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 0.001566/0.001566, allocations: 110 kB / 18.93 MB, free: 2.945 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 0.001685/0.001685, allocations: 191.4 kB / 22.23 MB, free: 5.16 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 1.402/1.402, allocations: 225.6 MB / 251 MB, free: 13.01 MB / 206.1 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 0.136/0.136, allocations: 12.43 MB / 318.7 MB, free: 12.93 MB / 254.1 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 0.001999/0.001999, allocations: 68.48 kB / 445.3 MB, free: 3.965 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1273/0.1293, allocations: 54.96 MB / 0.4885 GB, free: 12.93 MB / 366.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.007197/0.1365, allocations: 4.378 MB / 0.4928 GB, free: 8.531 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0004192/0.1369, allocations: 299.3 kB / 0.4931 GB, free: 8.238 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001154/0.137, allocations: 16 kB / 0.4931 GB, free: 8.223 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001245/0.1372, allocations: 55.53 kB / 0.4932 GB, free: 8.168 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0002015/0.1374, allocations: 75.28 kB / 0.4932 GB, free: 8.094 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002285/0.1376, allocations: 67.91 kB / 0.4933 GB, free: 8.027 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0003499/0.1379, allocations: 299.2 kB / 0.4936 GB, free: 7.734 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.000286/0.1382, allocations: 117 kB / 0.4937 GB, free: 7.621 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001438/0.1384, allocations: 131.5 kB / 0.4938 GB, free: 7.492 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002173/0.1386, allocations: 163.2 kB / 0.494 GB, free: 7.332 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.882e-05/0.1386, allocations: 32 kB / 0.494 GB, free: 7.301 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 5.614e-05/0.1387, allocations: 40 kB / 0.494 GB, free: 7.262 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 7.595e-05/0.1388, allocations: 75.75 kB / 0.4941 GB, free: 7.188 MB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001583/0.1389, allocations: 155.2 kB / 0.4943 GB, free: 7.035 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0004247/0.1393, allocations: 358.4 kB / 0.4946 GB, free: 6.684 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.893e-06/0.1394, allocations: 8 kB / 0.4946 GB, free: 6.676 MB / 366.1 MB
Notification: Performance of FrontEnd: time 2.245e-06/0.1394, allocations: 0 / 0.4946 GB, free: 6.676 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 9.077e-06/0.1394, allocations: 0 / 0.4946 GB, free: 6.676 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 0.001059/0.1404, allocations: 0.5369 MB / 0.4951 GB, free: 6.102 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.794e-05/0.1405, allocations: 8.031 kB / 0.4952 GB, free: 6.094 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.378e-05/0.1406, allocations: 36.7 kB / 0.4952 GB, free: 6.059 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001783/0.1407, allocations: 150.1 kB / 0.4953 GB, free: 5.887 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.915e-05/0.1408, allocations: 29.38 kB / 0.4954 GB, free: 5.859 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 8.06e-05/0.1409, allocations: 44.36 kB / 0.4954 GB, free: 5.816 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005417/0.1414, allocations: 303.1 kB / 0.4957 GB, free: 5.516 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.889e-05/0.1414, allocations: 192 / 0.4957 GB, free: 5.516 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.612e-05/0.1415, allocations: 19.94 kB / 0.4957 GB, free: 5.496 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.674e-05/0.1415, allocations: 8 kB / 0.4957 GB, free: 5.488 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0004381/0.1419, allocations: 239.9 kB / 0.4959 GB, free: 5.254 MB / 366.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001896/0.1438, allocations: 0.9955 MB / 0.4969 GB, free: 4.207 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003551/0.1442, allocations: 170.4 kB / 0.4971 GB, free: 4.031 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.000182/0.1444, allocations: 108.8 kB / 0.4972 GB, free: 3.922 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.201e-05/0.1444, allocations: 0 / 0.4972 GB, free: 3.922 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.121e-05/0.1444, allocations: 38.88 kB / 0.4972 GB, free: 3.875 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=22): time 3.015e-06/0.1444, allocations: 4 kB / 0.4972 GB, free: 3.871 MB / 366.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001991/0.1464, allocations: 0.8266 MB / 0.498 GB, free: 3.016 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.696e-05/0.1464, allocations: 55.41 kB / 0.4981 GB, free: 2.949 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001633/0.1466, allocations: 167.2 kB / 0.4982 GB, free: 2.77 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.495e-05/0.1466, allocations: 29.7 kB / 0.4983 GB, free: 2.734 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001444/0.1468, allocations: 219.9 kB / 0.4985 GB, free: 2.516 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 8.389e-05/0.1469, allocations: 103.2 kB / 0.4986 GB, free: 2.414 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.527e-05/0.1469, allocations: 57.7 kB / 0.4986 GB, free: 2.352 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001492/0.1471, allocations: 330.8 kB / 0.499 GB, free: 2.02 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001399/0.1472, allocations: 88.34 kB / 0.499 GB, free: 1.93 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002287/0.1475, allocations: 194.1 kB / 0.4992 GB, free: 1.691 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003053/0.1505, allocations: 0.8344 MB / 0.5 GB, free: 0.8047 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.843e-06/0.1505, allocations: 0 / 0.5 GB, free: 0.8047 MB / 366.