Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr BioChem_BioChem.Examples.GMO.cell.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.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell")
translateModel(BioChem.Examples.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001568/0.001568, allocations: 106.9 kB / 15.99 MB, free: 6.359 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001387/0.001387, allocations: 193.9 kB / 16.91 MB, free: 6.195 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.772/1.772, allocations: 222.9 MB / 240.6 MB, free: 15.4 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.09482/0.09482, allocations: 12.27 MB / 303 MB, free: 3.457 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0014/0.0014, allocations: 59.89 kB / 365.9 MB, free: 4.453 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.4008/0.4023, allocations: 52.07 MB / 418 MB, free: 21.98 MB / 302.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.006873/0.4092, allocations: 4.417 MB / 422.4 MB, free: 17.56 MB / 302.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003932/0.4097, allocations: 307.6 kB / 422.7 MB, free: 17.27 MB / 302.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000139/0.4098, allocations: 16 kB / 422.7 MB, free: 17.25 MB / 302.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001296/0.41, allocations: 40.94 kB / 422.8 MB, free: 17.21 MB / 302.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0002086/0.4102, allocations: 56.92 kB / 422.8 MB, free: 17.16 MB / 302.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002666/0.4105, allocations: 64.67 kB / 422.9 MB, free: 17.09 MB / 302.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002924/0.4108, allocations: 291.2 kB / 423.2 MB, free: 16.81 MB / 302.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002969/0.4111, allocations: 162.3 kB / 423.3 MB, free: 16.66 MB / 302.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001043/0.4112, allocations: 131.5 kB / 423.5 MB, free: 16.53 MB / 302.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001764/0.4114, allocations: 155.9 kB / 423.6 MB, free: 16.38 MB / 302.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.762e-05/0.4114, allocations: 36 kB / 423.6 MB, free: 16.34 MB / 302.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 4.622e-05/0.4115, allocations: 32.62 kB / 423.7 MB, free: 16.31 MB / 302.1 MB
Notification: Performance of NFScalarize.scalarize: time 5.692e-05/0.4115, allocations: 73.48 kB / 423.7 MB, free: 16.24 MB / 302.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001356/0.4117, allocations: 167.2 kB / 423.9 MB, free: 16.07 MB / 302.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002887/0.412, allocations: 269.3 kB / 424.2 MB, free: 15.81 MB / 302.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.524e-06/0.412, allocations: 0 / 424.2 MB, free: 15.81 MB / 302.1 MB
Notification: Performance of FrontEnd: time 3.316e-06/0.412, allocations: 0 / 424.2 MB, free: 15.81 MB / 302.1 MB
Notification: Performance of Transformations before backend: time 1.175e-05/0.412, allocations: 0.75 kB / 424.2 MB, free: 15.81 MB / 302.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 96
 * Number of variables: 96
Notification: Performance of Generate backend data structure: time 0.001102/0.4131, allocations: 0.6015 MB / 424.8 MB, free: 15.16 MB / 302.1 MB
Notification: Performance of prepare preOptimizeDAE: time 6.203e-05/0.4132, allocations: 9.062 kB / 424.8 MB, free: 15.16 MB / 302.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.947e-05/0.4133, allocations: 36.47 kB / 424.8 MB, free: 15.12 MB / 302.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001924/0.4135, allocations: 203.9 kB / 425 MB, free: 14.88 MB / 302.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.959e-05/0.4136, allocations: 29.94 kB / 425 MB, free: 14.86 MB / 302.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.743e-05/0.4136, allocations: 37.56 kB / 425.1 MB, free: 14.82 MB / 302.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005128/0.4142, allocations: 311 kB / 425.4 MB, free: 14.51 MB / 302.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.157e-05/0.4142, allocations: 4.172 kB / 425.4 MB, free: 14.51 MB / 302.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.661e-05/0.4142, allocations: 21.72 kB / 425.4 MB, free: 14.49 MB / 302.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.235e-05/0.4142, allocations: 8 kB / 425.4 MB, free: 14.48 MB / 302.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003476/0.4146, allocations: 243.9 kB / 425.7 MB, free: 14.24 MB / 302.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001563/0.4162, allocations: 1.035 MB / 426.7 MB, free: 13.17 MB / 302.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003175/0.4165, allocations: 187.8 kB / 426.9 MB, free: 12.98 MB / 302.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001816/0.4167, allocations: 128.5 kB / 427 MB, free: 12.85 MB / 302.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.663e-05/0.4167, allocations: 0.8438 kB / 427 MB, free: 12.85 MB / 302.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.739e-05/0.4168, allocations: 35.88 kB / 427 MB, free: 12.81 MB / 302.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.503e-06/0.4168, allocations: 0 / 427 MB, free: 12.81 MB / 302.1 MB
Notification: Performance of matching and sorting (n=26): time 0.002027/0.4188, allocations: 0.9041 MB / 427.9 MB, free: 11.86 MB / 302.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.595e-05/0.4189, allocations: 55.41 kB / 428 MB, free: 11.8 MB / 302.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001416/0.419, allocations: 167.3 kB / 428.2 MB, free: 11.62 MB / 302.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.903e-05/0.419, allocations: 25.7 kB / 428.2 MB, free: 11.59 MB / 302.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001032/0.4192, allocations: 211.4 kB / 428.4 MB, free: 11.38 MB / 302.1 MB
Notification: Performance of collectInitialBindings (initialization): time 6.921e-05/0.4192, allocations: 94.64 kB / 428.5 MB, free: 11.28 MB / 302.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.564e-05/0.4193, allocations: 69.59 kB / 428.6 MB, free: 11.21 MB / 302.1 MB
