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 0.001156/0.001156, allocations: 116.1 kB / 16.42 MB, free: 6.496 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001117/0.001117, allocations: 187.9 kB / 17.35 MB, free: 5.762 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.276/1.276, 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 0.06242/0.06242, allocations: 12.27 MB / 303.5 MB, free: 3.223 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.00125/0.00125, allocations: 65.12 kB / 420.7 MB, free: 17.01 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.0779/0.07916, allocations: 52.08 MB / 472.8 MB, free: 12.94 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.003869/0.08306, allocations: 2.815 MB / 475.6 MB, free: 10.11 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0002438/0.08332, allocations: 191.2 kB / 475.8 MB, free: 9.926 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 7.053e-05/0.0834, allocations: 8 kB / 475.8 MB, free: 9.918 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 6.7e-05/0.08347, allocations: 31.73 kB / 475.8 MB, free: 9.887 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001251/0.08361, allocations: 43.52 kB / 475.9 MB, free: 9.844 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001701/0.08378, allocations: 51.94 kB / 475.9 MB, free: 9.793 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0001784/0.08397, allocations: 183.2 kB / 476.1 MB, free: 9.613 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002136/0.08419, allocations: 99.59 kB / 476.2 MB, free: 9.512 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 7.915e-05/0.08428, allocations: 95.56 kB / 476.3 MB, free: 9.418 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000134/0.08442, allocations: 99.55 kB / 476.4 MB, free: 9.32 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 3.336e-05/0.08446, allocations: 20 kB / 476.4 MB, free: 9.301 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.184e-05/0.0845, allocations: 20 kB / 476.4 MB, free: 9.281 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 4.341e-05/0.08455, allocations: 47.84 kB / 476.5 MB, free: 9.234 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 8.852e-05/0.08464, allocations: 103.5 kB / 476.6 MB, free: 9.133 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002223/0.08487, allocations: 239.1 kB / 476.8 MB, free: 8.898 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.649e-06/0.08488, allocations: 0 / 476.8 MB, free: 8.898 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.273e-06/0.08489, allocations: 3.938 kB / 476.8 MB, free: 8.895 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 5.58e-06/0.0849, allocations: 0 / 476.8 MB, free: 8.895 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 0.0006647/0.08557, allocations: 0.4993 MB / 477.3 MB, free: 8.344 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.697e-05/0.08561, allocations: 8.031 kB / 477.3 MB, free: 8.336 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.823e-05/0.08567, allocations: 20.75 kB / 477.3 MB, free: 8.316 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000119/0.08579, allocations: 192 kB / 477.5 MB, free: 8.09 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.911e-05/0.08582, allocations: 16.88 kB / 477.6 MB, free: 8.074 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.672e-05/0.08587, allocations: 28.28 kB / 477.6 MB, free: 8.047 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003271/0.0862, allocations: 205.5 kB / 477.8 MB, free: 7.844 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.402e-05/0.08623, allocations: 4.125 kB / 477.8 MB, free: 7.84 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.61e-05/0.08626, allocations: 15.94 kB / 477.8 MB, free: 7.824 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.813e-06/0.08627, allocations: 4 kB / 477.8 MB, free: 7.82 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002417/0.08652, allocations: 138.2 kB / 477.9 MB, free: 7.684 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001262/0.08779, allocations: 0.7593 MB / 478.7 MB, free: 6.863 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001714/0.08797, allocations: 98.55 kB / 478.8 MB, free: 6.758 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002594/0.08824, allocations: 100.8 kB / 478.9 MB, free: 6.656 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.664e-05/0.08827, allocations: 8.219 kB / 478.9 MB, free: 6.648 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.037e-05/0.08829, allocations: 30.56 kB / 478.9 MB, free: 6.609 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=15): time 1.422e-06/0.0883, allocations: 0 / 478.9 MB, free: 6.609 MB / 350.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001229/0.08953, allocations: 0.5745 MB / 479.5 MB, free: 5.984 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.47e-05/0.08957, allocations: 59.41 kB / 479.6 MB, free: 5.914 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001159/0.08969, allocations: 146.4 kB / 479.7 MB, free: 5.754 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.968e-05/0.08972, allocations: 29.7 kB / 479.7 MB, free: 5.719 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 8.02e-05/0.08981, allocations: 159.9 kB / 479.9 MB, free: 5.559 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.297e-05/0.08986, allocations: 59.11 kB / 480 MB, free: 5.5 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.583e-05/0.08993, allocations: 49.61 kB / 480 MB, free: 5.445 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001055/0.09004, allocations: 326.8 kB / 480.3 MB, free: 5.117 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.304e-05/0.09013, allocations: 44.2 kB / 480.4 MB, free: 5.074 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000109/0.09024, allocations: 106.4 kB / 480.5 MB, free: 4.949 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001466/0.09171, allocations: 388.8 kB / 480.8 MB, free: 4.547 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.814e-06/0.09173, allocations: 0 / 480.8 MB, free: 4.547 MB / 350.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0003108/0.09204, allocations: 208.2 kB / 481 MB, free: 4.34 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.145e-05/0.09207, allocations: 11.94 kB / 481.1 MB, free: 4.328 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.114e-06/0.09208, allocations: 7.984 kB / 481.1 MB, free: 4.32 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.444e-05/0.0921, allocations: 7.938 kB / 481.1 MB, free: 4.312 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002217/0.09232, allocations: 47.97 kB / 481.1 MB, free: 4.266 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.807e-06/0.09234, allocations: 7.938 kB / 481.1 MB, free: 4.258 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.864e-05/0.09245, allocations: 8 kB / 481.1 MB, free: 4.25 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.913e-05/0.09247, allocations: 8 kB / 481.1 MB, free: 4.242 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 0.0001826/0.09266, allocations: 158 kB / 481.3 MB, free: 4.082 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.888e-05/0.0927, allocations: 11.81 kB / 481.3 MB, free: 4.07 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000289/0.093, allocations: 162.8 kB / 481.5 MB, free: 3.906 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.951e-06/0.09301, allocations: 3.938 kB / 481.5 MB, free: 3.902 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.182e-06/0.09302, allocations: 0 / 481.5 MB, free: 3.902 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 4.344e-05/0.09307, allocations: 88.92 kB / 481.6 MB, free: 3.797 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.484e-05/0.0931, allocations: 12 kB / 481.6 MB, free: 3.785 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001217/0.09323, allocations: 4 kB / 481.6 MB, free: 3.781 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.089e-05/0.09327, allocations: 11.92 kB / 481.6 MB, free: 3.77 MB / 350.1 MB
Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.0004586/0.09373, allocations: 256.6 kB / 481.8 MB, free: 3.512 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.0003956/0.09414, allocations: 384.5 kB / 482.2 MB, free: 3.121 MB / 350.1 MB
Notification: Performance of postOpt setEvaluationStage (simulation): time 9.265e-05/0.09424, allocations: 59.94 kB / 482.3 MB, free: 3.062 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 6.382e-05/0.09431, allocations: 111.2 kB / 482.4 MB, free: 2.953 MB / 350.1 MB
Notification: Performance of Backend: time 2.21e-07/0.09432, allocations: 0 / 482.4 MB, free: 2.953 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0004206/0.09474, allocations: 167.8 kB / 482.5 MB, free: 2.785 MB / 350.1 MB
Notification: Performance of SimCode: time 0.0008019/0.09555, allocations: 0.9248 MB / 483.5 MB, free: 1.812 MB / 350.1 MB
Notification: Performance of Templates: time 0.003803/0.09937, allocations: 1.535 MB / 485 MB, free: 288 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)