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 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo", uses=false)
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001309/0.001309, allocations: 110.4 kB / 16.42 MB, free: 6.508 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001375/0.001375, allocations: 185.5 kB / 17.35 MB, free: 5.738 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.307/1.307, allocations: 222.9 MB / 241 MB, free: 15.16 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06164/0.06164, allocations: 12.26 MB / 303.5 MB, free: 3.242 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001188/0.001188, allocations: 64.8 kB / 420.7 MB, free: 17.15 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.08119/0.08239, allocations: 52.08 MB / 472.8 MB, free: 13.07 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.00392/0.08634, allocations: 2.827 MB / 475.6 MB, free: 10.23 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0002481/0.08661, allocations: 183.2 kB / 475.8 MB, free: 10.05 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 7.071e-05/0.08669, allocations: 8 kB / 475.8 MB, free: 10.05 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 6.85e-05/0.08677, allocations: 35.69 kB / 475.8 MB, free: 10.01 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001327/0.0869, allocations: 43.56 kB / 475.9 MB, free: 9.969 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001748/0.08709, allocations: 51.88 kB / 475.9 MB, free: 9.918 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.000183/0.08729, allocations: 187.2 kB / 476.1 MB, free: 9.734 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002009/0.0875, allocations: 107.6 kB / 476.2 MB, free: 9.625 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 7.557e-05/0.08758, allocations: 79.66 kB / 476.3 MB, free: 9.547 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001351/0.08772, allocations: 99.53 kB / 476.4 MB, free: 9.449 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 3.477e-05/0.08776, allocations: 24 kB / 476.4 MB, free: 9.426 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.319e-05/0.0878, allocations: 20 kB / 476.4 MB, free: 9.406 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 4.31e-05/0.08785, allocations: 47.84 kB / 476.5 MB, free: 9.359 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 9.235e-05/0.08795, allocations: 103.4 kB / 476.6 MB, free: 9.258 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002168/0.08817, allocations: 231.2 kB / 476.8 MB, free: 9.031 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.589e-06/0.08818, allocations: 0 / 476.8 MB, free: 9.031 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.062e-06/0.08819, allocations: 11.94 kB / 476.8 MB, free: 9.02 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 8.466e-06/0.0882, allocations: 0 / 476.8 MB, free: 9.02 MB / 350.1 MB
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 0.0006535/0.08886, allocations: 0.4993 MB / 477.3 MB, free: 8.469 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.539e-05/0.0889, allocations: 8.031 kB / 477.3 MB, free: 8.461 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.223e-05/0.08896, allocations: 24.69 kB / 477.4 MB, free: 8.438 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001186/0.08909, allocations: 196 kB / 477.5 MB, free: 8.207 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.897e-05/0.08911, allocations: 20.94 kB / 477.6 MB, free: 8.188 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.564e-05/0.08916, allocations: 28.28 kB / 477.6 MB, free: 8.16 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003451/0.08951, allocations: 197.5 kB / 477.8 MB, free: 7.965 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.215e-05/0.08953, allocations: 192 / 477.8 MB, free: 7.965 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.647e-05/0.08957, allocations: 15.94 kB / 477.8 MB, free: 7.949 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.892e-06/0.08958, allocations: 4 kB / 477.8 MB, free: 7.945 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002459/0.08983, allocations: 134.2 kB / 477.9 MB, free: 7.812 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001267/0.0911, allocations: 0.7632 MB / 478.7 MB, free: 6.988 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001751/0.09129, allocations: 110.5 kB / 478.8 MB, free: 6.871 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002535/0.09155, allocations: 96.8 kB / 478.9 MB, free: 6.773 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.839e-05/0.09158, allocations: 4.281 kB / 478.9 MB, free: 6.77 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.647e-05/0.09161, allocations: 30.56 kB / 478.9 MB, free: 6.73 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=15): time 1.422e-06/0.09162, allocations: 0 / 478.9 MB, free: 6.73 MB / 350.