Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_master_Chemical.Examples.Diffusion.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"[<interactive>:1:22-1:33:writable] Warning: Modelica only supports 32-bit signed integers! Transforming: 13743895347 into a real
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.0002338/0.0002338, allocations: 0 / 0, free: 0 / 0
"
[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 0.0001744/0.0001744, allocations: 0 / 0, free: 0 / 0
"
[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 0.1002/0.1002, allocations: 0 / 0, free: 0 / 0
"
[Timeout remaining time 180]
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 0.005946/0.005946, allocations: 0 / 0, free: 0 / 0
"
[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: simulate(Chemical.Examples.Diffusion,startTime=0,stopTime=1,tolerance=1e-06,numberOfIntervals=2500,outputFormat="empty",variableFilter="",fileNamePrefix="Chemical_master_Chemical.Examples.Diffusion",simflags="-abortSlowSimulation -alarm=240   -lv LOG_STATS")
simulate(Chemical.Examples.Diffusion,startTime=0,stopTime=1,tolerance=1e-06,numberOfIntervals=2500,outputFormat="empty",variableFilter="",fileNamePrefix="Chemical_master_Chemical.Examples.Diffusion",simflags="-abortSlowSimulation -alarm=240   -lv LOG_STATS") [Timeout 900]
"Notification: Performance of FrontEnd - loaded program: time 3.206e-06/3.206e-06, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 2.992e-05/3.312e-05, allocations: 0 / 0, free: 0 / 0
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/Boundaries.mo:1361:7-1361:76:writable] Warning: An inner declaration for outer component dropOfCommons could not be found and was automatically generated.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/Boundaries.mo:1361:7-1361:76:writable] Notification: The diagnostics message for the missing inner is: 
Your model is using an outer \"dropOfCommons\" component but
an inner \"dropOfCommons\" component is not defined.
Use Chemical.DropOfCommons in your model
to specify system properties.
Notification: Performance of NFInst.instantiate(Chemical.Examples.Diffusion): time 0.04731/0.04734, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.03268/0.08002, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.006359/0.08638, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.007788/0.09417, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.01197/0.1061, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.01341/0.1195, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.02771/0.1473, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.004021/0.1513, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.009096/0.1604, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.006354/0.1667, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 0.001042/0.1678, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 0.005531/0.1733, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 0.003065/0.1764, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.003875/0.1802, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.01537/0.1956, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 0.001431/0.197, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 4.008e-06/0.197, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 3.14e-05/0.1971, allocations: 0 / 0, free: 0 / 0
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 3621
 * Number of variables: 3621
Notification: Performance of Generate backend data structure: time 0.01302/0.2101, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 0.0005108/0.2106, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.005756/0.2164, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.007001/0.2234, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.001085/0.2244, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001185/0.2256, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.01503/0.2407, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 0.0002285/0.2409, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0007704/0.2417, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.00189/0.2436, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.01455/0.2581, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0583/0.3164, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.003809/0.3202, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 0.001762/0.322, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 0.02349/0.3455, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 9.18e-05/0.3456, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=393): time 2.367e-05/0.3456, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=481): time 0.0533/0.3989, allocations: 0 / 0, free: 0 / 0
Error: Internal error IndexReduction.pantelidesIndexReduction failed! System is structurally singular and cannot be handled because the number of unassigned equations is larger than the number of states. Use -d=bltdump to get more information.
Error: Internal error Transformation Module PFPlusExt index Reduction Method Pantelides failed!
Error: Internal error IndexReduction.pantelidesIndexReduction failed! System is structurally singular and cannot be handled because the number of unassigned equations is larger than the number of states. Use -d=bltdump to get more information.
Error: Internal error Transformation Module PFPlusExt index Reduction Method Pantelides failed!
Error: Internal error IndexReduction.pantelidesIndexReduction failed! System is structurally singular and cannot be handled because the number of unassigned equations is larger than the number of states. Use -d=bltdump to get more information.
Error: Internal error Transformation Module PFPlusExt index Reduction Method Pantelides failed!
