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 0.001098/0.001098, allocations: 107.4 kB / 16.36 MB, free: 6.285 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001089/0.001089, allocations: 192.5 kB / 17.29 MB, free: 5.863 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.403/1.403, allocations: 222.9 MB / 241 MB, free: 15.19 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1197/0.1197, allocations: 12.28 MB / 303.4 MB, free: 3.242 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001291/0.001291, allocations: 63.91 kB / 367.2 MB, free: 3.383 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2318/0.2331, allocations: 52.09 MB / 419.3 MB, free: 21.66 MB / 302.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.005122/0.2383, allocations: 4.306 MB / 423.6 MB, free: 17.36 MB / 302.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003082/0.2387, allocations: 306.4 kB / 423.9 MB, free: 17.06 MB / 302.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001146/0.2388, allocations: 16.53 kB / 423.9 MB, free: 17.04 MB / 302.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001087/0.2389, allocations: 56.47 kB / 424 MB, free: 16.99 MB / 302.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001845/0.2391, allocations: 73.16 kB / 424 MB, free: 16.92 MB / 302.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.000212/0.2393, allocations: 63.91 kB / 424.1 MB, free: 16.86 MB / 302.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002487/0.2396, allocations: 300.3 kB / 424.4 MB, free: 16.56 MB / 302.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003191/0.2399, allocations: 165.2 kB / 424.5 MB, free: 16.41 MB / 302.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001004/0.24, allocations: 124.8 kB / 424.7 MB, free: 16.29 MB / 302.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001921/0.2402, allocations: 159.2 kB / 424.8 MB, free: 16.13 MB / 302.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.652e-05/0.2403, allocations: 35.98 kB / 424.9 MB, free: 16.09 MB / 302.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 4.633e-05/0.2403, allocations: 36 kB / 424.9 MB, free: 16.06 MB / 302.1 MB
Notification: Performance of NFScalarize.scalarize: time 5.899e-05/0.2404, allocations: 76.69 kB / 425 MB, free: 15.98 MB / 302.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001337/0.2405, allocations: 155.2 kB / 425.1 MB, free: 15.83 MB / 302.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002869/0.2408, allocations: 357 kB / 425.5 MB, free: 15.49 MB / 302.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.221e-06/0.2408, allocations: 4 kB / 425.5 MB, free: 15.48 MB / 302.1 MB
Notification: Performance of FrontEnd: time 2.215e-06/0.2408, allocations: 1.75 kB / 425.5 MB, free: 15.48 MB / 302.1 MB
Notification: Performance of Transformations before backend: time 1.364e-05/0.2409, allocations: 0 / 425.5 MB, free: 15.48 MB / 302.1 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 0.0007819/0.2417, allocations: 0.6081 MB / 426.1 MB, free: 14.83 MB / 302.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.514e-05/0.2417, allocations: 8.031 kB / 426.1 MB, free: 14.82 MB / 302.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.613e-05/0.2418, allocations: 45.03 kB / 426.1 MB, free: 14.78 MB / 302.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000118/0.2419, allocations: 203.9 kB / 426.3 MB, free: 14.54 MB / 302.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.393e-05/0.2419, allocations: 26.12 kB / 426.4 MB, free: 14.52 MB / 302.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.286e-05/0.242, allocations: 42.03 kB / 426.4 MB, free: 14.48 MB / 302.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003895/0.2424, allocations: 315.1 kB / 426.7 MB, free: 14.16 MB / 302.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.768e-05/0.2424, allocations: 192 / 426.7 MB, free: 14.16 MB / 302.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.722e-05/0.2424, allocations: 19.94 kB / 426.7 MB, free: 14.14 MB / 302.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.775e-06/0.2424, allocations: 12.72 kB / 426.7 MB, free: 14.13 MB / 302.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002951/0.2427, allocations: 239.9 kB / 427 MB, free: 13.89 MB / 302.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001383/0.2441, allocations: 1.022 MB / 428 MB, free: 12.83 MB / 302.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.000265/0.2444, allocations: 186 kB / 428.2 MB, free: 12.64 MB / 302.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001431/0.2446, allocations: 124.8 kB / 428.3 MB, free: 12.52 MB / 302.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.986e-05/0.2446, allocations: 4 kB / 428.3 MB, free: 12.51 MB / 302.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.845e-05/0.2446, allocations: 30.94 kB / 428.3 MB, free: 12.47 MB / 302.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.763e-06/0.2446, allocations: 0 / 428.3 MB, free: 12.47 MB / 302.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001601/0.2462, allocations: 0.8999 MB / 429.2 MB, free: 11.53 MB / 302.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.801e-05/0.2463, allocations: 57.91 kB / 429.3 MB, free: 11.46 MB / 302.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.649e-05/0.2464, allocations: 163.3 kB / 429.4 MB, free: 11.29 MB / 302.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.577e-05/0.2464, allocations: 29.7 kB / 429.5 MB, free: 11.25 MB / 302.1 MB
Notification: Performance of collectInitialEqns (initialization): time 6.486e-05/0.2465, allocations: 215.4 kB / 429.7 MB, free: 11.04 MB / 302.1 MB
Notification: Performance of collectInitialBindings (initialization): time 3.919e-05/0.2465, allocations: 90.66 kB / 429.8 MB, free: 10.95 MB / 302.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.715e-05/0.2466, allocations: 66.95 kB / 429.8 MB, free: 10.88 MB / 302.1 MB
