free: 12.44 MB / 410.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.939e-06/0.127, allocations: 4 kB / 435.3 MB, free: 12.43 MB / 410.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.361e-05/0.1271, allocations: 11.91 kB / 435.3 MB, free: 12.42 MB / 410.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.005173/0.1322, allocations: 2.603 MB / 437.9 MB, free: 9.785 MB / 410.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.809e-06/0.1322, allocations: 0 / 437.9 MB, free: 9.785 MB / 410.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0007096/0.1329, allocations: 363.5 kB / 438.2 MB, free: 9.43 MB / 410.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001761/0.1347, allocations: 0.6266 MB / 438.9 MB, free: 8.793 MB / 410.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 8.953e-05/0.1348, allocations: 63.94 kB / 438.9 MB, free: 8.73 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.00206/0.1369, allocations: 2.902 MB / 441.8 MB, free: 5.656 MB / 410.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.144e-06/0.1369, allocations: 3.938 kB / 441.8 MB, free: 5.652 MB / 410.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004379/0.1412, allocations: 2.148 MB / 444 MB, free: 3.477 MB / 410.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001145/0.1414, allocations: 123 kB / 444.1 MB, free: 3.355 MB / 410.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001294/0.1415, allocations: 36 kB / 444.1 MB, free: 3.32 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003778/0.1419, allocations: 36 kB / 444.2 MB, free: 3.285 MB / 410.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002417/0.1421, allocations: 193.6 kB / 444.4 MB, free: 3.098 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.18e-05/0.1422, allocations: 59.95 kB / 444.4 MB, free: 3.039 MB / 410.7 MB
Notification: Performance of sorting global known variables: time 0.0002459/0.1424, allocations: 360 kB / 444.8 MB, free: 2.676 MB / 410.7 MB
Notification: Performance of sort global known variables: time 8e-08/0.1424, allocations: 0 / 444.8 MB, free: 2.676 MB / 410.7 MB
Notification: Performance of remove unused functions: time 0.002004/0.1444, allocations: 1.2 MB / 446 MB, free: 1.473 MB / 410.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 8 (solution.temperature,H.logn,H3PO4.logn,H2PO4.logn,HPO4.logn,PO4.logn,H2O.logn,OH.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 (190):
 * Single equations (assignments): 187
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 1
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Equation system details (not torn):
 * Constant Jacobian (size): 0 systems
 * Linear Jacobian (size,density): 1 system
   {(4,100.0%)}
 * Non-linear Jacobian (size): 0 systems
 * Without analytic Jacobian (size): 0 systems
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 1 system
   {(1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of Backend phase and start with SimCode phase: time 0.1554/0.2998, allocations: 1.47 MB / 447.4 MB, free: 97.72 MB / 410.7 MB
Notification: Performance of simCode: created initialization part: time 0.002098/0.3019, allocations: 1.454 MB / 448.9 MB, free: 97.44 MB / 410.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.652e-05/0.3019, allocations: 17.06 kB / 448.9 MB, free: 97.44 MB / 410.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.000939/0.3029, allocations: 0.8889 MB / 449.8 MB, free: 97.2 MB / 410.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000922/0.3038, allocations: 352.9 kB / 450.1 MB, free: 97.19 MB / 410.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003642/0.3074, allocations: 2.954 MB / 453.1 MB, free: 95.98 MB / 410.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002432/0.3077, allocations: 322 kB / 453.4 MB, free: 95.89 MB / 410.7 MB
Notification: Performance of simCode: alias equations: time 0.0007947/0.3085, allocations: 372.3 kB / 453.8 MB, free: 95.88 MB / 410.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0007826/0.3092, allocations: 0.5086 MB / 454.3 MB, free: 95.82 MB / 410.7 MB
Notification: Performance of SimCode: time 7.42e-07/0.3092, allocations: 0 / 454.3 MB, free: 95.82 MB / 410.7 MB
Notification: Performance of Templates: time 0.03854/0.3478, allocations: 53.44 MB / 0.4958 GB, free: 61.88 MB / 410.7 MB
"
[Timeout remaining time 660]
make -j1 -f Chemical_master_Chemical.Obsolete.Examples.AcidBase.Phosphate.makefile [Timeout 660]
(rm -f Chemical_master_Chemical.Obsolete.Examples.AcidBase.Phosphate.pipe ; mkfifo Chemical_master_Chemical.Obsolete.Examples.AcidBase.Phosphate.pipe ; head -c 1048576 < Chemical_master_Chemical.Obsolete.Examples.AcidBase.Phosphate.pipe >> ../files/Chemical_master_Chemical.Obsolete.Examples.AcidBase.Phosphate.sim & ./Chemical_master_Chemical.Obsolete.Examples.AcidBase.Phosphate -abortSlowSimulation -alarm=240  -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.AcidBase.Phosphate.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 3.996209528762847]