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 0.008539/0.008539, allocations: 103.2 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 0.001549/0.001549, allocations: 190.5 kB / 16.67 MB, free: 5.977 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.449/1.449, allocations: 222.9 MB / 240.4 MB, free: 15.15 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1361/0.1361, allocations: 12.28 MB / 302.8 MB, free: 3.219 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.00141/0.00141, allocations: 60.62 kB / 420 MB, free: 17.14 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1164/0.1178, allocations: 52.08 MB / 472.1 MB, free: 13.07 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.007927/0.1258, allocations: 4.316 MB / 476.4 MB, free: 8.734 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0007344/0.1265, allocations: 299.2 kB / 476.7 MB, free: 8.441 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002554/0.1268, allocations: 16 kB / 476.7 MB, free: 8.426 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002164/0.1271, allocations: 55.53 kB / 476.8 MB, free: 8.371 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0003509/0.1274, allocations: 75.23 kB / 476.9 MB, free: 8.297 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003008/0.1277, allocations: 67.91 kB / 476.9 MB, free: 8.23 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0004062/0.1282, allocations: 303.2 kB / 477.2 MB, free: 7.934 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003135/0.1285, allocations: 148.5 kB / 477.4 MB, free: 7.785 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001784/0.1287, allocations: 135.5 kB / 477.5 MB, free: 7.652 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000231/0.1289, allocations: 155.3 kB / 477.7 MB, free: 7.5 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 6.324e-05/0.129, allocations: 36 kB / 477.7 MB, free: 7.465 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 6.104e-05/0.129, allocations: 32 kB / 477.7 MB, free: 7.434 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 7.176e-05/0.1291, allocations: 71.75 kB / 477.8 MB, free: 7.363 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.00017/0.1293, allocations: 171.1 kB / 478 MB, free: 7.195 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0003828/0.1297, allocations: 358.7 kB / 478.3 MB, free: 6.844 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.32e-06/0.1297, allocations: 0 / 478.3 MB, free: 6.844 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.014e-06/0.1297, allocations: 0 / 478.3 MB, free: 6.844 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.797e-05/0.1297, allocations: 0 / 478.3 MB, free: 6.844 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 0.001071/0.1308, allocations: 0.6049 MB / 478.9 MB, free: 6.188 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.366e-05/0.1309, allocations: 8.031 kB / 478.9 MB, free: 6.18 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 9.208e-05/0.131, allocations: 40.47 kB / 479 MB, free: 6.141 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001781/0.1311, allocations: 199.9 kB / 479.2 MB, free: 5.906 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.118e-05/0.1312, allocations: 33.38 kB / 479.2 MB, free: 5.875 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.689e-05/0.1313, allocations: 36.38 kB / 479.2 MB, free: 5.84 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005314/0.1318, allocations: 311.1 kB / 479.5 MB, free: 5.531 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.765e-05/0.1318, allocations: 192 / 479.5 MB, free: 5.531 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.361e-05/0.1319, allocations: 19.94 kB / 479.6 MB, free: 5.512 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.472e-05/0.1319, allocations: 12 kB / 479.6 MB, free: 5.5 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003933/0.1323, allocations: 231.9 kB / 479.8 MB, free: 5.27 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001823/0.1341, allocations: 1.039 MB / 480.8 MB, free: 4.18 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003263/0.1345, allocations: 182.5 kB / 481 MB, free: 3.992 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001657/0.1346, allocations: 120.8 kB / 481.1 MB, free: 3.871 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.819e-05/0.1347, allocations: 4 kB / 481.1 MB, free: 3.867 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.201e-05/0.1347, allocations: 38.94 kB / 481.2 MB, free: 3.82 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.483e-06/0.1347, allocations: 0 / 481.2 MB, free: 3.82 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001871/0.1366, allocations: 0.9093 MB / 482.1 MB, free: 2.859 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.452e-05/0.1366, allocations: 51.41 kB / 482.1 MB, free: 2.797 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001332/0.1368, allocations: 167.3 kB / 482.3 MB, free: 2.617 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.098e-05/0.1368, allocations: 29.7 kB / 482.3 MB, free: 2.582 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.00012/0.1369, allocations: 219.4 kB / 482.5 MB, free: 2.363 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 6.302e-05/0.137, allocations: 94.64 kB / 482.6 MB, free: 2.27 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.656e-05/0.1371, allocations: 65.61 kB / 482.7 