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 0.0007326/0.0007326, allocations: 98.88 kB / 16.02 MB, free: 76 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.0007917/0.0007917, allocations: 185.5 kB / 16.92 MB, free: 6.684 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.297/1.297, allocations: 223.3 MB / 241 MB, free: 5.344 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1669/0.1669, allocations: 12.25 MB / 304.3 MB, free: 2.094 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0002691/0.0002691, allocations: 4 kB / 368.2 MB, free: 9.461 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.07868/0.07896, allocations: 53.09 MB / 421.3 MB, free: 4.262 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.004816/0.08379, allocations: 3.975 MB / 425.3 MB, free: 276 kB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.1476/0.2314, allocations: 306.8 kB / 425.6 MB, free: 35.27 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002138/0.2316, allocations: 17.34 kB / 425.6 MB, free: 35.27 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.000121/0.2318, allocations: 35.98 kB / 425.6 MB, free: 35.27 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.00021/0.232, allocations: 59.19 kB / 425.7 MB, free: 35.27 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001883/0.2322, allocations: 58.86 kB / 425.7 MB, free: 35.27 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002262/0.2324, allocations: 285 kB / 426 MB, free: 35.27 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002244/0.2326, allocations: 141.5 kB / 426.1 MB, free: 35.27 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 9.934e-05/0.2328, allocations: 97.83 kB / 426.2 MB, free: 35.27 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001613/0.2329, allocations: 129.4 kB / 426.4 MB, free: 35.25 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.155e-05/0.233, allocations: 14.41 kB / 426.4 MB, free: 35.25 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.712e-05/0.233, allocations: 16.34 kB / 426.4 MB, free: 35.25 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 4.86e-05/0.2331, allocations: 52.7 kB / 426.4 MB, free: 35.23 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001136/0.2332, allocations: 162.2 kB / 426.6 MB, free: 35.16 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002124/0.2334, allocations: 252.3 kB / 426.9 MB, free: 35.15 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.068e-06/0.2334, allocations: 0.7188 kB / 426.9 MB, free: 35.15 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.924e-06/0.2334, allocations: 1 kB / 426.9 MB, free: 35.15 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 8.025e-06/0.2334, allocations: 0.75 kB / 426.9 MB, free: 35.15 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 0.0006996/0.2341, allocations: 0.5504 MB / 427.4 MB, free: 34.71 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.345e-05/0.2342, allocations: 10.06 kB / 427.4 MB, free: 34.71 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.319e-05/0.2343, allocations: 33.88 kB / 427.4 MB, free: 34.7 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 8.956e-05/0.2344, allocations: 207.2 kB / 427.7 MB, free: 34.48 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.566e-05/0.2344, allocations: 26 kB / 427.7 MB, free: 34.48 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.733e-05/0.2344, allocations: 41.62 kB / 427.7 MB, free: 34.48 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004523/0.2349, allocations: 305.4 kB / 428 MB, free: 34.44 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.541e-05/0.2349, allocations: 2.438 kB / 428 MB, free: 34.44 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.947e-05/0.235, allocations: 21.62 kB / 428 MB, free: 34.44 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.316e-06/0.235, allocations: 8.844 kB / 428 MB, free: 34.44 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003416/0.2353, allocations: 240.5 kB / 428.3 MB, free: 34.43 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001492/0.2368, allocations: 1.041 MB / 429.3 MB, free: 34.09 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002893/0.2371, allocations: 184.7 kB / 429.5 MB, free: 34.07 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001583/0.2373, allocations: 118.4 kB / 429.6 MB, free: 34.06 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.41e-05/0.2373, allocations: 4 kB / 429.6 MB, free: 34.06 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.684e-05/0.2373, allocations: 39.83 kB / 429.7 MB, free: 34.02 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.503e-06/0.2373, allocations: 0 / 429.7 MB, free: 34.02 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001778/0.2391, allocations: 0.8906 MB / 430.6 MB, free: 33.71 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.229e-05/0.2392, allocations: 58.22 kB / 430.6 MB, free: 33.65 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.559e-05/0.2393, allocations: 168 kB / 430.8 MB, free: 33.54 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.555e-05/0.2393, allocations: 29.2 kB / 430.8 MB, free: 33.51 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 6.179e-05/0.2394, allocations: 210.6 kB / 431 MB, free: 33.35 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.43e-05/0.2394, allocations: 102.6 kB / 431.1 