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 0.000923/0.000923, allocations: 80.94 kB / 19.94 MB, free: 4.547 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 0.0009677/0.0009677, allocations: 173 kB / 23.36 MB, free: 1.133 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 0.9492/0.9492, allocations: 177.2 MB / 203.8 MB, free: 5.457 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 0.08241/0.08241, allocations: 17.47 MB / 277.7 MB, free: 11.41 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 2.094e-06/2.094e-06, allocations: 0.6562 kB / 300.8 MB, free: 1.719 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.917e-05/2.126e-05, allocations: 2.859 kB / 300.8 MB, free: 1.715 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 0.03603/0.03605, allocations: 38.26 MB / 339 MB, free: 14.04 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.02534/0.0614, allocations: 28.63 MB / 367.7 MB, free: 1.301 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001531/0.06293, allocations: 35.69 kB / 367.7 MB, free: 1.266 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.001193/0.06412, allocations: 0.5425 MB / 368.3 MB, free: 0.7188 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.006149/0.07027, allocations: 2.61 MB / 370.9 MB, free: 14.09 MB / 346.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.009437/0.07971, allocations: 3.661 MB / 374.5 MB, free: 10.41 MB / 346.7 MB
Notification: Performance of NFFlatten.flatten: time 0.003326/0.08303, allocations: 2.804 MB / 377.3 MB, free: 7.59 MB / 346.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001609/0.08464, allocations: 1.431 MB / 378.8 MB, free: 6.109 MB / 346.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.00229/0.08693, allocations: 1.946 MB / 380.7 MB, free: 4.16 MB / 346.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001724/0.08865, allocations: 1.36 MB / 382.1 MB, free: 2.797 MB / 346.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0005324/0.08919, allocations: 252 kB / 382.3 MB, free: 2.551 MB / 346.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.006326/0.09551, allocations: 3.135 MB / 385.4 MB, free: 15.41 MB / 362.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0005158/0.09603, allocations: 0.6309 MB / 386.1 MB, free: 14.78 MB / 362.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0009656/0.09699, allocations: 0.9044 MB / 387 MB, free: 13.87 MB / 362.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.009767/0.1068, allocations: 5.603 MB / 392.6 MB, free: 8.246 MB / 362.7 MB
Notification: Performance of FrontEnd - DAE generated: time 4.298e-06/0.1068, allocations: 0 / 392.6 MB, free: 8.246 MB / 362.7 MB
Notification: Performance of FrontEnd: time 1.222e-06/0.1068, allocations: 0 / 392.6 MB, free: 8.246 MB / 362.7 MB
Notification: Performance of Transformations before backend: time 6.032e-05/0.1068, allocations: 0 / 392.6 MB, free: 8.246 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 0.004286/0.1111, allocations: 2.886 MB / 395.5 MB, free: 5.32 MB / 362.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.844e-05/0.1112, allocations: 8.031 kB / 395.5 MB, free: 5.312 MB / 362.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001499/0.1126, allocations: 0.7203 MB / 396.2 MB, free: 4.59 MB / 362.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.00112/0.1138, allocations: 0.8049 MB / 397 MB, free: 3.758 MB / 362.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001907/0.114, allocations: 361.8 kB / 397.4 MB, free: 3.355 MB / 362.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002273/0.1142, allocations: 188.3 kB / 397.5 MB, free: 3.172 MB / 362.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001777/0.116, allocations: 1.795 MB / 399.3 MB, free: 1.336 MB / 362.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.791e-05/0.116, allocations: 192 / 399.3 MB, free: 1.336 MB / 362.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001262/0.1161, allocations: 80.12 kB / 399.4 MB, free: 1.258 MB / 362.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.6e-05/0.1161, allocations: 44 kB / 399.5 MB, free: 1.215 MB / 362.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001689/0.1178, allocations: 1.542 MB / 401 MB, free: 15.66 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 0.006597/0.1244, allocations: 4.791 MB / 405.8 MB, free: 10.79 MB / 378.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.007537/0.132, allocations: 5.09 MB / 410.9 MB, free: 5.668 MB / 378.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0007761/0.1327, allocations: 0.5357 MB / 411.4 MB, free: 5.125 MB / 378.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.00817/0.1409, allocations: 4.544 MB / 416 MB, free: 0.5586 MB / 378.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.328e-05/0.141, allocations: 47.88 kB / 416 MB, free: 0.5 MB / 378.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0009979/0.142, allocations: 286.8 kB / 416.3 MB, free: 224 kB / 378.7 MB
Notification: Performance of pre-optimization done (n=158): time 5.25e-06/0.142, allocations: 0 / 416.3 MB, free: 224 kB / 378.7 MB
Notification: Performance of matching and sorting (n=187): time 0.01576/0.1577, allocations: 4.87 MB / 421.2 MB, free: 11.31 MB / 394.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.508e-05/0.1578, allocations: 73.41 kB / 421.2 MB, free: 11.23 MB / 394.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0006928/0.1585, allocations: 0.7854 MB / 422 MB, free: 10.42 MB / 394.7 MB
Notification: Performance of collectPreVariables (initialization): time 9.344e-05/0.1585, allocations: 57.7 kB / 422.1 MB, free: 10.36 MB / 394.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003692/0.1589, allocations: 0.7171 MB / 422.8 MB, free: 9.629 MB / 394.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0006435/0.1596, allocations: 0.6661 MB / 423.5 MB, free: 8.957 MB / 394.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0004798/0.16, allocations: 403.7 kB / 423.8 MB, free: 8.555 MB / 394.7 MB