Notification: Performance of setup shared object (initialization): time 9.182e-05/0.4194, allocations: 326.8 kB / 428.9 MB, free: 10.88 MB / 302.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000124/0.4196, allocations: 84.34 kB / 429 MB, free: 10.79 MB / 302.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001789/0.4198, allocations: 194.4 kB / 429.1 MB, free: 10.55 MB / 302.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.00294/0.4227, allocations: 0.8262 MB / 430 MB, free: 9.68 MB / 302.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.844e-06/0.4227, allocations: 0 / 430 MB, free: 9.68 MB / 302.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0004363/0.4232, allocations: 341.5 kB / 430.3 MB, free: 9.34 MB / 302.1 MB
Notification: Performance of prepare postOptimizeDAE: time 3.024e-05/0.4232, allocations: 8 kB / 430.3 MB, free: 9.332 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.176e-05/0.4232, allocations: 7.938 kB / 430.3 MB, free: 9.324 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.784e-05/0.4233, allocations: 4 kB / 430.3 MB, free: 9.32 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002942/0.4236, allocations: 79.91 kB / 430.4 MB, free: 9.242 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.352e-05/0.4236, allocations: 4 kB / 430.4 MB, free: 9.238 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001752/0.4238, allocations: 27.83 kB / 430.4 MB, free: 9.211 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.375e-05/0.4238, allocations: 12 kB / 430.4 MB, free: 9.199 MB / 302.1 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
         ambientSubstance.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         X.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         M.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         C.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: 16
 * 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 (46):
 * Single equations (assignments): 46
 * 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 0.0003775/0.4242, allocations: 177.6 kB / 430.6 MB, free: 9.016 MB / 302.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 5.669e-05/0.4242, allocations: 15.81 kB / 430.6 MB, free: 9 MB / 302.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 8.533e-05/0.4243, allocations: 29.88 kB / 430.7 MB, free: 8.969 MB / 302.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.527e-06/0.4243, allocations: 4 kB / 430.7 MB, free: 8.965 MB / 302.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.044e-05/0.4243, allocations: 4 kB / 430.7 MB, free: 8.961 MB / 302.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.123e-06/0.4244, allocations: 3.984 kB / 430.7 MB, free: 8.957 MB / 302.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004679/0.4248, allocations: 357.4 kB / 431 MB, free: 8.559 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.463e-06/0.4248, allocations: 0 / 431 MB, free: 8.559 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002538/0.4251, allocations: 47.91 kB / 431.1 MB, free: 8.512 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.956e-06/0.4251, allocations: 0 / 431.1 MB, free: 8.512 MB / 302.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.219e-05/0.4251, allocations: 7.938 kB / 431.1 MB, free: 8.504 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.966e-06/0.4252, allocations: 7.984 kB / 431.1 MB, free: 8.496 MB / 302.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.827e-06/0.4252, allocations: 4 kB / 431.1 MB, free: 8.492 MB / 302.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005028/0.4257, allocations: 451 kB / 431.5 MB, free: 8.035 MB / 302.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.843e-05/0.4257, allocations: 88.92 kB / 431.6 MB, free: 7.93 MB / 302.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.401e-05/0.4258, allocations: 4.062 kB / 431.6 MB, free: 7.926 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001604/0.4259, allocations: 8 kB / 431.6 MB, free: 7.918 MB / 302.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.059e-05/0.426, allocations: 19.91 kB / 431.6 MB, free: 7.898 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.341e-05/0.426, allocations: 8 kB / 431.7 MB, free: 7.891 MB / 302.1 MB
Notification: Performance of sorting global known variables: time 7.081e-05/0.4261, allocations: 122.5 kB / 431.8 MB, free: 7.773 MB / 302.1 MB
Notification: Performance of sort global known variables: time 1.11e-07/0.4261, allocations: 0 / 431.8 MB, free: 7.773 MB / 302.1 MB
Notification: Performance of remove unused functions: time 0.000329/0.4264, allocations: 64 kB / 431.8 MB, free: 7.711 MB / 302.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (V,C.n,M.n,X.n,ambientSubstance.n)
 * 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 (26):
 * Single equations (assignments): 26
 * 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 9.149e-05/0.4265, allocations: 95.52 kB / 431.9 MB, free: 7.605 MB / 302.1 MB
Notification: Performance of simCode: created initialization part: time 0.00035/0.4269, allocations: 256.5 kB / 432.2 MB, free: 7.355 MB / 302.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.675e-06/0.4269, allocations: 4 kB / 432.2 MB, free: 7.352 MB / 302.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.000115/0.427, allocations: 115.9 kB / 432.3 MB, free: 7.238 MB / 302.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000306/0.4273, allocations: 27.92 kB / 432.3 MB, free: 7.211 MB / 302.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001527/0.4288, allocations: 0.8986 MB / 433.2 MB, free: 6.281 MB / 302.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002952/0.4292, allocations: 0.7675 MB / 434 MB, free: 5.488 MB / 302.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 9.504e-05/0.4293, allocations: 27.42 kB / 434 MB, free: 5.461 MB / 302.1 MB
Notification: Performance of SimCode: time 1.363e-06/0.4293, allocations: 0 / 434 MB, free: 5.461 MB / 302.1 MB
Notification: Performance of Templates: time 0.004821/0.4341, allocations: 2.83 MB / 436.8 MB, free: 2.625 MB / 302.1 MB
make -j1 -f BioChem_BioChem.Examples.GMO.cell.makefile
(rm -f BioChem_BioChem.Examples.GMO.cell.pipe ; mkfifo BioChem_BioChem.Examples.GMO.cell.pipe ; head -c 1048576 < BioChem_BioChem.Examples.GMO.cell.pipe >> ../files/BioChem_BioChem.Examples.GMO.cell.sim & ./BioChem_BioChem.Examples.GMO.cell  -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1)