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/BioChem 1.1.2-master/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/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/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 BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/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/BioChem 1.1.2-master/package.mo): time 0.1713/0.1713, allocations: 12.25 MB / 27.21 MB, free: 0.9531 MB / 18.57 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.002269/0.002269, allocations: 177 kB / 30.74 MB, free: 3.973 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 2.49/2.49, allocations: 223.1 MB / 257.3 MB, free: 8.777 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001165/0.001165, allocations: 97.91 kB / 311.1 MB, free: 10.58 MB / 250.7 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0006648/0.000665, allocations: 10.91 kB / 374.7 MB, free: 53.3 MB / 298.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09884/0.09953, allocations: 53.07 MB / 427.7 MB, free: 12.29 MB / 298.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.005993/0.1056, allocations: 3.667 MB / 431.4 MB, free: 8.609 MB / 298.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0004477/0.1061, allocations: 327.2 kB / 431.7 MB, free: 8.289 MB / 298.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001309/0.1062, allocations: 16 kB / 431.7 MB, free: 8.273 MB / 298.7 MB
Notification: Performance of NFTyping.typeComponents: time 7.589e-05/0.1063, allocations: 47.66 kB / 431.8 MB, free: 8.227 MB / 298.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0002035/0.1065, allocations: 63.84 kB / 431.9 MB, free: 8.164 MB / 298.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002133/0.1067, allocations: 51.94 kB / 431.9 MB, free: 8.113 MB / 298.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0002568/0.107, allocations: 200 kB / 432.1 MB, free: 7.918 MB / 298.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002635/0.1073, allocations: 136.7 kB / 432.2 MB, free: 7.777 MB / 298.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 9.248e-05/0.1074, allocations: 91.64 kB / 432.3 MB, free: 7.688 MB / 298.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001901/0.1076, allocations: 127.4 kB / 432.4 MB, free: 7.562 MB / 298.7 MB
Notification: Performance of NFPackage.collectConstants: time 3.85e-05/0.1076, allocations: 15.94 kB / 432.5 MB, free: 7.547 MB / 298.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 5.336e-05/0.1077, allocations: 16 kB / 432.5 MB, free: 7.531 MB / 298.7 MB
Notification: Performance of NFScalarize.scalarize: time 4.884e-05/0.1078, allocations: 47.77 kB / 432.5 MB, free: 7.484 MB / 298.7 MB
Notification: Performance of NFVerifyModel.verify: time 6.739e-05/0.1078, allocations: 77.58 kB / 432.6 MB, free: 7.402 MB / 298.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002751/0.1081, allocations: 267.5 kB / 432.9 MB, free: 7.141 MB / 298.7 MB
Notification: Performance of FrontEnd - DAE generated: time 2.795e-06/0.1081, allocations: 0 / 432.9 MB, free: 7.141 MB / 298.7 MB
Notification: Performance of FrontEnd: time 2.615e-06/0.1081, allocations: 3.984 kB / 432.9 MB, free: 7.137 MB / 298.7 MB
Notification: Performance of Transformations before backend: time 6.101e-06/0.1082, allocations: 0 / 432.9 MB, free: 7.137 MB / 298.7 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 0.001027/0.1092, allocations: 0.5462 MB / 433.4 MB, free: 6.543 MB / 298.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.644e-05/0.1092, allocations: 8.031 kB / 433.4 MB, free: 6.535 MB / 298.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.711e-05/0.1093, allocations: 31.62 kB / 433.4 MB, free: 6.504 MB / 298.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001224/0.1095, allocations: 194.6 kB / 433.6 MB, free: 6.273 MB / 298.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.998e-05/0.1095, allocations: 29 kB / 433.7 MB, free: 6.246 MB / 298.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 7.718e-05/0.1096, allocations: 44 kB / 433.7 MB, free: 6.203 MB / 298.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0006406/0.1102, allocations: 302.5 kB / 434 MB, free: 5.898 MB / 298.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.294e-05/0.1103, allocations: 0 / 434 MB, free: 5.898 MB / 298.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.26e-05/0.1103, allocations: 19.95 kB / 434 MB, free: 5.879 MB / 298.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.248e-05/0.1103, allocations: 8 kB / 434 MB, free: 5.871 MB / 298.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0005547/0.1109, allocations: 239.8 kB / 434.3 MB, free: 5.637 MB / 298.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002428/0.1134, allocations: 1.028 MB / 435.3 MB, free: 4.559 MB / 298.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004506/0.1138, allocations: 186.2 kB / 435.5 MB, free: 4.371 MB / 298.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.162e-05/0.1139, allocations: 4.125 kB / 435.5 MB, free: 4.367 MB / 298.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.689e-05/0.1139, allocations: 34.75 kB / 435.5 MB, free: 4.324 MB / 298.7 MB
Notification: Performance of pre-optimization done (n=22): time 1.953e-06/0.1139, allocations: 4 kB / 435.5 MB, free: 4.32 MB / 298.7 MB
Notification: Performance of matching and sorting (n=26): time 0.002824/0.1167, allocations: 0.8987 MB / 436.4 MB, free: 3.375 MB / 298.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.665e-05/0.1168, allocations: 63.3 kB / 436.5 MB, free: 3.301 MB / 298.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001429/0.1169, allocations: 171.3 kB / 436.6 MB, free: 3.117 MB / 298.7 MB
Notification: Performance of collectPreVariables (initialization): time 2.458e-05/0.117, allocations: 37.64 kB / 436.7 MB, free: 3.074 MB / 298.7 MB
Notification: Performance of collectInitialEqns (initialization): time 9.439e-05/0.1171, allocations: 207.4 kB / 436.9 MB, free: 2.867 MB / 298.7 MB
Notification: Performance of collectInitialBindings (initialization): time 6.778e-05/0.1171, allocations: 90.72 kB / 437 MB, free: 2.777 MB / 298.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 1.862e-05/0.1172, allocations: 4 kB / 437 MB, free: 2.773 MB / 298.7 MB