Notification: Performance of setup shared object (initialization): time 7.229e-05/0.1601, allocations: 313.1 kB / 424.2 MB, free: 8.246 MB / 394.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000512/0.1606, allocations: 299.3 kB / 424.4 MB, free: 7.949 MB / 394.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0008005/0.1614, allocations: 0.891 MB / 425.3 MB, free: 6.797 MB / 394.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001574/0.163, allocations: 1.464 MB / 426.8 MB, free: 5.082 MB / 394.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.766e-06/0.163, allocations: 4 kB / 426.8 MB, free: 5.078 MB / 394.7 MB
Notification: Performance of matching and sorting (n=277) (initialization): time 0.005586/0.1686, allocations: 1.861 MB / 428.7 MB, free: 3.199 MB / 394.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.572e-05/0.1686, allocations: 14.34 kB / 428.7 MB, free: 3.188 MB / 394.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.176e-05/0.1686, allocations: 20 kB / 428.7 MB, free: 3.168 MB / 394.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002464/0.1711, allocations: 0.6505 MB / 429.3 MB, free: 2.508 MB / 394.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001408/0.1725, allocations: 0.5733 MB / 429.9 MB, free: 1.934 MB / 394.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.003156/0.1757, allocations: 3.026 MB / 432.9 MB, free: 14.74 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0008665/0.1765, allocations: 64 kB / 433 MB, free: 14.68 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001644/0.1767, allocations: 99.94 kB / 433.1 MB, free: 14.58 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 0.0004025/0.1771, allocations: 247.9 kB / 433.4 MB, free: 14.32 MB / 410.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002317/0.1773, allocations: 143.9 kB / 433.5 MB, free: 14.18 MB / 410.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.005729/0.1831, allocations: 1.912 MB / 435.4 MB, free: 12.25 MB / 410.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.351e-05/0.1831, allocations: 16 kB / 435.4 MB, free: 12.23 MB / 410.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.681e-06/0.1831, allocations: 4 kB / 435.4 MB, free: 12.23 MB / 410.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.662e-05/0.1831, allocations: 11.91 kB / 435.4 MB, free: 12.21 MB / 410.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.007049/0.1901, allocations: 2.603 MB / 438 MB, free: 9.578 MB / 410.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.581e-06/0.1902, allocations: 0 / 438 MB, free: 9.578 MB / 410.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00108/0.1912, allocations: 403.5 kB / 438.4 MB, free: 9.184 MB / 410.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.002371/0.1936, allocations: 0.6227 MB / 439.1 MB, free: 8.551 MB / 410.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001473/0.1938, allocations: 71.88 kB / 439.1 MB, free: 8.48 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002755/0.1965, allocations: 2.921 MB / 442 MB, free: 5.387 MB / 410.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.204e-06/0.1965, allocations: 3.938 kB / 442.1 MB, free: 5.383 MB / 410.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.006267/0.2028, allocations: 2.14 MB / 444.2 MB, free: 3.215 MB / 410.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001885/0.203, allocations: 123 kB / 444.3 MB, free: 3.094 MB / 410.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.000173/0.2031, allocations: 39.98 kB / 444.3 MB, free: 3.055 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005703/0.2037, allocations: 36 kB / 444.4 MB, free: 3.02 MB / 410.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.000657/0.2044, allocations: 193.6 kB / 444.6 MB, free: 2.832 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001381/0.2045, allocations: 59.95 kB / 444.6 MB, free: 2.773 MB / 410.7 MB
Notification: Performance of sorting global known variables: time 0.0003522/0.2049, allocations: 356 kB / 445 MB, free: 2.414 MB / 410.7 MB
Notification: Performance of sort global known variables: time 1.01e-07/0.2049, allocations: 3.938 kB / 445 MB, free: 2.41 MB / 410.7 MB
Notification: Performance of remove unused functions: time 0.002763/0.2076, allocations: 1.196 MB / 446.2 MB, free: 1.211 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 0.1166/0.3242, allocations: 1.466 MB / 447.6 MB, free: 97.81 MB / 410.7 MB
Notification: Performance of simCode: created initialization part: time 0.002338/0.3266, allocations: 1.458 MB / 449.1 MB, free: 97.53 MB / 410.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.997e-05/0.3266, allocations: 17.31 kB / 449.1 MB, free: 97.53 MB / 410.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.001107/0.3277, allocations: 0.8884 MB / 450 MB, free: 97.28 MB / 410.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0009754/0.3287, allocations: 351.4 kB / 450.4 MB, free: 97.27 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 0.004134/0.3328, allocations: 2.957 MB / 453.3 MB, free: 96.07 MB / 410.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002909/0.3331, allocations: 319 kB / 453.6 MB, free: 95.98 MB / 410.7 MB
Notification: Performance of simCode: alias equations: time 0.001326/0.3344, allocations: 371.8 kB / 454 MB, free: 95.96 MB / 410.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001099/0.3355, allocations: 0.5108 MB / 454.5 MB, free: 95.91 MB / 410.7 MB
Notification: Performance of SimCode: time 1.333e-06/0.3355, allocations: 0 / 454.5 MB, free: 95.91 MB / 410.7 MB
Notification: Performance of Templates: time 0.05677/0.3923, allocations: 53.44 MB / 0.496 GB, free: 61.65 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 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.AcidBase.Phosphate.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.112577124033123]