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]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.0007977/0.0007977, allocations: 80.94 kB / 19.94 MB, free: 4.547 MB / 18.57 MB
"
[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 0.0009623/0.0009623, allocations: 173 kB / 23.36 MB, free: 1.133 MB / 18.57 MB
"
[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 1.071/1.071, allocations: 177.1 MB / 203.8 MB, free: 5.48 MB / 186.7 MB
"
[Timeout remaining time 179]
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 0.04184/0.04184, allocations: 9.555 MB / 269.8 MB, free: 3.816 MB / 250.7 MB
"
[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: translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2400,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2400,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.064e-06/2.064e-06, allocations: 0.6562 kB / 290.1 MB, free: 18.43 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.921e-05/2.127e-05, allocations: 3.406 kB / 290.1 MB, free: 18.43 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.003611/0.003632, allocations: 2.47 MB / 292.6 MB, free: 17.78 MB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0005635/0.004196, allocations: 210.1 kB / 292.8 MB, free: 17.65 MB / 266.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 8.939e-05/0.004285, allocations: 7.219 kB / 292.8 MB, free: 17.65 MB / 266.7 MB
Notification: Performance of NFTyping.typeComponents: time 7.119e-05/0.004356, allocations: 30.38 kB / 292.8 MB, free: 17.63 MB / 266.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001527/0.004509, allocations: 51.06 kB / 292.9 MB, free: 17.59 MB / 266.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002044/0.004713, allocations: 52.31 kB / 292.9 MB, free: 17.56 MB / 266.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0001822/0.004896, allocations: 187.4 kB / 293.1 MB, free: 17.46 MB / 266.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001579/0.005054, allocations: 74.03 kB / 293.2 MB, free: 17.43 MB / 266.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001504/0.005204, allocations: 127.5 kB / 293.3 MB, free: 17.38 MB / 266.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001511/0.005355, allocations: 73.52 kB / 293.4 MB, free: 17.35 MB / 266.7 MB
Notification: Performance of NFPackage.collectConstants: time 3.512e-05/0.00539, allocations: 21.03 kB / 293.4 MB, free: 17.35 MB / 266.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 2.969e-05/0.00542, allocations: 22.94 kB / 293.4 MB, free: 17.35 MB / 266.7 MB
Notification: Performance of NFScalarize.scalarize: time 3.638e-05/0.005456, allocations: 49.67 kB / 293.5 MB, free: 17.32 MB / 266.7 MB
Notification: Performance of NFVerifyModel.verify: time 6.05e-05/0.005517, allocations: 67.42 kB / 293.5 MB, free: 17.29 MB / 266.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002168/0.005733, allocations: 153.8 kB / 293.7 MB, free: 17.2 MB / 266.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.336e-06/0.005737, allocations: 0 / 293.7 MB, free: 17.2 MB / 266.7 MB
Notification: Performance of FrontEnd: time 1.082e-06/0.005738, allocations: 0 / 293.7 MB, free: 17.2 MB / 266.7 MB
Notification: Performance of Transformations before backend: time 6.512e-06/0.005744, allocations: 1.969 kB / 293.7 MB, free: 17.2 MB / 266.7 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 0.0004552/0.0062, allocations: 418.5 kB / 294.1 MB, free: 16.88 MB / 266.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.665e-05/0.006236, allocations: 9.25 kB / 294.1 MB, free: 16.88 MB / 266.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.745e-05/0.006294, allocations: 37.27 kB / 294.1 MB, free: 16.87 MB / 266.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 7.506e-05/0.006369, allocations: 136.4 kB / 294.3 MB, free: 16.72 MB / 266.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.563e-05/0.006384, allocations: 18.59 kB / 294.3 MB, free: 16.71 MB / 266.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.564e-05/0.00642, allocations: 25.28 kB / 294.3 MB, free: 16.7 MB / 266.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002135/0.006634, allocations: 187.8 kB / 294.5 MB, free: 16.61 MB / 266.