Notification: Performance of setup shared object (initialization): time 6.455e-05/0.1172, allocations: 338.8 kB / 437.3 MB, free: 2.434 MB / 298.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001912/0.1174, allocations: 76.34 kB / 437.4 MB, free: 2.355 MB / 298.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002494/0.1177, allocations: 198.1 kB / 437.6 MB, free: 2.113 MB / 298.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002592/0.118, allocations: 120.9 kB / 437.7 MB, free: 1.996 MB / 298.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.776e-06/0.118, allocations: 0 / 437.7 MB, free: 1.996 MB / 298.7 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0006894/0.1187, allocations: 345.4 kB / 438 MB, free: 1.652 MB / 298.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.732e-05/0.1187, allocations: 12.09 kB / 438 MB, free: 1.641 MB / 298.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.674e-06/0.1187, allocations: 3.938 kB / 438 MB, free: 1.637 MB / 298.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.219e-05/0.1188, allocations: 8 kB / 438.1 MB, free: 1.629 MB / 298.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005378/0.1193, allocations: 83.89 kB / 438.1 MB, free: 1.547 MB / 298.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.168e-05/0.1193, allocations: 4 kB / 438.1 MB, free: 1.543 MB / 298.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002537/0.1196, allocations: 15.95 kB / 438.2 MB, free: 1.527 MB / 298.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.153e-05/0.1196, allocations: 16 kB / 438.2 MB, free: 1.512 MB / 298.7 MB
Warning: Assuming fixed start value for the following 5 variables:
         ambientSubstance.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
         C.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
         X.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 (linear and non-linear blocks): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0002573/0.1199, allocations: 168.8 kB / 438.3 MB, free: 1.34 MB / 298.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 5.119e-05/0.12, allocations: 15.81 kB / 438.4 MB, free: 1.324 MB / 298.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.777e-05/0.1201, allocations: 33.86 kB / 438.4 MB, free: 1.293 MB / 298.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.587e-06/0.1201, allocations: 4 kB / 438.4 MB, free: 1.289 MB / 298.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.402e-06/0.1201, allocations: 4 kB / 438.4 MB, free: 1.285 MB / 298.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.751e-06/0.1201, allocations: 7.984 kB / 438.4 MB, free: 1.277 MB / 298.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006029/0.1207, allocations: 369.3 kB / 438.8 MB, free: 0.8672 MB / 298.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.174e-06/0.1207, allocations: 0 / 438.8 MB, free: 0.8672 MB / 298.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004883/0.1212, allocations: 51.91 kB / 438.8 MB, free: 0.8164 MB / 298.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.496e-06/0.1212, allocations: 0 / 438.8 MB, free: 0.8164 MB / 298.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.592e-05/0.1213, allocations: 0 / 438.8 MB, free: 0.8164 MB / 298.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.908e-06/0.1213, allocations: 4 kB / 438.8 MB, free: 0.8125 MB / 298.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.233e-06/0.1213, allocations: 0 / 438.8 MB, free: 0.8125 MB / 298.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0007136/0.122, allocations: 435.2 kB / 439.2 MB, free: 380 kB / 298.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 4.151e-05/0.1221, allocations: 92.92 kB / 439.3 MB, free: 268 kB / 298.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.246e-05/0.1221, allocations: 4.062 kB / 439.3 MB, free: 264 kB / 298.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002499/0.1224, allocations: 11.98 kB / 439.3 MB, free: 252 kB / 298.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.156e-05/0.1224, allocations: 15.92 kB / 439.4 MB, free: 236 kB / 298.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.238e-05/0.1225, allocations: 11.98 kB / 439.4 MB, free: 224 kB / 298.7 MB
Notification: Performance of sorting global known variables: time 7.602e-05/0.1226, allocations: 115.9 kB / 439.5 MB, free: 108 kB / 298.7 MB
Notification: Performance of sort global known variables: time 4.31e-07/0.1226, allocations: 4 kB / 439.5 MB, free: 104 kB / 298.7 MB
Notification: Performance of remove unused functions: time 0.0004191/0.123, allocations: 68 kB / 439.6 MB, free: 36 kB / 298.7 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 (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 0.0001463/0.1232, allocations: 99.28 kB / 439.7 MB, free: 15.92 MB / 314.7 MB
Notification: Performance of simCode: created initialization part: time 0.0006074/0.1238, allocations: 244.5 kB / 439.9 MB, free: 15.68 MB / 314.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.465e-06/0.1238, allocations: 3.938 kB / 439.9 MB, free: 15.68 MB / 314.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002489/0.1241, allocations: 108 kB / 440 MB, free: 15.57 MB / 314.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002789/0.1243, allocations: 19.98 kB / 440 MB, free: 15.55 MB / 314.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002038/0.1264, allocations: 0.9115 MB / 440.9 MB, free: 14.61 MB / 314.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004287/0.1268, allocations: 0.7794 MB / 441.7 MB, free: 13.8 MB / 314.7 MB
Notification: Performance of simCode: alias equations: time 0.0001981/0.1271, allocations: 25.94 kB / 441.7 MB, free: 13.78 MB / 314.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001157/0.1272, allocations: 27.42 kB / 441.8 MB, free: 13.75 MB / 314.7 MB
Notification: Performance of SimCode: time 8.01e-07/0.1272, allocations: 0 / 441.8 MB, free: 13.75 MB / 314.7 MB
Notification: Performance of Templates: time 0.007066/0.1343, allocations: 1.843 MB / 443.6 MB, free: 11.93 MB / 314.7 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)