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 0.001112/0.001113, allocations: 107.9 kB / 16.41 MB, free: 6.5 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001115/0.001115, allocations: 188.1 kB / 17.34 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 1.359/1.359, 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 0.06257/0.06257, allocations: 12.28 MB / 303.5 MB, free: 3.211 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001213/0.001213, allocations: 60.03 kB / 420.7 MB, free: 17.01 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09163/0.09285, allocations: 52.08 MB / 472.8 MB, free: 12.93 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.004554/0.09746, allocations: 2.813 MB / 475.6 MB, free: 10.1 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003581/0.09785, allocations: 195.2 kB / 475.8 MB, free: 9.91 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001191/0.09798, allocations: 8 kB / 475.8 MB, free: 9.902 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001012/0.09809, allocations: 27.73 kB / 475.8 MB, free: 9.875 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001753/0.0983, allocations: 51.52 kB / 475.9 MB, free: 9.824 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002385/0.09855, allocations: 47.94 kB / 475.9 MB, free: 9.777 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002207/0.09878, allocations: 183.2 kB / 476.1 MB, free: 9.598 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002474/0.09903, allocations: 99.59 kB / 476.2 MB, free: 9.496 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001034/0.09914, allocations: 79.66 kB / 476.3 MB, free: 9.418 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000152/0.0993, allocations: 103.5 kB / 476.4 MB, free: 9.316 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.876e-05/0.09935, allocations: 20 kB / 476.4 MB, free: 9.297 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.795e-05/0.0994, allocations: 31.94 kB / 476.4 MB, free: 9.266 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 4.427e-05/0.09945, allocations: 43.84 kB / 476.5 MB, free: 9.223 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 9.861e-05/0.09956, allocations: 103.5 kB / 476.6 MB, free: 9.121 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002497/0.09981, allocations: 235.2 kB / 476.8 MB, free: 8.891 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.118e-06/0.09982, allocations: 0 / 476.8 MB, free: 8.891 MB / 350.1 MB
Notification: Performance of FrontEnd: time 3.186e-06/0.09983, allocations: 0 / 476.8 MB, free: 8.891 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 8.596e-06/0.09985, allocations: 3.938 kB / 476.8 MB, free: 8.887 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 0.0007456/0.1006, allocations: 0.4993 MB / 477.3 MB, free: 8.336 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.227e-05/0.1006, allocations: 12.03 kB / 477.3 MB, free: 8.324 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.996e-05/0.1007, allocations: 24.73 kB / 477.3 MB, free: 8.301 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001449/0.1009, allocations: 188 kB / 477.5 MB, free: 8.078 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.444e-05/0.1009, allocations: 20.94 kB / 477.5 MB, free: 8.059 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.574e-05/0.1009, allocations: 28.28 kB / 477.6 MB, free: 8.031 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003357/0.1013, allocations: 201.5 kB / 477.8 MB, free: 7.832 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.576e-05/0.1013, allocations: 4.172 kB / 477.8 MB, free: 7.828 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.481e-05/0.1013, allocations: 15.94 kB / 477.8 MB, free: 7.812 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.596e-06/0.1014, allocations: 11.94 kB / 477.8 MB, free: 7.801 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002387/0.1016, allocations: 130.2 kB / 477.9 MB, free: 7.672 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001316/0.1029, allocations: 0.7593 MB / 478.7 MB, free: 6.852 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001796/0.1031, allocations: 110.5 kB / 478.8 MB, free: 6.734 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002337/0.1034, allocations: 88.8 kB / 478.9 MB, free: 6.645 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.71e-05/0.1034, allocations: 8.219 kB / 478.9 MB, free: 6.637 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.285e-05/0.1034, allocations: 42.55 kB / 478.9 MB, free: 6.586 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=15): time 1.413e-06/0.1034, allocations: 0 / 478.9 MB, free: 6.586 MB / 350.