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001202/0.09282, allocations: 0.5805 MB / 479.5 MB, free: 6.102 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.127e-05/0.09288, allocations: 55.41 kB / 479.6 MB, free: 6.035 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001138/0.093, allocations: 142.4 kB / 479.7 MB, free: 5.879 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.911e-05/0.09302, allocations: 29.7 kB / 479.7 MB, free: 5.844 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 8.505e-05/0.09312, allocations: 159.9 kB / 479.9 MB, free: 5.684 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.62e-05/0.09317, allocations: 67.09 kB / 480 MB, free: 5.617 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.208e-05/0.09324, allocations: 45.61 kB / 480 MB, free: 5.566 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001028/0.09335, allocations: 326.8 kB / 480.3 MB, free: 5.238 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.388e-05/0.09344, allocations: 40.22 kB / 480.4 MB, free: 5.199 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000123/0.09357, allocations: 110.4 kB / 480.5 MB, free: 5.07 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001399/0.09498, allocations: 385.2 kB / 480.8 MB, free: 4.672 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.583e-06/0.09499, allocations: 0 / 480.8 MB, free: 4.672 MB / 350.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0003152/0.09532, allocations: 212 kB / 481.1 MB, free: 4.461 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.359e-05/0.09534, allocations: 7.938 kB / 481.1 MB, free: 4.453 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.913e-06/0.09536, allocations: 4 kB / 481.1 MB, free: 4.449 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.466e-05/0.09537, allocations: 3.938 kB / 481.1 MB, free: 4.445 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002153/0.0956, allocations: 56.11 kB / 481.1 MB, free: 4.391 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.217e-05/0.09562, allocations: 4 kB / 481.1 MB, free: 4.387 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.73e-05/0.09572, allocations: 15.98 kB / 481.1 MB, free: 4.371 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.43e-05/0.09574, allocations: 4 kB / 481.1 MB, free: 4.367 MB / 350.1 MB
Warning: Assuming fixed start value for the following 5 variables:
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         endoplasmicReticulum.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
         endoplasmicReticulum.CaER.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: 7
 * 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 0.0001915/0.09594, allocations: 155.3 kB / 481.3 MB, free: 4.207 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 5.095e-05/0.096, allocations: 11.81 kB / 481.3 MB, free: 4.195 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002934/0.09629, allocations: 164.7 kB / 481.5 MB, free: 4.031 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.511e-06/0.09631, allocations: 7.875 kB / 481.5 MB, free: 4.023 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.183e-06/0.09632, allocations: 0 / 481.5 MB, free: 4.023 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.787e-05/0.09638, allocations: 96.91 kB / 481.6 MB, free: 3.91 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.678e-05/0.09641, allocations: 0 / 481.6 MB, free: 3.91 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001142/0.09653, allocations: 8 kB / 481.6 MB, free: 3.902 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.607e-05/0.09656, allocations: 7.984 kB / 481.6 MB, free: 3.895 MB / 350.1 MB
Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.0004545/0.09702, allocations: 252.7 kB / 481.8 MB, free: 3.641 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.0004138/0.09745, allocations: 380.2 kB / 482.2 MB, free: 3.254 MB / 350.1 MB
Notification: Performance of postOpt setEvaluationStage (simulation): time 9.32e-05/0.09755, allocations: 62.28 kB / 482.3 MB, free: 3.195 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 6.877e-05/0.09763, allocations: 115.2 kB / 482.4 MB, free: 3.082 MB / 350.1 MB
Notification: Performance of Backend: time 4.8e-07/0.09764, allocations: 4 kB / 482.4 MB, free: 3.078 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0004478/0.09809, allocations: 170.3 kB / 482.6 MB, free: 2.906 MB / 350.1 MB
Notification: Performance of SimCode: time 0.0008673/0.09896, allocations: 0.9247 MB / 483.5 MB, free: 1.934 MB / 350.1 MB
Notification: Performance of Templates: time 0.004071/0.103, allocations: 1.533 MB / 485 MB, free: 412 kB / 350.1 MB
make -j1 -f BioChem_BioChem.Examples.CaOscillations.Cytosol.makefile
(rm -f BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe ; mkfifo BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe ; head -c 1048576 < BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe >> ../files/BioChem_BioChem.Examples.CaOscillations.Cytosol.sim & ./BioChem_BioChem.Examples.CaOscillations.Cytosol  -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe 2>&1)