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 0.0004098/0.0004098, 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 0.0002991/0.0002991, allocations: 0 / 0, free: 0 / 0
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[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 0.1756/0.1756, allocations: 0 / 0, free: 0 / 0
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[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 0.00683/0.00683, allocations: 0 / 0, free: 0 / 0
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[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 1.713e-06/1.713e-06, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 2.353e-05/2.525e-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 0.0323/0.03233, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.02342/0.05575, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.006653/0.0624, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.008429/0.07083, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.01234/0.08317, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.007533/0.0907, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.01155/0.1022, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.003438/0.1057, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.007044/0.1127, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.004192/0.1169, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 0.0008476/0.1178, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 0.004254/0.122, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 0.004222/0.1262, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.003316/0.1296, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.01621/0.1458, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 0.002356/0.1481, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 2.024e-06/0.1481, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 9.715e-05/0.1482, 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 0.01419/0.1624, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 0.0005513/0.163, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.004771/0.1677, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.00569/0.1734, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0007272/0.1742, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0008109/0.175, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02424/0.1992, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001212/0.1993, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0005938/0.1999, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.00157/0.2015, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.01294/0.2144, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.04318/0.2576, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.003138/0.2607, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 0.001316/0.2621, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 0.01534/0.2774, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.816e-05/0.2775, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=393): time 1.116e-05/0.2775, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=481): time 0.03755/0.315, 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 0.0008239/0.3158, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003467/0.3193, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 0.0006159/0.3199, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 0.00218/0.3221, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 0.0009835/0.3231, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 0.002239/0.3253, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 1.113e-05/0.3253, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 0.002076/0.3274, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.003025/0.3304, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.006772/0.3372, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.219e-05/0.3373, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=904) (initialization): time 0.01031/0.3476, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 6.919e-05/0.3477, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.541e-05/0.3478, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 0.003408/0.3512, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.006194/0.3574, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.016/0.3734, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00319/0.3766, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001428/0.378, 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 0.004273/0.3823, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001087/0.3833, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01322/0.3966, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.899e-05/0.3966, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.712e-05/0.3966, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.108e-05/0.3967, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02117/0.4178, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.128e-05/0.4178, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.003589/0.4214, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 0.004187/0.4256, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0002807/0.4259, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.01117/0.4371, 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 0.0005984/0.4377, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00804/0.4457, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 0.000676/0.4464, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001254/0.4476, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001218/0.4489, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0009537/0.4498, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002545/0.4501, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 0.001913/0.452, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 0.0002072/0.4522, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.005215/0.4574, 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 0.003362/0.4608, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.007164/0.4679, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 8.425e-06/0.4679, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.003459/0.4714, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004601/0.476, 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 900]
[Calling sys.exit(0), Time elapsed: 1.0722419675439596]