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 0.001638/0.001637, allocations: 112.6 kB / 16.37 MB, free: 6 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001229/0.001229, allocations: 196 kB / 17.31 MB, free: 5.613 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.325/1.325, allocations: 222.9 MB / 241 MB, free: 15.16 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1711/0.1711, allocations: 12.26 MB / 303.4 MB, free: 3.219 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001312/0.001312, allocations: 63.91 kB / 367.2 MB, free: 3.359 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2017/0.203, allocations: 52.09 MB / 419.3 MB, free: 21.67 MB / 302.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.005309/0.2084, allocations: 4.312 MB / 423.6 MB, free: 17.36 MB / 302.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0002703/0.2086, allocations: 304.8 kB / 423.9 MB, free: 17.06 MB / 302.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 9.627e-05/0.2087, allocations: 16 kB / 423.9 MB, free: 17.05 MB / 302.1 MB
Notification: Performance of NFTyping.typeComponents: time 9.284e-05/0.2088, allocations: 47.61 kB / 424 MB, free: 17 MB / 302.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001422/0.209, allocations: 71.28 kB / 424 MB, free: 16.93 MB / 302.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001657/0.2092, allocations: 68.95 kB / 424.1 MB, free: 16.86 MB / 302.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0001931/0.2094, allocations: 303.1 kB / 424.4 MB, free: 16.57 MB / 302.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002401/0.2096, allocations: 167.7 kB / 424.6 MB, free: 16.41 MB / 302.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 9.279e-05/0.2097, allocations: 119.6 kB / 424.7 MB, free: 16.29 MB / 302.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001482/0.2099, allocations: 159.3 kB / 424.8 MB, free: 16.14 MB / 302.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.194e-05/0.2099, allocations: 32 kB / 424.9 MB, free: 16.11 MB / 302.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.868e-05/0.21, allocations: 36 kB / 424.9 MB, free: 16.07 MB / 302.1 MB
Notification: Performance of NFScalarize.scalarize: time 4.733e-05/0.21, allocations: 67.77 kB / 425 MB, free: 16 MB / 302.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001126/0.2102, allocations: 168.1 kB / 425.1 MB, free: 15.84 MB / 302.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002344/0.2104, allocations: 360.4 kB / 425.5 MB, free: 15.49 MB / 302.1 MB
Notification: Performance of FrontEnd - DAE generated: time 3.577e-06/0.2104, allocations: 9.25 kB / 425.5 MB, free: 15.48 MB / 302.1 MB
Notification: Performance of FrontEnd: time 7.31e-07/0.2104, allocations: 0 / 425.5 MB, free: 15.48 MB / 302.1 MB
Notification: Performance of Transformations before backend: time 6.873e-06/0.2104, 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 0.0007569/0.2112, allocations: 0.6044 MB / 426.1 MB, free: 14.83 MB / 302.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.277e-05/0.2112, allocations: 8.625 kB / 426.1 MB, free: 14.82 MB / 302.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.753e-05/0.2113, allocations: 37.09 kB / 426.1 MB, free: 14.79 MB / 302.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001127/0.2114, allocations: 202.8 kB / 426.3 MB, free: 14.55 MB / 302.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.336e-05/0.2115, allocations: 27.03 kB / 426.4 MB, free: 14.53 MB / 302.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.692e-05/0.2115, allocations: 40.38 kB / 426.4 MB, free: 14.49 MB / 302.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004105/0.2119, allocations: 315 kB / 426.7 MB, free: 14.18 MB / 302.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.502e-05/0.212, allocations: 192 / 426.7 MB, free: 14.18 MB / 302.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.671e-05/0.212, allocations: 20.84 kB / 426.7 MB, free: 14.16 MB / 302.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.063e-05/0.212, allocations: 8 kB / 426.7 MB, free: 14.15 MB / 302.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003272/0.2123, allocations: 240.8 kB / 427 MB, free: 13.91 MB / 302.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001477/0.2138, allocations: 1.033 MB / 428 MB, free: 12.84 MB / 302.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002992/0.2141, allocations: 187.5 kB / 428.2 MB, free: 12.65 MB / 302.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001526/0.2143, allocations: 124.8 kB / 428.3 MB, free: 12.52 MB / 302.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.436e-05/0.2143, allocations: 4 kB / 428.3 MB, free: 12.52 MB / 302.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.47e-05/0.2144, allocations: 37.44 kB / 428.4 MB, free: 12.48 MB / 302.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.362e-06/0.2144, allocations: 0 / 428.4 MB, free: 12.48 MB / 302.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001754/0.2161, allocations: 0.8971 MB / 429.3 MB, free: 11.54 MB / 302.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.217e-05/0.2162, allocations: 55.41 kB / 429.3 MB, free: 11.47 MB / 302.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.82e-05/0.2163, allocations: 163.3 kB / 429.5 MB, free: 11.3 MB / 302.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.516e-05/0.2163, allocations: 25.7 kB / 429.5 MB, free: 11.27 MB / 302.1 MB
Notification: Performance of collectInitialEqns (initialization): time 6.792e-05/0.2164, allocations: 215 kB / 429.7 MB, free: 11.05 MB / 302.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.313e-05/0.2164, allocations: 98.62 kB / 429.8 MB, free: 10.96 MB / 302.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.016e-05/0.2165, allocations: 65.61 kB / 429.9 MB, free: 10.89 MB / 302.1 MB
