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) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001623/0.001623, allocations: 110.1 kB / 17.13 MB, free: 6.008 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001631/0.001631, allocations: 194.6 kB / 20.08 MB, free: 3.074 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.459/1.459, allocations: 225.6 MB / 248.5 MB, free: 3.637 MB / 190.1 MB
"
[Timeout remaining time 178]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1182/0.1182, allocations: 12.41 MB / 315.8 MB, free: 304 kB / 238.1 MB
"
[Timeout remaining time 180]
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=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell")
translateModel(BioChem.Examples.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell") [Timeout 660]
"Warning: Ignoring unknown experiment annotation option: Algorithm = \"dassl\"
Notification: Performance of FrontEnd - loaded program: time 0.002081/0.002081, allocations: 71.89 kB / 440.7 MB, free: 5.66 MB / 366.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2314/0.2335, allocations: 54.91 MB / 495.6 MB, free: 23.45 MB / 366.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.005523/0.239, allocations: 4.336 MB / 500 MB, free: 20.64 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003567/0.2393, allocations: 291.6 kB / 0.4885 GB, free: 20.43 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001112/0.2394, allocations: 16.41 kB / 0.4885 GB, free: 20.43 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 9.787e-05/0.2395, allocations: 50.47 kB / 0.4886 GB, free: 20.39 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001734/0.2397, allocations: 71.64 kB / 0.4886 GB, free: 20.33 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001883/0.2399, allocations: 76.88 kB / 0.4887 GB, free: 20.29 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0003003/0.2402, allocations: 295 kB / 0.489 GB, free: 20.15 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002209/0.2404, allocations: 120.2 kB / 0.4891 GB, free: 20.08 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001045/0.2405, allocations: 132.6 kB / 0.4892 GB, free: 20.02 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001732/0.2407, allocations: 159.2 kB / 0.4894 GB, free: 19.93 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 5.265e-05/0.2408, allocations: 33.5 kB / 0.4894 GB, free: 19.93 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 5.03e-05/0.2408, allocations: 33.22 kB / 0.4895 GB, free: 19.93 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 7.916e-05/0.2409, allocations: 70.22 kB / 0.4895 GB, free: 19.89 MB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001232/0.241, allocations: 171.1 kB / 0.4897 GB, free: 19.78 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0003056/0.2413, allocations: 365.2 kB / 0.49 GB, free: 19.62 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 2.916e-06/0.2413, allocations: 0 / 0.49 GB, free: 19.62 MB / 366.1 MB
Notification: Performance of FrontEnd: time 1.673e-06/0.2413, allocations: 1.438 kB / 0.49 GB, free: 19.62 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 6.763e-06/0.2413, allocations: 0 / 0.49 GB, free: 19.62 MB / 366.1 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 0.0008309/0.2422, allocations: 0.6122 MB / 0.4906 GB, free: 19.12 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.246e-05/0.2422, allocations: 9.5 kB / 0.4906 GB, free: 19.12 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.962e-05/0.2423, allocations: 42.02 kB / 0.4907 GB, free: 19.09 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001033/0.2424, allocations: 206.8 kB / 0.4909 GB, free: 18.87 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.276e-05/0.2424, allocations: 28.78 kB / 0.4909 GB, free: 18.86 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.266e-05/0.2424, allocations: 41 kB / 0.491 GB, free: 18.84 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005074/0.243, allocations: 312.7 kB / 0.4912 GB, free: 18.7 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.83e-05/0.243, allocations: 1.375 kB / 0.4913 GB, free: 18.7 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.947e-05/0.243, allocations: 19.12 kB / 0.4913 GB, free: 18.68 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.758e-06/0.243, allocations: 8.906 kB / 0.4913 GB, free: 18.68 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003666/0.2434, allocations: 242.8 kB / 0.4915 GB, free: 18.57 MB / 366.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001687/0.2451, allocations: 1.034 MB / 0.4925 GB, free: 17.78 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003205/0.2454, allocations: 167.3 kB / 0.4927 GB, free: 17.69 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001615/0.2455, allocations: 110.4 kB / 0.4928 GB, free: 17.63 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.769e-05/0.2456, allocations: 6.609 kB / 0.4928 GB, free: 17.63 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.258e-05/0.2456, allocations: 32.47 kB / 0.4928 GB, free: 17.59 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.302e-06/0.2456, allocations: 0 / 0.4928 GB, free: 17.59 MB / 366.