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.189e-05/0.006646, allocations: 1.062 kB / 294.5 MB, free: 16.61 MB / 266.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.356e-05/0.006659, allocations: 11 kB / 294.5 MB, free: 16.61 MB / 266.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.144e-06/0.006666, allocations: 7.141 kB / 294.5 MB, free: 16.61 MB / 266.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 8.948e-05/0.006756, allocations: 65.73 kB / 294.6 MB, free: 16.59 MB / 266.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007859/0.007542, allocations: 0.5936 MB / 295.2 MB, free: 16.19 MB / 266.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.000112/0.007654, allocations: 86.28 kB / 295.3 MB, free: 16.13 MB / 266.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.000142/0.007796, allocations: 78.88 kB / 295.3 MB, free: 16.11 MB / 266.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.833e-05/0.007814, allocations: 4.312 kB / 295.4 MB, free: 16.11 MB / 266.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.616e-05/0.00783, allocations: 32.55 kB / 295.4 MB, free: 16.07 MB / 266.7 MB
Notification: Performance of pre-optimization done (n=15): time 2.164e-06/0.007832, allocations: 2.031 kB / 295.4 MB, free: 16.07 MB / 266.7 MB
Notification: Performance of matching and sorting (n=17): time 0.000775/0.008607, allocations: 0.5027 MB / 295.9 MB, free: 15.73 MB / 266.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.099e-05/0.008628, allocations: 84.17 kB / 296 MB, free: 15.64 MB / 266.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 7.05e-05/0.008699, allocations: 142 kB / 296.1 MB, free: 15.52 MB / 266.7 MB
Notification: Performance of collectPreVariables (initialization): time 8.597e-06/0.008707, allocations: 31.48 kB / 296.1 MB, free: 15.48 MB / 266.7 MB
Notification: Performance of collectInitialEqns (initialization): time 4.533e-05/0.008753, allocations: 153.8 kB / 296.3 MB, free: 15.35 MB / 266.7 MB
Notification: Performance of collectInitialBindings (initialization): time 3.146e-05/0.008784, allocations: 74.02 kB / 296.4 MB, free: 15.29 MB / 266.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.028e-05/0.008834, allocations: 41.58 kB / 296.4 MB, free: 15.26 MB / 266.7 MB
Notification: Performance of setup shared object (initialization): time 3.913e-05/0.008874, allocations: 330.6 kB / 296.7 MB, free: 14.94 MB / 266.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 3.33e-05/0.008907, allocations: 18.67 kB / 296.7 MB, free: 14.94 MB / 266.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 5.643e-05/0.008963, allocations: 74.03 kB / 296.8 MB, free: 14.87 MB / 266.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001768/0.00914, allocations: 156.1 kB / 297 MB, free: 14.79 MB / 266.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.344e-06/0.009142, allocations: 3.875 kB / 297 MB, free: 14.79 MB / 266.7 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0001812/0.009324, allocations: 130.4 kB / 297.1 MB, free: 14.74 MB / 266.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.704e-05/0.009341, allocations: 9.688 kB / 297.1 MB, free: 14.74 MB / 266.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.192e-06/0.009347, allocations: 2.062 kB / 297.1 MB, free: 14.74 MB / 266.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.644e-05/0.009363, allocations: 9.109 kB / 297.1 MB, free: 14.74 MB / 266.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000189/0.009552, allocations: 62.5 kB / 297.2 MB, free: 14.73 MB / 266.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 5.25e-06/0.009557, allocations: 4.406 kB / 297.2 MB, free: 14.73 MB / 266.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 4.844e-05/0.009606, allocations: 7.344 kB / 297.2 MB, free: 14.73 MB / 266.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.266e-05/0.009619, allocations: 7.234 kB / 297.2 MB, free: 14.73 MB / 266.7 MB
