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: "" <> buildModelFMU(BioChem.Examples.GMO.cell,fileNamePrefix="BioChem_BioChem_Examples_GMO_cell",fmuType="me",version="2.0",platforms={"static"})
"" <> buildModelFMU(BioChem.Examples.GMO.cell,fileNamePrefix="BioChem_BioChem_Examples_GMO_cell",fmuType="me",version="2.0",platforms={"static"})
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.007751/0.007751, allocations: 101 kB / 15.73 MB, free: 6.059 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.00202/0.00202, allocations: 194 kB / 16.67 MB, free: 5.969 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.491/1.491, allocations: 222.9 MB / 240.4 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 0.1457/0.1457, allocations: 12.27 MB / 302.8 MB, free: 3.223 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001896/0.001896, allocations: 67.12 kB / 419.5 MB, free: 17.49 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09459/0.0965, allocations: 52.07 MB / 471.6 MB, free: 13.44 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.006819/0.1033, allocations: 4.319 MB / 475.9 MB, free: 9.105 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0005187/0.1039, allocations: 299.3 kB / 476.2 MB, free: 8.812 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001519/0.104, allocations: 15.94 kB / 476.2 MB, free: 8.797 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001361/0.1042, allocations: 55.55 kB / 476.3 MB, free: 8.742 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0002155/0.1044, allocations: 71.3 kB / 476.4 MB, free: 8.672 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.000224/0.1047, allocations: 67.89 kB / 476.4 MB, free: 8.605 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0003465/0.105, allocations: 303.1 kB / 476.7 MB, free: 8.309 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003012/0.1053, allocations: 164.5 kB / 476.9 MB, free: 8.145 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001421/0.1055, allocations: 119.6 kB / 477 MB, free: 8.027 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002353/0.1057, allocations: 167.3 kB / 477.2 MB, free: 7.863 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 7.305e-05/0.1058, allocations: 32 kB / 477.2 MB, free: 7.832 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 6.077e-05/0.1059, allocations: 32 kB / 477.2 MB, free: 7.801 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 7.787e-05/0.1059, allocations: 71.77 kB / 477.3 MB, free: 7.73 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001617/0.1061, allocations: 163.2 kB / 477.5 MB, free: 7.57 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0004218/0.1065, allocations: 366.6 kB / 477.8 MB, free: 7.211 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.178e-06/0.1065, allocations: 0 / 477.8 MB, free: 7.211 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.094e-06/0.1066, allocations: 4 kB / 477.8 MB, free: 7.207 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.218e-05/0.1066, allocations: 0 / 477.8 MB, free: 7.207 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: 96
 * Number of variables: 96
Notification: Performance of Generate backend data structure: time 0.001069/0.1076, allocations: 0.6045 MB / 478.4 MB, free: 6.551 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.961e-05/0.1077, allocations: 11.97 kB / 478.4 MB, free: 6.539 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 8.167e-05/0.1078, allocations: 78.7 kB / 478.5 MB, free: 6.453 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.925e-05/0.1079, allocations: 44.7 kB / 478.6 MB, free: 6.41 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001802/0.108, allocations: 200 kB / 478.8 MB, free: 6.176 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.334e-05/0.1081, allocations: 25.38 kB / 478.8 MB, free: 6.152 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.846e-05/0.1082, allocations: 40.38 kB / 478.8 MB, free: 6.113 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005395/0.1087, allocations: 311 kB / 479.1 MB, free: 5.805 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.111e-05/0.1087, allocations: 3.938 kB / 479.1 MB, free: 5.801 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.11e-05/0.1088, allocations: 16 kB / 479.1 MB, free: 5.785 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.139e-05/0.1088, allocations: 8 kB / 479.1 MB, free: 5.777 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0004312/0.1092, allocations: 239.9 kB / 479.4 MB, free: 5.539 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002003/0.1112, allocations: 1.039 MB / 480.4 MB, free: 4.449 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003684/0.1116, allocations: 182.5 kB / 480.6 MB, free: 4.262 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001943/0.1118, allocations: 120.8 kB / 480.7 MB, free: 4.141 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.849e-05/0.1119, allocations: 8 kB / 480.7 MB, free: 4.133 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.264e-05/0.1119, allocations: 42.88 kB / 480.8 MB, free: 4.082 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.593e-06/0.1119, allocations: 0 / 480.8 MB, free: 4.082 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.002277/0.1142, allocations: 0.9001 MB / 481.7 MB, free: 3.133 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.814e-05/0.1143, allocations: 59.34 kB / 481.7 MB, free: 3.062 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001808/0.1144, allocations: 163.3 kB / 481.9 MB, free: 2.887 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.208e-05/0.1145, allocations: 29.7 kB / 481.9 MB, free: 2.852 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001629/0.1146, allocations: 216 kB / 482.1 MB, free: 2.637 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 8.94e-05/0.1147, allocations: 107.1 kB / 482.2 MB, free: 2.531 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.97e-05/0.1149, allocations: 