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 0.0008812/0.0008813, allocations: 86.25 kB / 15.06 MB, free: 1.09 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.0009868/0.000987, allocations: 168.7 kB / 15.95 MB, free: 204 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.518/1.518, allocations: 223.3 MB / 240 MB, free: 5.418 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.2831/0.2831, allocations: 12.26 MB / 303.3 MB, free: 2.105 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.000394/0.0003944, allocations: 8 kB / 366.9 MB, free: 9.781 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1217/0.1222, allocations: 53.09 MB / 420 MB, free: 4.582 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.006313/0.1285, allocations: 3.832 MB / 423.9 MB, free: 0.7344 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0007945/0.1293, allocations: 307.2 kB / 424.2 MB, free: 440 kB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001698/0.1295, allocations: 16 kB / 424.2 MB, free: 424 kB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001112/0.1296, allocations: 43.72 kB / 424.2 MB, free: 380 kB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001897/0.1298, allocations: 59.47 kB / 424.3 MB, free: 320 kB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002533/0.1301, allocations: 51.94 kB / 424.3 MB, free: 268 kB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.205/0.3351, allocations: 277.1 kB / 424.6 MB, free: 35 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.000367/0.3355, allocations: 126.3 kB / 424.7 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001576/0.3357, allocations: 95.86 kB / 424.8 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001543/0.3358, allocations: 117.4 kB / 424.9 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 3.522e-05/0.3359, allocations: 17.41 kB / 424.9 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.888e-05/0.3359, allocations: 17.91 kB / 425 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 4.01e-05/0.336, allocations: 47.69 kB / 425 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 5.563e-05/0.336, allocations: 76.05 kB / 425.1 MB, free: 34.96 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0003096/0.3363, allocations: 256.5 kB / 425.3 MB, free: 34.95 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.238e-06/0.3364, allocations: 0.6875 kB / 425.3 MB, free: 34.95 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.403e-06/0.3364, allocations: 0 / 425.3 MB, free: 34.95 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 7.764e-06/0.3364, allocations: 1.062 kB / 425.3 MB, free: 34.95 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 0.000797/0.3372, allocations: 0.5472 MB / 425.9 MB, free: 34.53 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.136e-05/0.3372, allocations: 8.812 kB / 425.9 MB, free: 34.53 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.478e-05/0.3373, allocations: 33.91 kB / 425.9 MB, free: 34.51 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001272/0.3374, allocations: 200.1 kB / 426.1 MB, free: 34.3 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.109e-05/0.3375, allocations: 27.42 kB / 426.1 MB, free: 34.3 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 7.262e-05/0.3375, allocations: 42.38 kB / 426.2 MB, free: 34.3 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005376/0.3381, allocations: 312 kB / 426.5 MB, free: 34.25 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.676e-05/0.3381, allocations: 2.5 kB / 426.5 MB, free: 34.25 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.318e-05/0.3382, allocations: 16.44 kB / 426.5 MB, free: 34.25 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.415e-05/0.3382, allocations: 18.78 kB / 426.5 MB, free: 34.25 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003513/0.3385, allocations: 230.9 kB / 426.8 MB, free: 34.25 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001538/0.3401, allocations: 1.044 MB / 427.8 MB, free: 33.91 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002724/0.3404, allocations: 179.5 kB / 428 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001672/0.3405, allocations: 126.6 kB / 428.1 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.033e-05/0.3406, allocations: 3.125 kB / 428.1 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.893e-05/0.3406, allocations: 34.77 kB / 428.1 MB, free: 33.84 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 2.174e-06/0.3406, allocations: 1.344 kB / 428.1 MB, free: 33.84 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001847/0.3425, allocations: 0.8881 MB / 429 MB, free: 33.54 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.711e-05/0.3425, allocations: 59.36 kB / 429.1 MB, free: 33.47 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001479/0.3427, allocations: 168.8 kB / 429.2 MB, free: 33.36 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.208e-05/0.3427, allocations: 30.27 kB / 429.3 MB, free: 33.32 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001165/0.3428, allocations: 217.4 kB / 429.5 MB, free: 33.16 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 5.402e-05/0.3429, allocations: 93.17 kB / 429.6 MB, free: 33.11 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 1.464e-05/0.3429, allocations: 10.97 kB / 429.6 MB, free: 33.11 