MB, free: 33.29 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 3.818e-05/0.2395, allocations: 32.41 kB / 431.1 MB, free: 33.27 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 4.018e-05/0.2395, allocations: 333.8 kB / 431.5 MB, free: 32.96 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001192/0.2396, allocations: 83.25 kB / 431.5 MB, free: 32.96 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001447/0.2398, allocations: 195 kB / 431.7 MB, free: 32.83 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003412/0.2432, allocations: 0.8532 MB / 432.6 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.275e-06/0.2432, allocations: 3.656 kB / 432.6 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0004176/0.2436, allocations: 344.2 kB / 432.9 MB, free: 32.65 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.34e-05/0.2437, allocations: 6.344 kB / 432.9 MB, free: 32.65 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.772e-06/0.2437, allocations: 7.375 kB / 432.9 MB, free: 32.65 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.48e-05/0.2437, allocations: 5.688 kB / 432.9 MB, free: 32.65 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002989/0.244, allocations: 81.61 kB / 433 MB, free: 32.65 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.866e-06/0.244, allocations: 7.438 kB / 433 MB, free: 32.65 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000166/0.2442, allocations: 16.86 kB / 433.1 MB, free: 32.65 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.874e-05/0.2442, allocations: 16.28 kB / 433.1 MB, free: 32.65 MB / 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 0.0001826/0.2444, allocations: 168.7 kB / 433.2 MB, free: 32.53 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.1e-05/0.2444, allocations: 23.33 kB / 433.3 MB, free: 32.51 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.828e-05/0.2445, allocations: 32.78 kB / 433.3 MB, free: 32.5 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.806e-06/0.2445, allocations: 2.906 kB / 433.3 MB, free: 32.5 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.979e-06/0.2445, allocations: 5.031 kB / 433.3 MB, free: 32.5 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.987e-06/0.2446, allocations: 4.219 kB / 433.3 MB, free: 32.5 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000366/0.2449, allocations: 365.9 kB / 433.7 MB, free: 32.31 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.751e-06/0.2449, allocations: 0 / 433.7 MB, free: 32.31 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002684/0.2452, allocations: 48.05 kB / 433.7 MB, free: 32.3 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.906e-06/0.2452, allocations: 1.172 kB / 433.7 MB, free: 32.3 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.681e-05/0.2452, allocations: 7 kB / 433.7 MB, free: 32.3 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.835e-06/0.2453, allocations: 3.719 kB / 433.7 MB, free: 32.3 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.052e-06/0.2453, allocations: 0.625 kB / 433.7 MB, free: 32.3 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000469/0.2457, allocations: 437.4 kB / 434.1 MB, free: 32.15 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.938e-05/0.2458, allocations: 87.89 kB / 434.2 MB, free: 32.05 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.126e-05/0.2458, allocations: 7.781 kB / 434.2 MB, free: 32.05 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001666/0.246, allocations: 17.78 kB / 434.3 MB, free: 32.04 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.279e-05/0.246, allocations: 13.36 kB / 434.3 MB, free: 32.04 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.445e-05/0.246, allocations: 8.25 kB / 434.3 MB, free: 32.04 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 6.26e-05/0.2461, allocations: 115.4 kB / 434.4 MB, free: 31.97 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.5e-07/0.2461, allocations: 4 kB / 434.4 MB, free: 31.96 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0003443/0.2465, allocations: 64.78 kB / 434.5 MB, free: 31.96 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 (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 7.668e-05/0.2466, allocations: 102.8 kB / 434.6 MB, free: 31.87 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003805/0.2469, allocations: 246.4 kB / 434.8 MB, free: 31.86 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.284e-06/0.2469, allocations: 0 / 434.8 MB, free: 31.86 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001399/0.2471, allocations: 107 kB / 434.9 MB, free: 31.85 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003182/0.2474, allocations: 34.81 kB / 434.9 MB, free: 31.84 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001161/0.2486, allocations: 0.9844 MB / 435.9 MB, free: 31.21 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001609/0.2488, allocations: 0.7695 MB / 436.7 MB, free: 30.52 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 8.308e-05/0.2489, allocations: 24.55 kB / 436.7 MB, free: 30.51 MB / 350.1 MB
Notification: Performance of SimCode: time 3.41e-07/0.2489, allocations: 0 / 436.7 MB, free: 30.51 MB / 350.1 MB
Notification: Performance of Templates: time 0.003545/0.2524, allocations: 2.804 MB / 439.5 MB, free: 30.36 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)