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 0.001119/0.001119, allocations: 116 kB / 16.42 MB, free: 6.473 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001092/0.001092, allocations: 186.6 kB / 17.35 MB, free: 5.75 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.328/1.328, allocations: 222.9 MB / 241 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 0.1157/0.1157, allocations: 12.27 MB / 303.5 MB, free: 3.23 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0012/0.0012, allocations: 65.22 kB / 420.7 MB, free: 17.02 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.07537/0.07658, allocations: 52.08 MB / 472.8 MB, free: 12.95 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.005726/0.08234, allocations: 4.305 MB / 477.1 MB, free: 8.625 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003416/0.0827, allocations: 307.2 kB / 477.4 MB, free: 8.324 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 9.668e-05/0.0828, allocations: 16 kB / 477.4 MB, free: 8.309 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001022/0.08292, allocations: 47.55 kB / 477.5 MB, free: 8.262 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001708/0.08309, allocations: 79.2 kB / 477.5 MB, free: 8.184 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001882/0.08329, allocations: 71.91 kB / 477.6 MB, free: 8.113 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002715/0.08357, allocations: 299.2 kB / 477.9 MB, free: 7.82 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002655/0.08384, allocations: 156.5 kB / 478.1 MB, free: 7.664 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001119/0.08396, allocations: 131.6 kB / 478.2 MB, free: 7.535 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001819/0.08415, allocations: 155.3 kB / 478.3 MB, free: 7.383 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.773e-05/0.0842, allocations: 36 kB / 478.4 MB, free: 7.348 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 4.869e-05/0.08426, allocations: 32 kB / 478.4 MB, free: 7.316 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 6.604e-05/0.08433, allocations: 75.69 kB / 478.5 MB, free: 7.242 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001317/0.08447, allocations: 163.2 kB / 478.6 MB, free: 7.082 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0003182/0.08479, allocations: 362.7 kB / 479 MB, free: 6.727 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 3.416e-06/0.0848, allocations: 0 / 479 MB, free: 6.727 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.232e-06/0.08481, allocations: 0 / 479 MB, free: 6.727 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 5.791e-06/0.08482, allocations: 0 / 479 MB, free: 6.727 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 0.0008899/0.08572, allocations: 0.6049 MB / 479.6 MB, free: 6.07 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.204e-05/0.08576, allocations: 8.031 kB / 479.6 MB, free: 6.062 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.26e-05/0.08583, allocations: 40.41 kB / 479.6 MB, free: 6.023 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001384/0.08597, allocations: 203.9 kB / 479.8 MB, free: 5.785 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.254e-05/0.086, allocations: 29.38 kB / 479.9 MB, free: 5.758 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.852e-05/0.08606, allocations: 36.38 kB / 479.9 MB, free: 5.723 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004703/0.08654, allocations: 311.1 kB / 480.2 MB, free: 5.414 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.566e-05/0.08656, allocations: 4.188 kB / 480.2 MB, free: 5.41 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.209e-05/0.0866, allocations: 19.94 kB / 480.2 MB, free: 5.391 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.001e-05/0.08662, allocations: 8 kB / 480.2 MB, free: 5.383 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003819/0.087, allocations: 235.9 kB / 480.5 MB, free: 5.148 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001718/0.08873, allocations: 1.031 MB / 481.5 MB, free: 4.066 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003212/0.08907, allocations: 192.8 kB / 481.7 MB, free: 3.871 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001779/0.08926, allocations: 120.8 kB / 481.8 MB, free: 3.75 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.568e-05/0.08928, allocations: 4 kB / 481.8 MB, free: 3.746 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.962e-05/0.08931, allocations: 34.94 kB / 481.8 MB, free: 3.703 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.453e-06/0.08931, allocations: 0 / 481.8 MB, free: 3.703 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001955/0.09127, allocations: 0.9014 MB / 482.7 MB, free: 2.75 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.484e-05/0.09132, allocations: 63.41 kB / 482.8 MB, free: 2.676 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001255/0.09145, allocations: 163.3 kB / 483 MB, free: 2.5 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.089e-05/0.09148, allocations: 29.7 kB / 483 MB, free: 2.465 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001092/0.0916, allocations: 211.4 kB / 483.2 MB, free: 2.254 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 6.95e-05/0.09167, allocations: 94.64 kB / 483.3 MB, free: 2.16 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.589e-05/0.09177, allocations: 65.61 kB / 483.4 MB, free: 2.09 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001078/0.09188, allocations: 330.8 kB / 483.7 MB, free: 1.758 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001381/0.09203, allocations: 80.34 kB / 483.8 MB, free: 1.676 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002041/0.09224, allocations: 198.4 kB / 484 MB, free: 1.434 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003349/0.09559, allocations: 0.8182 MB / 484.8 MB, free: 0.5625 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.206e-06/0.09561, allocations: 7.938 kB / 484.8 MB, free: 0.5547 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0004797/0.09609, allocations: 341.1 kB / 485.1 MB, free: 220 kB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.455e-05/0.09612, allocations: 8 kB / 485.1 MB, free: 212 kB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.783e-06/0.09613, allocations: 4.469 kB / 485.1 MB, free: 208 kB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.434e-05/0.09615, allocations: 8 kB / 485.1 MB, free: 200 kB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003297/0.09649, allocations: 83.89 kB / 485.2 MB, free: 116 kB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.144e-05/0.09651, allocations: 7.938 kB / 485.2 MB, free: 108 kB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001512/0.09666, allocations: 8 kB / 485.2 MB, free: 100 kB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.268e-05/0.09669, allocations: 23.94 kB / 485.3 MB, free: 76 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 0.0002133/0.09691, allocations: 170.2 kB / 485.4 MB, free: 15.9 MB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.885e-05/0.09697, allocations: 23.72 kB / 485.4 MB, free: 15.88 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.412e-05/0.09704, allocations: 29.88 kB / 485.5 MB, free: 15.85 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.983e-06/0.09705, allocations: 3.984 kB / 485.5 MB, free: 15.84 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.262e-06/0.09706, allocations: 3.938 kB / 485.5 MB, free: 15.84 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 4.426e-05/0.09711, allocations: 88.92 kB / 485.6 MB, free: 15.73 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.06e-05/0.09714, allocations: 8 kB / 485.6 MB, free: 15.73 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001521/0.0973, allocations: 4 kB / 485.6 MB, free: 15.72 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.843e-05/0.09735, allocations: 23.91 kB / 485.6 MB, free: 15.7 MB / 366.1 MB
Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.000563/0.09792, allocations: 304.8 kB / 485.9 MB, free: 15.39 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.0005451/0.09848, allocations: 0.4908 MB / 486.4 MB, free: 14.89 MB / 366.1 MB
Notification: Performance of postOpt setEvaluationStage (simulation): time 0.0001302/0.09862, allocations: 88.02 kB / 486.5 MB, free: 14.8 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 7.971e-05/0.0987, allocations: 120 kB / 486.6 MB, free: 14.68 MB / 366.1 MB
Notification: Performance of Backend: time 3.11e-07/0.09871, allocations: 0 / 486.6 MB, free: 14.68 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.0005243/0.09924, allocations: 242.2 kB / 486.8 MB, free: 14.44 MB / 366.1 MB
Notification: Performance of SimCode: time 0.001047/0.1003, allocations: 1.098 MB / 487.9 MB, free: 13.3 MB / 366.1 MB
Notification: Performance of Templates: time 0.00504/0.1053, allocations: 2.248 MB / 490.2 MB, free: 11.05 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)