Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.CaOscillations.Cytosol.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 0.0003351/0.0003351, 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 0.0002286/0.0002286, 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 0.1253/0.1253, 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 0.01119/0.01119, 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.CaOscillations.Cytosol,startTime=0,stopTime=120,tolerance=1e-06,numberOfIntervals=2400,outputFormat="empty",variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol",simflags="-abortSlowSimulation -alarm=240   -lv LOG_STATS")
simulate(BioChem.Examples.CaOscillations.Cytosol,startTime=0,stopTime=120,tolerance=1e-06,numberOfIntervals=2400,outputFormat="empty",variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol",simflags="-abortSlowSimulation -alarm=240   -lv LOG_STATS") [Timeout 900]
"Notification: Performance of FrontEnd - loaded program: time 9.71e-07/9.71e-07, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 1.096e-05/1.193e-05, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.002971/0.002983, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.0003514/0.003335, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 6.552e-05/0.0034, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 7.118e-05/0.003471, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.0001413/0.003613, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.0001306/0.003743, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.0001501/0.003893, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.0001416/0.004035, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.0001426/0.004178, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.0001046/0.004282, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 2.332e-05/0.004306, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 2.035e-05/0.004326, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 4.948e-05/0.004375, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 6.253e-05/0.004438, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.0002993/0.004737, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 2.314e-05/0.00476, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 1.443e-06/0.004762, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 5.781e-06/0.004768, 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: 60
 * Number of variables: 60
Notification: Performance of Generate backend data structure: time 0.000383/0.005151, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 5.082e-05/0.005201, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.752e-05/0.005259, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001143/0.005373, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.894e-05/0.005402, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 4.066e-05/0.005443, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002465/0.005689, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 1.318e-05/0.005702, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.035e-05/0.005733, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.883e-06/0.00574, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 9.91e-05/0.005839, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007541/0.006593, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.0001079/0.006701, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001282/0.006829, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 9.869e-06/0.006839, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.337e-05/0.006852, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=15): time 2.996e-06/0.006855, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=17): time 0.0007993/0.007654, allocations: 0 / 0, free: 0 / 0
Notification: Performance of inlineWhenForInitialization (initialization): time 1.858e-05/0.007673, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 4.666e-05/0.00772, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 1.89e-05/0.007739, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 5.144e-05/0.00779, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 4.514e-05/0.007835, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 5.027e-05/0.007885, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 1.413e-05/0.0079, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 2.659e-05/0.007926, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 4.529e-05/0.007971, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001387/0.00811, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.006e-06/0.008113, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0001609/0.008274, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 1.402e-05/0.008288, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.13e-06/0.008293, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 1.083e-05/0.008304, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001445/0.008449, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.194e-05/0.00846, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.006e-05/0.008531, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.597e-05/0.008546, allocations: 0 / 0, free: 0 / 0
Warning: Assuming fixed start value for the following 5 variables:
         endoplasmicReticulum.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         endoplasmicReticulum.CaER.c:VARIABLE(min = 0.0 start = 0.0 unit = \"mol/l\" fixed = true stateSelect=StateSelect.prefer )  \"Current concentration of substance (mM)\" type: Real
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         p3_sbml:VARIABLE(start = 0.95 fixed = true )  type: Real
         Ca_Cyt.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: 8
 * 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 (28):
 * Single equations (assignments): 28
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0001023/0.008649, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.499e-05/0.008684, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001531/0.008837, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.976e-06/0.00884, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.2e-06/0.008845, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.379e-06/0.008849, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006637/0.009513, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.445e-06/0.009515, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001081/0.009624, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 3.807e-06/0.009627, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.75e-05/0.009645, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.679e-06/0.00965, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.384e-06/0.009652, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0001865/0.009838, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 2.047e-05/0.009859, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.18e-05/0.009911, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001181/0.01003, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.302e-05/0.01006, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.099e-05/0.01007, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 1.995e-05/0.01009, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 2.174e-06/0.01009, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.0004764/0.01057, allocations: 0 / 0, free: 0 / 0
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 3
 * Number of states: 5 (V,Ca_Cyt.n,p3_sbml,endoplasmicReticulum.V,endoplasmicReticulum.CaER.c)
 * 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 (18):
 * Single equations (assignments): 18
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.0001037/0.01068, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.0001423/0.01082, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 1.783e-06/0.01082, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 5.01e-05/0.01087, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005566/0.01143, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.000537/0.01196, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.031e-05/0.01201, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: alias equations: time 4.817e-05/0.01206, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: all other stuff during SimCode phase: time 8.737e-05/0.01215, allocations: 0 / 0, free: 0 / 0
Notification: Performance of SimCode: time 1.671e-05/0.01217, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Templates: time 0.0005279/0.01269, allocations: 0 / 0, free: 0 / 0
"
[Timeout remaining time 900]
[Calling sys.exit(0), Time elapsed: 0.6839707647450268]