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001928/0.2475, allocations: 0.9005 MB / 0.4937 GB, free: 17 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.096e-05/0.2475, allocations: 58.53 kB / 0.4938 GB, free: 16.93 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001074/0.2476, allocations: 168.4 kB / 0.4939 GB, free: 16.79 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.554e-05/0.2477, allocations: 30.77 kB / 0.4939 GB, free: 16.75 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 6.632e-05/0.2477, allocations: 213.3 kB / 0.4941 GB, free: 16.55 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.833e-05/0.2478, allocations: 110.8 kB / 0.4943 GB, free: 16.46 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.544e-05/0.2479, allocations: 58.17 kB / 0.4943 GB, free: 16.42 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 5.009e-05/0.2479, allocations: 326.8 kB / 0.4946 GB, free: 16.09 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001394/0.248, allocations: 88.11 kB / 0.4947 GB, free: 16.05 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001786/0.2482, allocations: 190 kB / 0.4949 GB, free: 15.87 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.00315/0.2514, allocations: 0.8308 MB / 0.4957 GB, free: 15.38 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.344e-06/0.2514, allocations: 1.062 kB / 0.4957 GB, free: 15.38 MB / 366.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0004888/0.2519, allocations: 345.8 kB / 0.496 GB, free: 15.2 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.688e-05/0.2519, allocations: 6.031 kB / 0.496 GB, free: 15.2 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.256e-06/0.2519, allocations: 8 kB / 0.496 GB, free: 15.19 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.036e-05/0.2519, allocations: 9.969 kB / 0.4961 GB, free: 15.19 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003079/0.2522, allocations: 74 kB / 0.4961 GB, free: 15.18 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.116e-05/0.2522, allocations: 9.484 kB / 0.4961 GB, free: 15.17 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001475/0.2524, allocations: 12.34 kB / 0.4961 GB, free: 15.16 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.213e-05/0.2524, allocations: 17.06 kB / 0.4962 GB, free: 15.16 MB / 366.1 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 0.0002534/0.2526, allocations: 176 kB / 0.4963 GB, free: 15 MB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.397e-05/0.2527, allocations: 19.58 kB / 0.4963 GB, free: 14.99 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.654e-05/0.2528, allocations: 29.94 kB / 0.4964 GB, free: 14.96 MB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.316e-06/0.2528, allocations: 2.562 kB / 0.4964 GB, free: 14.96 MB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.831e-06/0.2528, allocations: 0 / 0.4964 GB, free: 14.96 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.709e-06/0.2528, allocations: 7.969 kB / 0.4964 GB, free: 14.95 MB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003887/0.2532, allocations: 370.5 kB / 0.4967 GB, free: 14.63 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.532e-06/0.2532, allocations: 4 kB / 0.4967 GB, free: 14.62 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002885/0.2535, allocations: 47.38 kB / 0.4968 GB, free: 14.61 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.655e-06/0.2535, allocations: 1.094 kB / 0.4968 GB, free: 14.61 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.999e-05/0.2535, allocations: 10.56 kB / 0.4968 GB, free: 14.61 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.275e-06/0.2535, allocations: 0.875 kB / 0.4968 GB, free: 14.61 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.714e-06/0.2535, allocations: 3.984 kB / 0.4968 GB, free: 14.6 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004776/0.254, allocations: 426.9 kB / 0.4972 GB, free: 14.32 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.834e-05/0.254, allocations: 97.52 kB / 0.4973 GB, free: 14.21 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.949e-05/0.254, allocations: 10.25 kB / 0.4973 GB, free: 14.21 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001643/0.2542, allocations: 5.188 kB / 0.4973 GB, free: 14.2 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.976e-05/0.2542, allocations: 15.77 kB / 0.4973 GB, free: 14.2 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.462e-05/0.2542, allocations: 8.391 kB / 0.4973 GB, free: 14.19 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 6.057e-05/0.2543, allocations: 118.7 kB / 0.4975 GB, free: 14.1 MB / 366.1 MB
Notification: Performance of sort global known variables: time 9e-08/0.2543, allocations: 1.062 kB / 0.4975 GB, free: 14.1 MB / 366.1 MB
Notification: Performance of remove unused functions: time 0.0003448/0.2546, allocations: 62.81 kB / 0.4975 GB, free: 14.09 MB / 366.1 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 8.815e-05/0.2547, allocations: 96.22 kB / 0.4976 GB, free: 14 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003739/0.2551, allocations: 234.2 kB / 0.4978 GB, free: 13.89 MB / 366.1 MB
Notification: Performance of simCode: created event and clocks part: time 1.683e-06/0.2551, allocations: 0 / 0.4978 GB, free: 13.89 MB / 366.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001323/0.2552, allocations: 105 kB / 0.4979 GB, free: 13.85 MB / 366.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002998/0.2555, allocations: 22.16 kB / 0.498 GB, free: 13.84 MB / 366.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001148/0.2567, allocations: 0.7746 MB / 0.4987 GB, free: 13.25 MB / 366.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002112/0.2569, allocations: 0.7651 MB / 0.4995 GB, free: 12.52 MB / 366.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 9.085e-05/0.257, allocations: 27.42 kB / 0.4995 GB, free: 12.52 MB / 366.1 MB
Notification: Performance of SimCode: time 4.31e-07/0.257, allocations: 0 / 0.4995 GB, free: 12.52 MB / 366.1 MB
Notification: Performance of Templates: time 0.00447/0.2615, allocations: 2.876 MB / 0.5023 GB, free: 11 MB / 366.1 MB
"
[Timeout remaining time 660]
make -j1 -f BioChem_BioChem.Examples.GMO.cell.makefile [Timeout 660]
(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) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 7.244272356037982]
Failed to read output from testmodel.py, exit status != 0:
0.2690406140172854 0.27741169299999996 0.034005709
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7f08ba5757e0>