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 0.0002287/0.0002287, 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 0.0002009/0.0002009, 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 0.1401/0.1401, 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 0.01268/0.01268, 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 6.71e-07/6.71e-07, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 8.146e-06/8.817e-06, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instantiate(BioChem.Examples.centralMetabolism.extra_cellular): time 0.009945/0.009954, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.003401/0.01335, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.0004288/0.01378, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.0006001/0.01438, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.001205/0.01559, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.001038/0.01663, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.001223/0.01785, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.0008579/0.01871, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.001206/0.01991, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.0005739/0.02049, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 0.000198/0.02069, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 0.0001298/0.02082, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 0.0003179/0.02113, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.0004308/0.02156, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.001513/0.02308, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 0.0001665/0.02324, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 1.223e-06/0.02325, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 8.426e-06/0.02325, 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 0.002259/0.02551, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 9.516e-05/0.02561, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0003479/0.02596, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0006927/0.02665, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001548/0.0268, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000239/0.02704, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002111/0.02915, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 7.924e-05/0.02923, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001784/0.02941, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.596e-05/0.02945, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009299/0.03038, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.005651/0.03603, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.0009896/0.03702, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003137/0.03733, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 3.625e-05/0.03737, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.964e-05/0.03743, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=96): time 1.548e-05/0.03744, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=114): time 0.00673/0.04417, allocations: 0 / 0, free: 0 / 0
Notification: Performance of inlineWhenForInitialization (initialization): time 5.459e-05/0.04423, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002717/0.0445, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 0.0001232/0.04462, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 0.0002739/0.0449, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 0.0003177/0.04521, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003408/0.04555, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 6.656e-05/0.04562, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000274/0.04589, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004234/0.04632, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.001365/0.04768, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.406e-05/0.04771, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=165) (initialization): time 0.001786/0.04949, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 4.225e-05/0.04953, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.355e-05/0.04956, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 0.0004236/0.04998, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001004/0.05099, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002132/0.05312, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0005228/0.05364, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.000109/0.05375, 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 0.0004603/0.05421, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001535/0.05436, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002215/0.05459, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.23e-05/0.0546, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.973e-06/0.0546, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.807e-05/0.05462, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.00305/0.05767, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.276e-05/0.05769, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0008076/0.05849, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 0.0004113/0.0589, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001059/0.05901, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.001825/0.06083, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.455e-06/0.06084, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001743/0.06258, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 8.31e-05/0.06266, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0002182/0.06288, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003896/0.06327, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0003099/0.06358, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.597e-05/0.06367, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 0.0001433/0.06381, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 1.357e-05/0.06382, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.001375/0.0652, 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 0.0003533/0.06555, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.001378/0.06693, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 2.325e-06/0.06693, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.0006944/0.06763, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0009444/0.06857, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003102/0.07167, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002178/0.07189, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: alias equations: time 0.0003433/0.07223, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0005242/0.07276, allocations: 0 / 0, free: 0 / 0
Notification: Performance of SimCode: time 4.097e-05/0.0728, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Templates: time 0.002497/0.0753, allocations: 0 / 0, free: 0 / 0
"
[Timeout remaining time 900]
[Calling sys.exit(0), Time elapsed: 0.7965623922646046]