MB, free: 2.199 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001063/0.1372, allocations: 334.8 kB / 483 MB, free: 1.863 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001214/0.1373, allocations: 80.34 kB / 483.1 MB, free: 1.781 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001931/0.1375, allocations: 198.4 kB / 483.3 MB, free: 1.539 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003016/0.1405, allocations: 0.8104 MB / 484.1 MB, free: 0.6758 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.878e-06/0.1406, allocations: 4 kB / 484.1 MB, free: 0.6719 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0004908/0.1411, allocations: 349.3 kB / 484.4 MB, free: 332 kB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.319e-05/0.1411, allocations: 7.984 kB / 484.5 MB, free: 324 kB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.011e-05/0.1411, allocations: 4 kB / 484.5 MB, free: 320 kB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.431e-05/0.1411, allocations: 8 kB / 484.5 MB, free: 312 kB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002945/0.1414, allocations: 75.91 kB / 484.5 MB, free: 236 kB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.552e-05/0.1415, allocations: 11.94 kB / 484.5 MB, free: 224 kB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001381/0.1416, allocations: 8 kB / 484.6 MB, free: 216 kB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.102e-05/0.1416, allocations: 16 kB / 484.6 MB, free: 200 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 0.0003518/0.142, allocations: 175.7 kB / 484.7 MB, free: 16 kB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 6.562e-05/0.1421, allocations: 19.89 kB / 484.8 MB, free: 15.99 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 8.772e-05/0.1422, allocations: 37.86 kB / 484.8 MB, free: 15.95 MB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.846e-06/0.1422, allocations: 4 kB / 484.8 MB, free: 15.95 MB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.172e-06/0.1422, allocations: 0 / 484.8 MB, free: 15.95 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.017e-06/0.1422, allocations: 0 / 484.8 MB, free: 15.95 MB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005134/0.1427, allocations: 365.3 kB / 485.2 MB, free: 15.54 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.827e-06/0.1427, allocations: 0 / 485.2 MB, free: 15.54 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002588/0.143, allocations: 47.91 kB / 485.2 MB, free: 15.5 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.576e-06/0.143, allocations: 4 kB / 485.2 MB, free: 15.49 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.129e-05/0.143, allocations: 4 kB / 485.2 MB, free: 15.49 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.577e-06/0.143, allocations: 4 kB / 485.2 MB, free: 15.48 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.382e-06/0.143, allocations: 0 / 485.2 MB, free: 15.48 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005976/0.1436, allocations: 439.2 kB / 485.6 MB, free: 15.04 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 7.868e-05/0.1437, allocations: 88.92 kB / 485.7 MB, free: 14.93 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.998e-05/0.1438, allocations: 4.062 kB / 485.7 MB, free: 14.93 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001383/0.1439, allocations: 8 kB / 485.7 MB, free: 14.92 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.129e-05/0.144, allocations: 15.97 kB / 485.8 MB, free: 14.91 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.299e-05/0.144, allocations: 8 kB / 485.8 MB, free: 14.9 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 9.132e-05/0.1441, allocations: 116 kB / 485.9 MB, free: 14.79 MB / 366.1 MB
Notification: Performance of sort global known variables: time 1e-07/0.1441, allocations: 0 / 485.9 MB, free: 14.79 MB / 366.1 MB
Notification: Performance of remove unused functions: time 0.0003658/0.1444, allocations: 64 kB / 485.9 MB, free: 14.72 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 0.0001164/0.1446, allocations: 103.2 kB / 486 MB, free: 14.61 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.0004537/0.145, allocations: 243.7 kB / 486.3 MB, free: 14.37 MB / 366.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.186e-06/0.145, allocations: 0 / 486.3 MB, free: 14.37 MB / 366.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001456/0.1452, allocations: 104.8 kB / 486.4 MB, free: 14.27 MB / 366.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003288/0.1455, allocations: 44.03 kB / 486.4 MB, free: 14.23 MB / 366.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001393/0.1469, allocations: 0.7357 MB / 487.2 MB, free: 13.47 MB / 366.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003677/0.1473, allocations: 0.7714 MB / 487.9 MB, free: 12.67 MB / 366.1 MB
Notification: Performance of simCode: alias equations: time 0.0001008/0.1474, allocations: 29.94 kB / 488 MB, free: 12.64 MB / 366.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.642e-05/0.1475, allocations: 19.44 kB / 488 MB, free: 12.63 MB / 366.1 MB
Notification: Performance of SimCode: time 3.4e-07/0.1475, allocations: 0 / 488 MB, free: 12.63 MB / 366.1 MB
Notification: Performance of Templates: time 0.005637/0.1532, allocations: 2.079 MB / 490.1 MB, free: 10.56 MB / 366.1 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)