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0008646/0.3997, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003942/0.4037, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 0.0007566/0.4044, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 0.003215/0.4077, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 0.001526/0.4092, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 0.002858/0.412, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 1.235e-05/0.4121, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 0.002711/0.4148, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.00352/0.4183, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.00915/0.4274, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 9.468e-05/0.4275, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=904) (initialization): time 0.01591/0.4434, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 0.0001244/0.4436, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0001412/0.4437, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 0.004667/0.4484, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01031/0.4587, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01515/0.4738, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.01103/0.4849, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.005041/0.4899, allocations: 0 / 0, free: 0 / 0
Warning: Assuming fixed start value for the following 5 variables:
         d5.rear.n_flow:VARIABLE(flow=true unit = \"mol/s\" fixed = true )  \"Molar change of the substance\" type: Real
         d4.rear.n_flow:VARIABLE(flow=true unit = \"mol/s\" fixed = true )  \"Molar change of the substance\" type: Real
         d3.rear.n_flow:VARIABLE(flow=true unit = \"mol/s\" fixed = true )  \"Molar change of the substance\" type: Real
         d1.rear.n_flow:VARIABLE(flow=true unit = \"mol/s\" fixed = true )  \"Molar change of the substance\" type: Real
         d2.rear.n_flow:VARIABLE(flow=true unit = \"mol/s\" fixed = true )  \"Molar change of the substance\" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 420
 * Number of states: 0 ()
 * Number of discrete variables: 12 (s2.substanceDefinitionVar.data.phase,s2.substanceDefinitionVar.SelfClustering,s1.substanceDefinitionVar.data.phase,s1.substanceDefinitionVar.SelfClustering,s3.substanceDefinitionVar.data.phase,s3.substanceDefinitionVar.SelfClustering,s4.substanceDefinitionVar.data.phase,s4.substanceDefinitionVar.SelfClustering,solvent.substanceDefinitionVar.data.phase,solvent.substanceDefinitionVar.SelfClustering,s5.substanceDefinitionVar.data.phase,s5.substanceDefinitionVar.SelfClustering)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (848):
 * Single equations (assignments): 828
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 20
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 14 systems
   {(2,2,100.0%), (1,4,100.0%), (1,1,100.0%), (1,4,100.0%), (1,1,100.0%), (2,1,100.0%), (2,2,100.0%), (1,4,100.0%), (1,1,100.0%), (1,4,100.0%), (1,1,100.0%), (1,1,100.0%), (1,4,100.0%), (1,1,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 6 systems
   {(1,6), (2,2), (1,2), (2,1), (1,6), (2,2)}
Notification: Performance of prepare postOptimizeDAE: time 0.0083/0.4982, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.004675/0.5029, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.02934/0.5322, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.423e-05/0.5323, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.142e-05/0.5323, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.739e-05/0.5323, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.03024/0.5626, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.477e-05/0.5626, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.006228/0.5688, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 0.005071/0.5739, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0004149/0.5743, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.01473/0.5891, allocations: 0 / 0, free: 0 / 0
Error: Internal error IndexReduction.pantelidesIndexReduction failed! System is structurally singular and cannot be handled because the number of unassigned equations is larger than the number of states. Use -d=bltdump to get more information.
Error: Internal error Transformation Module PFPlusExt index Reduction Method Pantelides failed!
Error: Internal error IndexReduction.pantelidesIndexReduction failed! System is structurally singular and cannot be handled because the number of unassigned equations is larger than the number of states. Use -d=bltdump to get more information.
Error: Internal error Transformation Module PFPlusExt index Reduction Method Pantelides failed!
Error: Internal error IndexReduction.pantelidesIndexReduction failed! System is structurally singular and cannot be handled because the number of unassigned equations is larger than the number of states. Use -d=bltdump to get more information.
Error: Internal error Transformation Module PFPlusExt index Reduction Method Pantelides failed!
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 0.0007094/0.5898, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01287/0.6026, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 0.0009113/0.6036, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001858/0.6054, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002119/0.6075, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.00108/0.6086, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0004224/0.609, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 0.002425/0.6115, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 0.0002419/0.6117, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.009021/0.6207, allocations: 0 / 0, free: 0 / 0
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 52
 * Number of states: 19 (s2.logm,p2.logm,d2.rear.n_flow,s1.logm,p1.logm,d1.rear.n_flow,$STATESET3.x,s3.logm,p3.logm,d3.rear.n_flow,$STATESET2.x,s4.logm,p4.logm,d4.rear.n_flow,solvent.logm,$STATESET1.x,s5.logm,p5.logm,d5.rear.n_flow)
 * 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 (429):
 * Single equations (assignments): 409
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 20
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 14 systems
   {(1,4,100.0%), (1,1,100.0%), (1,1,100.0%), (1,4,100.0%), (1,1,100.0%), (1,1,100.0%), (2,2,100.0%), (1,4,100.0%), (1,4,100.0%), (1,1,100.0%), (1,1,100.0%), (2,1,100.0%), (2,2,100.0%), (1,4,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 6 systems
   {(1,5), (3,4), (1,2), (3,3), (1,5), (3,4)}
Notification: Performance of Backend phase and start with SimCode phase: time 0.00259/0.6233, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.008582/0.6319, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 6.001e-06/0.6319, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.005083/0.637, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.00616/0.6431, allocations: 0 / 0, free: 0 / 0
[SimCode/SimCodeUtil.mo:0:0-0:0:writable] Error: Internal error function createStateSetsSets failed.
[SimCode/SimCodeUtil.mo:0:0-0:0:writable] Error: Internal error function createSimCode failed [Transformation from optimised DAE to simulation code structure failed]
"
[Timeout remaining time 899]
[Calling sys.exit(0), Time elapsed: 1.2429320779629052]