Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.centralMetabolism.extra_cellular.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 0.0002933/0.0002933, 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 0.0002169/0.0002169, 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 0.1615/0.1615, allocations: 0 / 0, free: 0 / 0
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo): time 0.01941/0.01941, allocations: 0 / 0, free: 0 / 0
"
[Timeout remaining time 180]
Using package BioChem with version 1.1.3 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/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(BioChem.Examples.centralMetabolism.extra_cellular,startTime=0,stopTime=0.5,tolerance=1e-05,numberOfIntervals=2500,outputFormat="empty",variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.centralMetabolism.extra_cellular",simflags="-abortSlowSimulation -alarm=240   -lv LOG_STATS")
simulate(BioChem.Examples.centralMetabolism.extra_cellular,startTime=0,stopTime=0.5,tolerance=1e-05,numberOfIntervals=2500,outputFormat="empty",variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.centralMetabolism.extra_cellular",simflags="-abortSlowSimulation -alarm=240   -lv LOG_STATS") [Timeout 900]
"Notification: Performance of FrontEnd - loaded program: time 7.42e-07/7.42e-07, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 2.265e-05/2.339e-05, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instantiate(BioChem.Examples.centralMetabolism.extra_cellular): time 0.005026/0.005049, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.001657/0.006707, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002131/0.00692, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.0002976/0.007217, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.0004526/0.00767, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.0004273/0.008097, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.0006009/0.008698, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.0004311/0.009129, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.0006756/0.009805, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.0003658/0.01017, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 0.0001022/0.01027, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 8.061e-05/0.01035, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 0.0002036/0.01056, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.0002848/0.01084, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.000761/0.0116, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 9.518e-05/0.0117, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 1.423e-06/0.0117, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 1.557e-05/0.01171, 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: 353
 * Number of variables: 353
Notification: Performance of Generate backend data structure: time 0.001308/0.01302, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 6.662e-05/0.01309, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001648/0.01325, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003542/0.01361, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 7.239e-05/0.01368, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 9.915e-05/0.01378, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0009058/0.01469, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 3.305e-05/0.01472, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 8.68e-05/0.01481, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.913e-05/0.01482, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0004943/0.01532, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003204/0.01852, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.0006168/0.01914, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002016/0.01934, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 2.297e-05/0.01936, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.766e-05/0.01939, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=96): time 5.721e-06/0.0194, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=114): time 0.004163/0.02356, allocations: 0 / 0, free: 0 / 0
Notification: Performance of inlineWhenForInitialization (initialization): time 3.492e-05/0.0236, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001762/0.02377, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 7.833e-05/0.02385, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 0.000152/0.024, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 0.0001763/0.02418, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002009/0.02438, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 4.265e-05/0.02442, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001814/0.0246, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002686/0.02487, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.0007921/0.02566, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.456e-06/0.02567, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=165) (initialization): time 0.0008948/0.02657, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 2.55e-05/0.02659, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.203e-05/0.0266, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 0.0002918/0.0269, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005767/0.02747, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.001319/0.02879, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002761/0.02907, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.321e-05/0.02912, allocations: 0 / 0, free: 0 / 0
Warning: Assuming fixed start value for the following 15 variables:
         V:VARIABLE(start = 2.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         cytosol.V:VARIABLE(start = 2.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         cytosol.GLY.c:VARIABLE(min = 0.0 start = 1.0 unit = \"mol/l\" fixed = true stateSelect=StateSelect.prefer )  \"Current concentration of substance (mM)\" type: Real
         cytosol.mitochondria.V:VARIABLE(start = 2.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         LACext.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytosol.mitochondria.NADm.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytosol.mitochondria.NADHm.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytosol.CP.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytosol.LAC.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytosol.AMP.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytosol.IMP.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytosol.ADP.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytosol.PYR.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytosol.FDP.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         cytosol.NADH.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 35
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (157):
 * Single equations (assignments): 155
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 2 systems
   {(1,4,100.0%), (1,4,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 0 systems
Notification: Performance of prepare postOptimizeDAE: time 0.0003325/0.02945, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.611e-05/0.02954, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001403/0.02968, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.832e-06/0.02969, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.221e-06/0.02969, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.714e-06/0.0297, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001709/0.03141, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.269e-06/0.03142, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000504/0.03192, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 0.0002457/0.03217, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 5.709e-05/0.03222, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.00121/0.03343, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.224e-06/0.03344, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00101/0.03445, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 5.443e-05/0.0345, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001238/0.03462, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.00022/0.03484, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001903/0.03503, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.345e-05/0.03508, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 9.091e-05/0.03517, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 6.943e-06/0.03518, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.0006763/0.03585, allocations: 0 / 0, free: 0 / 0
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 2
 * Number of states: 17 (V,cytosol.V,cytosol.NADH.n,cytosol.FDP.n,cytosol.PYR.n,cytosol.ADP.n,cytosol.IMP.n,cytosol.AMP.n,cytosol.LAC.n,cytosol.CP.n,cytosol.GLY.c,cytosol.G6P.c,cytosol.mitochondria.V,cytosol.mitochondria.NADHm.n,cytosol.mitochondria.NADm.n,cytosol.DHAP.c,LACext.n)
 * 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 (106):
 * Single equations (assignments): 104
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 2 systems
   {(1,4,100.0%), (1,4,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 0 systems
Notification: Performance of Backend phase and start with SimCode phase: time 0.0002766/0.03613, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.0008849/0.03701, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 2.515e-06/0.03702, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.0004982/0.03751, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005616/0.03808, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002022/0.0401, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001504/0.04025, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: alias equations: time 0.000288/0.04054, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003249/0.04086, allocations: 0 / 0, free: 0 / 0
Notification: Performance of SimCode: time 2.572e-05/0.04089, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Templates: time 0.002554/0.04344, allocations: 0 / 0, free: 0 / 0
"
[Timeout remaining time 900]
[Calling sys.exit(0), Time elapsed: 0.7489723768085241]