Notification: Performance of setup shared object (initialization): time 5.005e-05/0.2466, allocations: 330.8 kB / 430.2 MB, free: 10.55 MB / 302.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001032/0.2468, allocations: 84.34 kB / 430.2 MB, free: 10.46 MB / 302.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001369/0.2469, allocations: 191.4 kB / 430.4 MB, free: 10.23 MB / 302.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.002647/0.2495, allocations: 0.8281 MB / 431.3 MB, free: 9.363 MB / 302.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.623e-06/0.2496, allocations: 0 / 431.3 MB, free: 9.363 MB / 302.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0003627/0.2499, allocations: 345.5 kB / 431.6 MB, free: 9.02 MB / 302.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.38e-05/0.2499, allocations: 11.98 kB / 431.6 MB, free: 9.008 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.724e-06/0.25, allocations: 4 kB / 431.6 MB, free: 9.004 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.776e-05/0.25, allocations: 4 kB / 431.6 MB, free: 9 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000265/0.2503, allocations: 79.84 kB / 431.7 MB, free: 8.922 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.357e-06/0.2503, allocations: 4 kB / 431.7 MB, free: 8.918 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001275/0.2504, allocations: 12 kB / 431.7 MB, free: 8.906 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.731e-05/0.2504, allocations: 15.94 kB / 431.7 MB, free: 8.891 MB / 302.1 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 0.000229/0.2507, allocations: 182.6 kB / 431.9 MB, free: 8.707 MB / 302.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.683e-05/0.2507, allocations: 15.81 kB / 431.9 MB, free: 8.691 MB / 302.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.687e-05/0.2508, allocations: 33.86 kB / 432 MB, free: 8.656 MB / 302.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.866e-06/0.2508, allocations: 4 kB / 432 MB, free: 8.652 MB / 302.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.813e-06/0.2508, allocations: 4 kB / 432 MB, free: 8.648 MB / 302.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.988e-06/0.2508, allocations: 0 / 432 MB, free: 8.648 MB / 302.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003417/0.2511, allocations: 373.4 kB / 432.3 MB, free: 8.234 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.293e-06/0.2512, allocations: 3.938 kB / 432.3 MB, free: 8.23 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002351/0.2514, allocations: 47.91 kB / 432.4 MB, free: 8.184 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.024e-06/0.2514, allocations: 0 / 432.4 MB, free: 8.184 MB / 302.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.78e-05/0.2514, allocations: 8 kB / 432.4 MB, free: 8.176 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.633e-06/0.2514, allocations: 0 / 432.4 MB, free: 8.176 MB / 302.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.82e-07/0.2514, allocations: 0 / 432.4 MB, free: 8.176 MB / 302.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003926/0.2518, allocations: 439.1 kB / 432.8 MB, free: 7.73 MB / 302.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.834e-05/0.2519, allocations: 92.83 kB / 432.9 MB, free: 7.621 MB / 302.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.822e-05/0.2519, allocations: 8.062 kB / 432.9 MB, free: 7.613 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001309/0.252, allocations: 0 / 432.9 MB, free: 7.613 MB / 302.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.578e-05/0.2521, allocations: 19.97 kB / 432.9 MB, free: 7.594 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.166e-05/0.2521, allocations: 4 kB / 432.9 MB, free: 7.59 MB / 302.1 MB
Notification: Performance of sorting global known variables: time 4.835e-05/0.2522, allocations: 116 kB / 433.1 MB, free: 7.477 MB / 302.1 MB
Notification: Performance of sort global known variables: time 1.21e-07/0.2522, allocations: 3.938 kB / 433.1 MB, free: 7.473 MB / 302.1 MB
Notification: Performance of remove unused functions: time 0.0002935/0.2525, allocations: 64 kB / 433.1 MB, free: 7.41 MB / 302.1 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 7.499e-05/0.2525, allocations: 103.2 kB / 433.2 MB, free: 7.297 MB / 302.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003011/0.2528, allocations: 239.7 kB / 433.5 MB, free: 7.062 MB / 302.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.364e-06/0.2529, allocations: 4 kB / 433.5 MB, free: 7.059 MB / 302.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001092/0.253, allocations: 112.8 kB / 433.6 MB, free: 6.949 MB / 302.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002815/0.2533, allocations: 27.92 kB / 433.6 MB, free: 6.922 MB / 302.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0009488/0.2542, allocations: 0.7212 MB / 434.3 MB, free: 6.176 MB / 302.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001501/0.2544, allocations: 0.7713 MB / 435.1 MB, free: 5.379 MB / 302.1 MB
Notification: Performance of simCode: alias equations: time 8.588e-05/0.2545, allocations: 29.94 kB / 435.1 MB, free: 5.348 MB / 302.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.981e-05/0.2545, allocations: 19.44 kB / 435.1 MB, free: 5.328 MB / 302.1 MB
Notification: Performance of SimCode: time 3e-07/0.2545, allocations: 3.938 kB / 435.1 MB, free: 5.324 MB / 302.1 MB
Notification: Performance of Templates: time 0.00417/0.2587, allocations: 2.036 MB / 437.2 MB, free: 3.301 MB / 302.1 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 -s cvode -lv LOG_STATS > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1)