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 0.0002177/0.0002177, 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 0.0001821/0.0001821, 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 0.1437/0.1437, 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 0.005444/0.005444, 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 1.022e-06/1.022e-06, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 2.319e-05/2.422e-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 0.04958/0.04961, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.03799/0.0876, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.007566/0.09516, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.009619/0.1048, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.01608/0.1209, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.0112/0.1321, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.01769/0.1498, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.005961/0.1557, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.01529/0.171, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.01281/0.1838, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 0.004348/0.1882, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 0.01631/0.2045, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 0.01313/0.2176, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.01867/0.2363, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.01913/0.2554, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 0.001785/0.2572, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 1.953e-06/0.2572, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 4.443e-05/0.2572, 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 0.01472/0.272, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 0.0005838/0.2725, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006542/0.2791, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.009207/0.2883, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.001192/0.2895, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001294/0.2908, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.01791/0.3087, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 0.0002691/0.309, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0008996/0.3099, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.002421/0.3123, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02047/0.3328, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.1033/0.436, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.004483/0.4405, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 0.002/0.4425, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 0.02633/0.4688, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001121/0.4689, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=393): time 2.702e-05/0.469, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=481): time 0.05928/0.5283, 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 0.001064/0.5293, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004347/0.5337, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 0.001336/0.535, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 0.003365/0.5384, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 0.001956/0.5403, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 0.002907/0.5432, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 1.575e-05/0.5432, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 0.002853/0.5461, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.003755/0.5499, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.009696/0.5595, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0001134/0.5597, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=904) (initialization): time 0.01579/0.5755, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 0.0001382/0.5756, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0001215/0.5757, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 0.004462/0.5802, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01258/0.5928, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01488/0.6076, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00495/0.6126, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001906/0.6145, 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 0.004889/0.6194, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001354/0.6207, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01833/0.6391, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.544e-05/0.6391, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.909e-05/0.6391, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.745e-05/0.6392, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02839/0.6675, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.451e-05/0.6676, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.008268/0.6759, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 0.005135/0.681, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0003418/0.6813, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.01588/0.6972, 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 0.0008091/0.698, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0146/0.7126, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 0.001127/0.7137, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.002039/0.7158, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002313/0.7181, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001299/0.7194, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0005324/0.7199, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 0.002825/0.7228, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 0.0003553/0.7231, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.01071/0.7338, 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 0.003451/0.7373, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.009781/0.747, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 1.67e-05/0.7471, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.005577/0.7526, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.007279/0.7599, 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: 1.3850775980390608]