65.7 kB / 482.3 MB, free: 2.461 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001843/0.115, allocations: 334.8 kB / 482.6 MB, free: 2.125 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001573/0.1152, allocations: 80.34 kB / 482.7 MB, free: 2.043 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002565/0.1155, allocations: 198.4 kB / 482.9 MB, free: 1.801 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003295/0.1188, allocations: 0.8143 MB / 483.7 MB, free: 0.9336 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.944e-06/0.1188, allocations: 0 / 483.7 MB, free: 0.9336 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.000612/0.1194, allocations: 345.3 kB / 484 MB, free: 0.5898 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.103e-05/0.1194, allocations: 8 kB / 484.1 MB, free: 0.582 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.787e-06/0.1194, allocations: 7.938 kB / 484.1 MB, free: 0.5742 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.354e-05/0.1195, allocations: 7.984 kB / 484.1 MB, free: 0.5664 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003147/0.1198, allocations: 79.91 kB / 484.1 MB, free: 500 kB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.144e-05/0.1198, allocations: 11.88 kB / 484.2 MB, free: 488 kB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001496/0.12, allocations: 8 kB / 484.2 MB, free: 480 kB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.821e-05/0.12, allocations: 16.38 kB / 484.2 MB, free: 464 kB / 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
         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 0.0003219/0.1203, allocations: 175.6 kB / 484.4 MB, free: 280 kB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.79e-05/0.1204, allocations: 19.86 kB / 484.4 MB, free: 260 kB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 8.723e-05/0.1205, allocations: 37.86 kB / 484.4 MB, free: 220 kB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 8.205e-06/0.1205, allocations: 4 kB / 484.4 MB, free: 216 kB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.759e-06/0.1205, allocations: 0 / 484.4 MB, free: 216 kB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.248e-06/0.1205, allocations: 0 / 484.4 MB, free: 216 kB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005513/0.1211, allocations: 365.5 kB / 484.8 MB, free: 15.8 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.386e-06/0.1211, allocations: 0 / 484.8 MB, free: 15.8 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002679/0.1214, allocations: 43.92 kB / 484.8 MB, free: 15.76 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 6.321e-06/0.1214, allocations: 3.984 kB / 484.8 MB, free: 15.75 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.434e-05/0.1214, allocations: 8 kB / 484.8 MB, free: 15.75 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.485e-06/0.1214, allocations: 0 / 484.8 MB, free: 15.75 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.062e-06/0.1214, allocations: 0 / 484.8 MB, free: 15.75 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005985/0.122, allocations: 443.5 kB / 485.3 MB, free: 15.3 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 6.69e-05/0.1221, allocations: 89.02 kB / 485.3 MB, free: 15.19 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.389e-05/0.1222, allocations: 12.06 kB / 485.4 MB, free: 15.18 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001381/0.1223, allocations: 4 kB / 485.4 MB, free: 15.18 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.806e-05/0.1223, allocations: 23.84 kB / 485.4 MB, free: 15.15 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.846e-05/0.1224, allocations: 8 kB / 485.4 MB, free: 15.14 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 8.64e-05/0.1225, allocations: 112 kB / 485.5 MB, free: 15.04 MB / 366.1 MB
Notification: Performance of sort global known variables: time 1.4e-07/0.1225, allocations: 4 kB / 485.5 MB, free: 15.03 MB / 366.1 MB
Notification: Performance of remove unused functions: time 0.0003474/0.1228, allocations: 68 kB / 485.6 MB, free: 14.96 MB / 366.1 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 0.0008821/0.1237, allocations: 0.9543 MB / 486.5 MB, free: 13.98 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.0004192/0.1241, allocations: 252.2 kB / 486.8 MB, free: 13.73 MB / 366.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.655e-06/0.1241, allocations: 3.938 kB / 486.8 MB, free: 13.73 MB / 366.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001524/0.1243, allocations: 107.8 kB / 486.9 MB, free: 13.62 MB / 366.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003034/0.1246, allocations: 19.98 kB / 486.9 MB, free: 13.61 MB / 366.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003443/0.1281, allocations: 2.757 MB / 489.7 MB, free: 10.68 MB / 366.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004169/0.1285, allocations: 0.7675 MB / 490.4 MB, free: 9.891 MB / 366.1 MB
Notification: Performance of simCode: alias equations: time 0.0001102/0.1286, allocations: 25.94 kB / 490.4 MB, free: 9.867 MB / 366.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001582/0.1288, allocations: 91.41 kB / 490.5 MB, free: 9.781 MB / 366.1 MB
Notification: Performance of SimCode: time 4.61e-07/0.1288, allocations: 0 / 490.5 MB, free: 9.781 MB / 366.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.0278/0.1566, allocations: 4.364 MB / 494.9 MB, free: 5.48 MB / 366.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 8.2/8.357, allocations: 8.359 kB / 494.9 MB, free: 5.477 MB / 366.1 MB
(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 & python3 -m fmpy simulate  --output-file BioChem_BioChem.Examples.GMO.cell_res.csv --start-time 0 --stop-time 100 --timeout 50 --relative-tolerance 1e-06 --interface-type ModelExchange --solver CVode --output-interval 100 BioChem_BioChem_Examples_GMO_cell.fmu > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1)