Notification: Performance of setup shared object (initialization): time 5.365e-05/0.2165, allocations: 330.8 kB / 430.2 MB, free: 10.55 MB / 302.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001087/0.2167, allocations: 84.34 kB / 430.3 MB, free: 10.47 MB / 302.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001463/0.2168, allocations: 192.2 kB / 430.5 MB, free: 10.24 MB / 302.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.002881/0.2197, allocations: 0.8236 MB / 431.3 MB, free: 9.367 MB / 302.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.874e-06/0.2197, allocations: 0 / 431.3 MB, free: 9.367 MB / 302.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.000381/0.2201, allocations: 341.1 kB / 431.6 MB, free: 9.027 MB / 302.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.38e-05/0.2201, allocations: 8 kB / 431.6 MB, free: 9.02 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.893e-06/0.2201, allocations: 7.938 kB / 431.6 MB, free: 9.012 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.634e-05/0.2202, allocations: 4.469 kB / 431.6 MB, free: 9.008 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002835/0.2204, allocations: 91.83 kB / 431.7 MB, free: 8.918 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.228e-06/0.2205, allocations: 4 kB / 431.7 MB, free: 8.914 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001363/0.2206, allocations: 12 kB / 431.7 MB, free: 8.902 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.031e-05/0.2206, allocations: 12 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 0.0002572/0.2209, allocations: 179.5 kB / 431.9 MB, free: 8.707 MB / 302.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.834e-05/0.2209, allocations: 15.81 kB / 431.9 MB, free: 8.691 MB / 302.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.11e-05/0.221, allocations: 29.88 kB / 432 MB, free: 8.66 MB / 302.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.458e-06/0.221, allocations: 7.984 kB / 432 MB, free: 8.652 MB / 302.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.561e-06/0.221, allocations: 3.938 kB / 432 MB, free: 8.648 MB / 302.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.757e-06/0.221, allocations: 0 / 432 MB, free: 8.648 MB / 302.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003573/0.2214, allocations: 361.4 kB / 432.3 MB, free: 8.246 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.563e-06/0.2214, allocations: 0 / 432.3 MB, free: 8.246 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002549/0.2217, allocations: 55.91 kB / 432.4 MB, free: 8.191 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.364e-06/0.2217, allocations: 0 / 432.4 MB, free: 8.191 MB / 302.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.014e-05/0.2217, allocations: 11.98 kB / 432.4 MB, free: 8.18 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.114e-06/0.2217, allocations: 0 / 432.4 MB, free: 8.18 MB / 302.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.413e-06/0.2217, allocations: 0 / 432.4 MB, free: 8.18 MB / 302.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004253/0.2222, allocations: 435.1 kB / 432.8 MB, free: 7.738 MB / 302.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.082e-05/0.2222, allocations: 92.83 kB / 432.9 MB, free: 7.629 MB / 302.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.85e-05/0.2222, allocations: 4.062 kB / 432.9 MB, free: 7.625 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001387/0.2224, allocations: 8 kB / 432.9 MB, free: 7.617 MB / 302.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.463e-05/0.2224, allocations: 23.91 kB / 433 MB, free: 7.594 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.22e-05/0.2224, allocations: 4 kB / 433 MB, free: 7.59 MB / 302.1 MB
Notification: Performance of sorting global known variables: time 5.482e-05/0.2225, allocations: 116 kB / 433.1 MB, free: 7.477 MB / 302.1 MB
Notification: Performance of sort global known variables: time 1e-07/0.2225, allocations: 0 / 433.1 MB, free: 7.477 MB / 302.1 MB
Notification: Performance of remove unused functions: time 0.0003121/0.2228, allocations: 64 kB / 433.1 MB, free: 7.414 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 9.181e-05/0.2229, allocations: 95.25 kB / 433.2 MB, free: 7.309 MB / 302.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003233/0.2232, allocations: 243.9 kB / 433.5 MB, free: 7.07 MB / 302.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.695e-06/0.2233, allocations: 4 kB / 433.5 MB, free: 7.066 MB / 302.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001167/0.2234, allocations: 115.8 kB / 433.6 MB, free: 6.953 MB / 302.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000303/0.2237, allocations: 19.94 kB / 433.6 MB, free: 6.934 MB / 302.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001003/0.2247, allocations: 0.7414 MB / 434.3 MB, free: 6.168 MB / 302.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001505/0.2249, allocations: 0.7675 MB / 435.1 MB, free: 5.375 MB / 302.1 MB
Notification: Performance of simCode: alias equations: time 8.618e-05/0.225, allocations: 21.95 kB / 435.1 MB, free: 5.352 MB / 302.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.152e-05/0.225, allocations: 23.42 kB / 435.2 MB, free: 5.328 MB / 302.1 MB
Notification: Performance of SimCode: time 2.21e-07/0.225, allocations: 3.938 kB / 435.2 MB, free: 5.324 MB / 302.1 MB
Notification: Performance of Templates: time 0.004053/0.2291, allocations: 2.035 MB / 437.2 MB, free: 3.305 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 gbode -lv LOG_STATS > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1)