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 0.0002307/0.0002307, 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 0.0002225/0.0002225, 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 0.1105/0.1105, 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 0.04313/0.04313, 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 8.72e-07/8.72e-07, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 1.665e-05/1.752e-05, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instantiate(BioChem.Examples.centralMetabolism.extra_cellular): time 0.007391/0.007409, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.002457/0.009866, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003345/0.0102, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.0004347/0.01064, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.000731/0.01137, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.0006582/0.01202, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.0009726/0.013, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.0006695/0.01367, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.0009504/0.01462, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.0005553/0.01517, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 0.0001406/0.01531, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 0.0001261/0.01544, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 0.0003051/0.01574, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.0003996/0.01614, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.001086/0.01723, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 0.0001481/0.01738, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 9.62e-07/0.01738, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 8.807e-06/0.01739, 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 0.002045/0.01943, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 0.0001044/0.01954, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002462/0.01978, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0006212/0.02041, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001182/0.02052, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001462/0.02067, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001131/0.0218, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 3.866e-05/0.02184, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 9.232e-05/0.02193, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.055e-05/0.02196, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0005497/0.02251, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004102/0.02661, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.0007344/0.02735, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002268/0.02757, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 2.421e-05/0.0276, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.062e-05/0.02764, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=96): time 8.496e-06/0.02765, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=114): time 0.004976/0.03262, allocations: 0 / 0, free: 0 / 0
Notification: Performance of inlineWhenForInitialization (initialization): time 3.646e-05/0.03266, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002025/0.03286, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 8.119e-05/0.03294, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 0.000247/0.03319, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 0.0002659/0.03346, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002306/0.03369, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 3.878e-05/0.03373, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001925/0.03392, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002854/0.0342, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.0009152/0.03512, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.216e-05/0.03513, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=165) (initialization): time 0.001053/0.03618, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 2.53e-05/0.03621, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.426e-05/0.03622, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 0.0003653/0.03659, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007886/0.03738, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.001511/0.03889, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003783/0.03927, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.58e-05/0.03933, 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 0.0003391/0.03967, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000104/0.03978, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001666/0.03994, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.063e-05/0.03995, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.29e-06/0.03996, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.979e-06/0.03997, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.002119/0.04209, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 7.213e-06/0.0421, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0006528/0.04275, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 0.0003472/0.0431, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 6.679e-05/0.04316, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.001201/0.04436, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.715e-06/0.04437, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001141/0.04551, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 7.481e-05/0.04558, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.000171/0.04575, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003057/0.04606, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001694/0.04623, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.721e-05/0.04629, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 9.745e-05/0.04638, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 1.001e-05/0.04639, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.001175/0.04757, 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 0.0002971/0.04786, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.0009164/0.04878, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 2.154e-06/0.04878, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.0005496/0.04933, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006509/0.04998, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002494/0.05248, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002131/0.05269, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: alias equations: time 0.0002713/0.05296, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0004094/0.05337, allocations: 0 / 0, free: 0 / 0
Notification: Performance of SimCode: time 3.328e-05/0.0534, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Templates: time 0.002336/0.05574, allocations: 0 / 0, free: 0 / 0
"
[Timeout remaining time 900]
[Calling sys.exit(0), Time elapsed: 0.749847155995667]