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 7.577e-05/0.343, allocations: 330.1 kB / 429.9 MB, free: 32.79 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001154/0.3431, allocations: 86.62 kB / 430 MB, free: 32.79 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001693/0.3433, allocations: 194.5 kB / 430.2 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.000171/0.3434, allocations: 120.3 kB / 430.3 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.403e-06/0.3435, allocations: 0 / 430.3 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0004391/0.3439, allocations: 347.6 kB / 430.6 MB, free: 32.61 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.916e-05/0.3439, allocations: 6.062 kB / 430.7 MB, free: 32.61 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.255e-06/0.3439, allocations: 3.594 kB / 430.7 MB, free: 32.61 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.644e-05/0.344, allocations: 7.156 kB / 430.7 MB, free: 32.61 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003041/0.3443, allocations: 82.08 kB / 430.7 MB, free: 32.61 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.336e-05/0.3443, allocations: 6.828 kB / 430.7 MB, free: 32.61 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000153/0.3445, allocations: 26.22 kB / 430.8 MB, free: 32.61 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.666e-05/0.3445, allocations: 13.81 kB / 430.8 MB, free: 32.61 MB / 350.1 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 0.0002623/0.3448, allocations: 166.9 kB / 431 MB, free: 32.49 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.023e-05/0.3448, allocations: 16.28 kB / 431 MB, free: 32.48 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 8.115e-05/0.3449, allocations: 32.11 kB / 431 MB, free: 32.48 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.418e-06/0.3449, allocations: 2.906 kB / 431 MB, free: 32.48 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.816e-06/0.3449, allocations: 1.781 kB / 431 MB, free: 32.48 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.268e-06/0.3449, allocations: 3.031 kB / 431 MB, free: 32.48 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004122/0.3454, allocations: 363 kB / 431.4 MB, free: 32.29 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.335e-06/0.3454, allocations: 5.125 kB / 431.4 MB, free: 32.29 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002286/0.3456, allocations: 46.47 kB / 431.4 MB, free: 32.29 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.266e-06/0.3456, allocations: 4.656 kB / 431.4 MB, free: 32.29 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.781e-05/0.3456, allocations: 12.53 kB / 431.4 MB, free: 32.29 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.545e-06/0.3457, allocations: 0.6875 kB / 431.4 MB, free: 32.29 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.032e-06/0.3457, allocations: 0 / 431.4 MB, free: 32.29 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004045/0.3461, allocations: 434.7 kB / 431.9 MB, free: 32.13 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.886e-05/0.3461, allocations: 92.06 kB / 431.9 MB, free: 32.03 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.889e-05/0.3461, allocations: 12 kB / 432 MB, free: 32.03 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000144/0.3463, allocations: 7.5 kB / 432 MB, free: 32.03 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.689e-05/0.3463, allocations: 13.17 kB / 432 MB, free: 32.03 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.249e-05/0.3463, allocations: 13.77 kB / 432 MB, free: 32.03 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 5.267e-05/0.3464, allocations: 114.6 kB / 432.1 MB, free: 31.95 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.2e-07/0.3464, allocations: 1.125 kB / 432.1 MB, free: 31.95 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0003086/0.3467, allocations: 63.88 kB / 432.2 MB, free: 31.95 MB / 350.1 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 (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 7.395e-05/0.3468, allocations: 105.7 kB / 432.3 MB, free: 31.86 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002994/0.3471, allocations: 248.2 kB / 432.5 MB, free: 31.86 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 1.903e-06/0.3471, allocations: 0 / 432.5 MB, free: 31.86 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001122/0.3472, allocations: 107.8 kB / 432.6 MB, free: 31.86 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003082/0.3475, allocations: 22.94 kB / 432.6 MB, free: 31.86 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001312/0.3489, allocations: 0.927 MB / 433.6 MB, free: 31.31 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001777/0.3491, allocations: 0.7701 MB / 434.3 MB, free: 30.61 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0001184/0.3492, allocations: 22.48 kB / 434.4 MB, free: 30.61 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.281e-05/0.3492, allocations: 24.45 kB / 434.4 MB, free: 30.6 MB / 350.1 MB
Notification: Performance of SimCode: time 4.01e-07/0.3492, allocations: 0 / 434.4 MB, free: 30.6 MB / 350.1 MB
Notification: Performance of Templates: time 0.004046/0.3533, allocations: 1.847 MB / 436.2 MB, free: 30.52 MB / 350.1 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)