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 0.0002057/0.0002057, 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 0.0001994/0.0001994, 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 0.1183/0.1183, 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 0.006789/0.006789, 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 9.31e-07/9.31e-07, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 1.284e-05/1.377e-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 0.04687/0.04688, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.03958/0.08646, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.009931/0.09639, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.009962/0.1064, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.01694/0.1233, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.01068/0.134, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.01578/0.1498, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.004717/0.1545, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.0118/0.1663, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.00658/0.1729, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 0.001146/0.174, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 0.005568/0.1796, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 0.003094/0.1827, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.004219/0.1869, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.01501/0.2019, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 0.001522/0.2034, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 1.823e-06/0.2034, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 3.556e-05/0.2035, 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 0.01369/0.2171, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 0.0005398/0.2177, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006102/0.2238, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.007276/0.2311, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.001103/0.2322, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 0.00123/0.2334, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.01619/0.2496, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 0.0002419/0.2498, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0008239/0.2506, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.002001/0.2526, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.01587/0.2685, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.06254/0.3311, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.003985/0.335, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 0.001836/0.3369, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 0.02429/0.3612, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001073/0.3613, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=393): time 2.51e-05/0.3613, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=481): time 0.05794/0.4192, 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 0.0009804/0.4202, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004305/0.4245, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 0.0008041/0.4253, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 0.006564/0.4319, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 0.00163/0.4335, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 0.00295/0.4365, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 1.509e-05/0.4365, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 0.002987/0.4395, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004135/0.4436, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.01016/0.4538, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0001104/0.4539, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=904) (initialization): time 0.01608/0.47, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 0.0001308/0.4701, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0001406/0.4702, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 0.004845/0.4751, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0107/0.4858, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01456/0.5003, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004206/0.5046, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001573/0.5061, 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 0.004069/0.5102, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001312/0.5115, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01725/0.5288, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.25e-05/0.5288, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.764e-05/0.5288, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.536e-05/0.5288, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02644/0.5553, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.281e-05/0.5553, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.006071/0.5614, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 0.00475/0.5661, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0003129/0.5665, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.01469/0.5812, 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 0.0007402/0.5819, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01286/0.5948, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 0.0008475/0.5956, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0019/0.5975, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002251/0.5998, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001057/0.6008, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0004491/0.6013, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 0.002084/0.6033, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 0.0001898/0.6035, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.009507/0.613, 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 0.002943/0.616, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.01484/0.6308, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 5.22e-06/0.6308, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.007974/0.6388, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.005663/0.6445, 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: 1.2246096320450306]