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
[<interactive>:1:1-1:33:writable] Error: Class GC_set_max_heap_size not found in scope <global scope> (looking for a function or record).
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.0003005/0.0003005, 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 0.0003228/0.0003228, 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 0.2783/0.2783, 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 0.02107/0.02107, 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 5.21e-07/5.21e-07, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 1.512e-05/1.564e-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 0.1739/0.174, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.1139/0.2879, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.01433/0.3022, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.01612/0.3183, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.03047/0.3488, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.01988/0.3687, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.0283/0.397, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.01127/0.4082, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.02493/0.4332, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.01426/0.4474, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 0.003702/0.4511, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 0.01259/0.4637, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 0.005512/0.4692, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.01038/0.4796, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.04864/0.5282, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 0.005593/0.5338, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 2.725e-06/0.5338, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 0.0002839/0.5341, 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 0.05937/0.5935, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 0.001131/0.5946, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02544/0.6201, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.03279/0.6529, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002574/0.6554, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 0.005762/0.6612, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.08286/0.7441, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 0.000745/0.7448, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.003026/0.7478, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.00454/0.7524, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.09014/0.8425, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.2177/1.06, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.01927/1.079, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 0.01099/1.09, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 0.09442/1.185, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002334/1.185, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=393): time 5.351e-05/1.185, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=481): time 0.2105/1.396, 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 0.0028/1.398, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.02119/1.42, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 0.002579/1.422, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 0.009492/1.432, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 0.004108/1.436, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 0.008778/1.445, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 9.691e-05/1.445, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 0.01092/1.456, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.01447/1.47, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.03796/1.508, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002224/1.508, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=904) (initialization): time 0.05765/1.566, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 0.0002494/1.566, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002493/1.566, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 0.0129/1.579, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.02803/1.607, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.05727/1.665, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.01/1.675, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.003879/1.679, 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 (s5.substanceDefinitionVar.SelfClustering,s5.substanceDefinitionVar.data.phase,solvent.substanceDefinitionVar.SelfClustering,solvent.substanceDefinitionVar.data.phase,s4.substanceDefinitionVar.SelfClustering,s4.substanceDefinitionVar.data.phase,s3.substanceDefinitionVar.SelfClustering,s3.substanceDefinitionVar.data.phase,s1.substanceDefinitionVar.SelfClustering,s1.substanceDefinitionVar.data.phase,s2.substanceDefinitionVar.SelfClustering,s2.substanceDefinitionVar.data.phase)
 * 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 0.01212/1.691, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.006839/1.697, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.05989/1.757, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.889e-05/1.757, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.656e-05/1.758, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001083/1.758, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.1211/1.879, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 8.735e-05/1.879, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01784/1.897, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 0.01294/1.91, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001482/1.911, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.06239/1.974, 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 0.002332/1.976, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.04854/2.024, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 0.00521/2.03, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.004053/2.034, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.006044/2.04, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.004366/2.044, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.001296/2.045, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 0.01195/2.057, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 0.0002968/2.058, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.02518/2.083, 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 0.007037/2.09, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.03409/2.124, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 2.407e-05/2.124, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.01848/2.142, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02124/2.164, 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 898]
[Calling sys.exit(0), Time elapsed: 3.300951285753399]