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 0.0008755/0.0008755, allocations: 91.61 kB / 15.06 MB, free: 1.098 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.000812/0.000812, allocations: 172.7 kB / 15.95 MB, free: 208 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.521/1.521, allocations: 223.3 MB / 240 MB, free: 5.426 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1866/0.1866, allocations: 12.25 MB / 303.3 MB, free: 2.102 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0003222/0.0003223, allocations: 8 kB / 366.9 MB, free: 9.824 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1064/0.1067, allocations: 53.09 MB / 420 MB, free: 4.625 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.003213/0.11, allocations: 2.41 MB / 422.4 MB, free: 2.203 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003347/0.1104, allocations: 195.2 kB / 422.6 MB, free: 2.012 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 9.594e-05/0.1105, allocations: 8 kB / 422.6 MB, free: 2.004 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 6.806e-05/0.1105, allocations: 23.86 kB / 422.6 MB, free: 1.98 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001666/0.1107, allocations: 31.7 kB / 422.7 MB, free: 1.949 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002352/0.111, allocations: 39.89 kB / 422.7 MB, free: 1.91 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002302/0.1112, allocations: 163.3 kB / 422.9 MB, free: 1.75 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002472/0.1115, allocations: 81.44 kB / 423 MB, free: 1.668 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001466/0.1116, allocations: 59.7 kB / 423 MB, free: 1.609 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001641/0.1118, allocations: 79.56 kB / 423.1 MB, free: 1.531 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 3.276e-05/0.1118, allocations: 8 kB / 423.1 MB, free: 1.523 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.182e-05/0.1119, allocations: 12 kB / 423.1 MB, free: 1.512 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 3.898e-05/0.1119, allocations: 31.84 kB / 423.1 MB, free: 1.48 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 6.678e-05/0.112, allocations: 61.58 kB / 423.2 MB, free: 1.414 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002028/0.1122, allocations: 175.8 kB / 423.4 MB, free: 1.242 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.991e-06/0.1122, allocations: 4 kB / 423.4 MB, free: 1.238 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.044e-06/0.1122, allocations: 0 / 423.4 MB, free: 1.238 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 8.977e-06/0.1122, allocations: 0 / 423.4 MB, free: 1.238 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 0.0008622/0.1131, allocations: 471.2 kB / 423.8 MB, free: 0.7305 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.612e-05/0.1132, allocations: 12.03 kB / 423.8 MB, free: 0.7188 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.678e-05/0.1132, allocations: 23.72 kB / 423.9 MB, free: 0.6953 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001609/0.1134, allocations: 190.7 kB / 424.1 MB, free: 480 kB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.669e-05/0.1134, allocations: 20.56 kB / 424.1 MB, free: 460 kB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.855e-05/0.1135, allocations: 24 kB / 424.1 MB, free: 436 kB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004113/0.1139, allocations: 200.8 kB / 424.3 MB, free: 228 kB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.817e-05/0.1139, allocations: 0 / 424.3 MB, free: 228 kB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.505e-05/0.114, allocations: 12 kB / 424.3 MB, free: 216 kB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.223e-05/0.114, allocations: 4 kB / 424.3 MB, free: 212 kB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002625/0.1143, allocations: 134.2 kB / 424.4 MB, free: 80 kB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.2453/0.3595, allocations: 0.7599 MB / 425.2 MB, free: 38.12 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.000215/0.3598, allocations: 103.4 kB / 425.3 MB, free: 38.1 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002428/0.36, allocations: 94.88 kB / 425.4 MB, free: 38.09 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.58e-05/0.3601, allocations: 3.844 kB / 425.4 MB, free: 38.09 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.445e-05/0.3601, allocations: 37.95 kB / 425.4 MB, free: 38.05 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=15): time 2.986e-06/0.3601, allocations: 1.031 kB / 425.4 MB, free: 38.05 MB / 350.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001346/0.3615, allocations: 0.5806 MB / 426 MB, free: 37.76 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.435e-05/0.3615, allocations: 53.97 kB / 426.1 MB, free: 37.7 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001618/0.3617, allocations: 148.5 kB / 426.2 MB, free: 37.59 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.549e-05/0.3617, allocations: 26.7 kB / 426.2 MB, free: 37.56 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 8.937e-05/0.3618, allocations: 158.8 kB / 426.4 MB, free: 37.44 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.272e-05/0.3619, allocations: 63.55 kB / 426.5 MB, free: 37.4 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 1.017e-05/0.3619, allocations: 4.312 kB / 426.5 MB, free: 37.4 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 8.126e-05/0.362, allocations: 323.5 kB / 426.8 MB, free: 37.09 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.252e-05/0.362, allocations: 45.59 kB / 426.8 MB, free: 37.09 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001234/0.3622, allocations: 97.14 kB / 426.9 MB, free: 37.03 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.000125/0.3623, allocations: 72.41 kB / 427 MB, free: 37.02 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.022e-06/0.3623, allocations: 0 / 427 MB, free: 37.02 MB / 350.