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 0.0001771/0.009796, allocations: 148.1 kB / 297.3 MB, free: 14.59 MB / 266.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.802e-05/0.009844, allocations: 11.17 kB / 297.4 MB, free: 14.59 MB / 266.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001741/0.01002, allocations: 111.1 kB / 297.5 MB, free: 14.52 MB / 266.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.839e-06/0.01002, allocations: 3.969 kB / 297.5 MB, free: 14.52 MB / 266.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.597e-06/0.01003, allocations: 0 / 297.5 MB, free: 14.52 MB / 266.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.752e-06/0.01003, allocations: 2.156 kB / 297.5 MB, free: 14.52 MB / 266.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005101/0.01054, allocations: 393.5 kB / 297.9 MB, free: 14.23 MB / 266.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.567e-06/0.01055, allocations: 1.844 kB / 297.9 MB, free: 14.23 MB / 266.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001597/0.01071, allocations: 54.88 kB / 297.9 MB, free: 14.22 MB / 266.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 5.871e-06/0.01071, allocations: 1.125 kB / 297.9 MB, free: 14.22 MB / 266.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.537e-05/0.01073, allocations: 6.625 kB / 297.9 MB, free: 14.21 MB / 266.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.827e-06/0.01073, allocations: 2.562 kB / 297.9 MB, free: 14.21 MB / 266.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.046e-06/0.01073, allocations: 0 / 297.9 MB, free: 14.21 MB / 266.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002681/0.011, allocations: 317.5 kB / 298.2 MB, free: 13.99 MB / 266.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 1.727e-05/0.01102, allocations: 12.67 kB / 298.2 MB, free: 13.98 MB / 266.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 1.934e-05/0.01104, allocations: 7.844 kB / 298.2 MB, free: 13.98 MB / 266.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.483e-05/0.01111, allocations: 7.453 kB / 298.3 MB, free: 13.97 MB / 266.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.899e-05/0.01114, allocations: 14.14 kB / 298.3 MB, free: 13.97 MB / 266.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.695e-06/0.01115, allocations: 4.234 kB / 298.3 MB, free: 13.97 MB / 266.7 MB
Notification: Performance of sorting global known variables: time 3.2e-05/0.01118, allocations: 37.7 kB / 298.3 MB, free: 13.95 MB / 266.7 MB
Notification: Performance of sort global known variables: time 7e-08/0.01118, allocations: 0.5312 kB / 298.3 MB, free: 13.95 MB / 266.7 MB
Notification: Performance of remove unused functions: time 0.0002236/0.01141, allocations: 39.47 kB / 298.3 MB, free: 13.95 MB / 266.7 MB
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 0.0001019/0.01151, allocations: 78.16 kB / 298.4 MB, free: 13.88 MB / 266.7 MB
Notification: Performance of simCode: created initialization part: time 0.0001799/0.01169, allocations: 105.8 kB / 298.5 MB, free: 13.84 MB / 266.7 MB
Notification: Performance of simCode: created event and clocks part: time 5.29e-06/0.01169, allocations: 2.125 kB / 298.5 MB, free: 13.84 MB / 266.7 MB
Notification: Performance of simCode: created simulation system equations: time 5.775e-05/0.01175, allocations: 48.64 kB / 298.6 MB, free: 13.83 MB / 266.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002404/0.01199, allocations: 29.8 kB / 298.6 MB, free: 13.82 MB / 266.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0006888/0.01268, allocations: 448.5 kB / 299 MB, free: 13.52 MB / 266.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 7.207e-05/0.01275, allocations: 78.55 kB / 299.1 MB, free: 13.45 MB / 266.7 MB
Notification: Performance of simCode: alias equations: time 8.213e-05/0.01283, allocations: 17.94 kB / 299.1 MB, free: 13.45 MB / 266.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001024/0.01294, allocations: 73.92 kB / 299.2 MB, free: 13.4 MB / 266.7 MB
Notification: Performance of SimCode: time 1.433e-06/0.01294, allocations: 0 / 299.2 MB, free: 13.4 MB / 266.7 MB
Notification: Performance of Templates: time 0.004131/0.01707, allocations: 1.4 MB / 300.6 MB, free: 13.23 MB / 266.7 MB
"
[Timeout remaining time 660]
make -j1 -f BioChem_BioChem.Examples.CaOscillations.Cytosol.makefile [Timeout 660]
(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=240 -s gbode -gbm=radauIIA3 -lv LOG_STATS > BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 2.793219876009971]