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001221/0.1047, allocations: 0.5775 MB / 479.5 MB, free: 5.957 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.294e-05/0.1047, allocations: 51.41 kB / 479.6 MB, free: 5.895 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001306/0.1048, allocations: 156.2 kB / 479.7 MB, free: 5.727 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.679e-05/0.1049, allocations: 25.7 kB / 479.7 MB, free: 5.695 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 9.102e-05/0.105, allocations: 155.9 kB / 479.9 MB, free: 5.539 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.714e-05/0.105, allocations: 67.08 kB / 480 MB, free: 5.473 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.354e-05/0.1051, allocations: 41.61 kB / 480 MB, free: 5.426 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001129/0.1052, allocations: 330.8 kB / 480.3 MB, free: 5.094 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.263e-05/0.1053, allocations: 44.22 kB / 480.4 MB, free: 5.051 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001088/0.1054, allocations: 94.44 kB / 480.5 MB, free: 4.938 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.00135/0.1068, allocations: 388.9 kB / 480.8 MB, free: 4.535 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.533e-06/0.1068, allocations: 0 / 480.8 MB, free: 4.535 MB / 350.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0003207/0.1071, allocations: 216.1 kB / 481 MB, free: 4.32 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.66e-05/0.1071, allocations: 6.031 kB / 481 MB, free: 4.316 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.56e-06/0.1071, allocations: 3.938 kB / 481.1 MB, free: 4.312 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.526e-05/0.1072, allocations: 7.938 kB / 481.1 MB, free: 4.305 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002033/0.1074, allocations: 55.89 kB / 481.1 MB, free: 4.25 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.906e-06/0.1074, allocations: 4 kB / 481.1 MB, free: 4.246 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.968e-05/0.1075, allocations: 4 kB / 481.1 MB, free: 4.242 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.672e-05/0.1075, allocations: 12 kB / 481.1 MB, free: 4.23 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 0.0002393/0.1078, allocations: 155.2 kB / 481.3 MB, free: 4.074 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.042e-05/0.1078, allocations: 15.81 kB / 481.3 MB, free: 4.059 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0003077/0.1081, allocations: 174.7 kB / 481.5 MB, free: 3.883 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.765e-06/0.1081, allocations: 4 kB / 481.5 MB, free: 3.879 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.981e-06/0.1081, allocations: 3.984 kB / 481.5 MB, free: 3.875 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.707e-06/0.1082, allocations: 0 / 481.5 MB, free: 3.875 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007247/0.1089, allocations: 0.516 MB / 482 MB, free: 3.305 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.887e-06/0.1089, allocations: 3.984 kB / 482 MB, free: 3.301 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002075/0.1091, allocations: 31.92 kB / 482 MB, free: 3.27 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.036e-06/0.1091, allocations: 0 / 482 MB, free: 3.27 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.796e-05/0.1091, allocations: 8 kB / 482 MB, free: 3.262 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.883e-06/0.1092, allocations: 0 / 482 MB, free: 3.262 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.363e-06/0.1092, allocations: 4 kB / 482 MB, free: 3.258 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000382/0.1095, allocations: 303.8 kB / 482.3 MB, free: 2.945 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.178e-05/0.1096, allocations: 88.92 kB / 482.4 MB, free: 2.84 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.553e-05/0.1097, allocations: 15.94 kB / 482.4 MB, free: 2.824 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000108/0.1098, allocations: 3.984 kB / 482.4 MB, free: 2.82 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3e-05/0.1098, allocations: 11.98 kB / 482.5 MB, free: 2.809 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 9.648e-06/0.1098, allocations: 4 kB / 482.5 MB, free: 2.805 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 7.192e-05/0.1099, allocations: 111.3 kB / 482.6 MB, free: 2.695 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.2e-07/0.1099, allocations: 0 / 482.6 MB, free: 2.695 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0002805/0.1102, allocations: 40 kB / 482.6 MB, free: 2.656 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 (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.0001065/0.1103, allocations: 95.77 kB / 482.7 MB, free: 2.555 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002599/0.1106, allocations: 146 kB / 482.8 MB, free: 2.414 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.605e-06/0.1106, allocations: 4 kB / 482.9 MB, free: 2.41 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 9.657e-05/0.1107, allocations: 59.92 kB / 482.9 MB, free: 2.352 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002819/0.111, allocations: 20.36 kB / 482.9 MB, free: 2.332 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0008672/0.1118, allocations: 0.5415 MB / 483.5 MB, free: 1.758 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003033/0.1122, allocations: 0.7397 MB / 484.2 MB, free: 0.9922 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.137e-05/0.1122, allocations: 19.44 kB / 484.2 MB, free: 0.9727 MB / 350.1 MB
Notification: Performance of SimCode: time 2.21e-07/0.1122, allocations: 0 / 484.2 MB, free: 0.9727 MB / 350.1 MB
Notification: Performance of Templates: time 0.003743/0.116, allocations: 2.031 MB / 486.3 MB, free: 14.94 MB / 366.1 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)