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0003286/0.3626, allocations: 209.5 kB / 427.2 MB, free: 36.98 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.348e-05/0.3627, allocations: 7.391 kB / 427.2 MB, free: 36.98 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.906e-06/0.3627, allocations: 1.562 kB / 427.2 MB, free: 36.98 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.211e-05/0.3627, allocations: 7.609 kB / 427.2 MB, free: 36.98 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001961/0.3629, allocations: 48.95 kB / 427.3 MB, free: 36.98 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.907e-06/0.3629, allocations: 3.969 kB / 427.3 MB, free: 36.98 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.357e-05/0.363, allocations: 11.22 kB / 427.3 MB, free: 36.98 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.782e-05/0.3631, allocations: 9.172 kB / 427.3 MB, free: 36.98 MB / 350.1 MB
Warning: Assuming fixed start value for the following 5 variables:
         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
         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
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 (linear and non-linear blocks): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0002121/0.3633, allocations: 150 kB / 427.4 MB, free: 36.86 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.383e-05/0.3633, allocations: 14.94 kB / 427.4 MB, free: 36.86 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002858/0.3636, allocations: 172.2 kB / 427.6 MB, free: 36.82 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.457e-06/0.3636, allocations: 10.44 kB / 427.6 MB, free: 36.82 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.911e-06/0.3636, allocations: 0.5 kB / 427.6 MB, free: 36.82 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.599e-06/0.3636, allocations: 1.219 kB / 427.6 MB, free: 36.82 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005852/0.3642, allocations: 0.5148 MB / 428.1 MB, free: 36.52 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.495e-06/0.3643, allocations: 0.5625 kB / 428.1 MB, free: 36.52 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001708/0.3644, allocations: 33.31 kB / 428.2 MB, free: 36.52 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.887e-06/0.3644, allocations: 5.328 kB / 428.2 MB, free: 36.52 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.645e-05/0.3645, allocations: 5.781 kB / 428.2 MB, free: 36.52 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.986e-06/0.3645, allocations: 3.734 kB / 428.2 MB, free: 36.52 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.41e-07/0.3645, allocations: 0.75 kB / 428.2 MB, free: 36.52 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003636/0.3649, allocations: 305.3 kB / 428.5 MB, free: 36.38 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.374e-05/0.3649, allocations: 87.86 kB / 428.6 MB, free: 36.28 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.784e-05/0.3649, allocations: 13.86 kB / 428.6 MB, free: 36.27 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001004/0.365, allocations: 3.234 kB / 428.6 MB, free: 36.27 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.737e-05/0.3651, allocations: 13.95 kB / 428.6 MB, free: 36.27 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.416e-06/0.3651, allocations: 7.562 kB / 428.6 MB, free: 36.27 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 5.523e-05/0.3651, allocations: 113.6 kB / 428.7 MB, free: 36.2 MB / 350.1 MB
Notification: Performance of sort global known variables: time 2.5e-07/0.3651, allocations: 2.188 kB / 428.7 MB, free: 36.2 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0002666/0.3654, allocations: 36.88 kB / 428.8 MB, free: 36.2 MB / 350.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (V,endoplasmicReticulum.V,endoplasmicReticulum.CaER.n,Ca_Cyt.n,p3_sbml)
 * 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 (linear and non-linear blocks): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 8.851e-05/0.3655, allocations: 98.16 kB / 428.9 MB, free: 36.11 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.000245/0.3658, allocations: 137.1 kB / 429 MB, free: 36.1 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.104e-06/0.3658, allocations: 0 / 429 MB, free: 36.1 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 7.922e-05/0.3659, allocations: 69.12 kB / 429.1 MB, free: 36.09 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002832/0.3661, allocations: 13.06 kB / 429.1 MB, free: 36.09 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0008382/0.367, allocations: 0.636 MB / 429.7 MB, free: 35.76 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001834/0.3672, allocations: 0.7367 MB / 430.4 MB, free: 35.06 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 7.538e-05/0.3673, allocations: 19.38 kB / 430.5 MB, free: 35.06 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.116e-05/0.3673, allocations: 13.62 kB / 430.5 MB, free: 35.05 MB / 350.1 MB
Notification: Performance of SimCode: time 2.21e-07/0.3673, allocations: 6.719 kB / 430.5 MB, free: 35.05 MB / 350.1 MB
Notification: Performance of Templates: time 0.003605/0.3709, allocations: 1.257 MB / 431.7 MB, free: 34.99 MB / 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)