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0005152/0.151, allocations: 341.6 kB / 0.5004 GB, free: 476 kB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.969e-05/0.1511, allocations: 12.06 kB / 0.5004 GB, free: 464 kB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.123e-05/0.1511, allocations: 8 kB / 0.5004 GB, free: 456 kB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.122e-05/0.1511, allocations: 4 kB / 0.5004 GB, free: 452 kB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003151/0.1514, allocations: 83.83 kB / 0.5005 GB, free: 368 kB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.12e-05/0.1514, allocations: 4 kB / 0.5005 GB, free: 364 kB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001378/0.1516, allocations: 12 kB / 0.5005 GB, free: 352 kB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.484e-05/0.1516, allocations: 16 kB / 0.5005 GB, free: 336 kB / 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 0.0003429/0.1519, allocations: 172.2 kB / 0.5007 GB, free: 152 kB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.857e-05/0.152, allocations: 19.86 kB / 0.5007 GB, free: 132 kB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.882e-05/0.152, allocations: 29.97 kB / 0.5007 GB, free: 104 kB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.66e-06/0.1521, allocations: 4 kB / 0.5007 GB, free: 100 kB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.504e-06/0.1521, allocations: 0 / 0.5007 GB, free: 100 kB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.601e-06/0.1521, allocations: 7.984 kB / 0.5007 GB, free: 92 kB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005011/0.1526, allocations: 344.3 kB / 0.501 GB, free: 15.71 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.242e-06/0.1526, allocations: 0 / 0.501 GB, free: 15.71 MB / 382.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002594/0.1528, allocations: 43.97 kB / 0.5011 GB, free: 15.67 MB / 382.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.264e-06/0.1528, allocations: 0 / 0.5011 GB, free: 15.67 MB / 382.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.412e-05/0.1529, allocations: 15.92 kB / 0.5011 GB, free: 15.65 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 6.762e-06/0.1529, allocations: 3.938 kB / 0.5011 GB, free: 15.65 MB / 382.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.233e-06/0.1529, allocations: 0 / 0.5011 GB, free: 15.65 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005642/0.1534, allocations: 431.4 kB / 0.5015 GB, free: 15.21 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.502e-05/0.1534, allocations: 19.86 kB / 0.5015 GB, free: 15.19 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.018e-05/0.1535, allocations: 8.062 kB / 0.5015 GB, free: 15.18 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001354/0.1536, allocations: 4 kB / 0.5015 GB, free: 15.18 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.544e-05/0.1537, allocations: 15.97 kB / 0.5016 GB, free: 15.16 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.595e-05/0.1537, allocations: 11.98 kB / 0.5016 GB, free: 15.15 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 8.896e-05/0.1538, allocations: 112 kB / 0.5017 GB, free: 15.04 MB / 382.1 MB
Notification: Performance of sort global known variables: time 6e-08/0.1538, allocations: 0 / 0.5017 GB, free: 15.04 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.0003363/0.1541, allocations: 64 kB / 0.5017 GB, free: 14.98 MB / 382.1 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 0.0001243/0.1542, allocations: 107.3 kB / 0.5018 GB, free: 14.87 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.0004057/0.1546, allocations: 231.9 kB / 0.5021 GB, free: 14.64 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 4.688e-06/0.1546, allocations: 4 kB / 0.5021 GB, free: 14.64 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001524/0.1548, allocations: 99.84 kB / 0.5022 GB, free: 14.54 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003131/0.1551, allocations: 31.83 kB / 0.5022 GB, free: 14.51 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001331/0.1564, allocations: 0.7398 MB / 0.5029 GB, free: 13.75 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004274/0.1569, allocations: 0.7675 MB / 0.5037 GB, free: 12.95 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.0001099/0.157, allocations: 29.94 kB / 0.5037 GB, free: 12.92 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 7.447e-05/0.157, allocations: 19.44 kB / 0.5037 GB, free: 12.91 MB / 382.1 MB
Notification: Performance of SimCode: time 4.1e-07/0.157, allocations: 0 / 0.5037 GB, free: 12.91 MB / 382.1 MB
Notification: Performance of Templates: time 0.005903/0.1629, allocations: 2.31 MB / 0.506 GB, free: 10.61 MB / 382.1 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: 4.84436890296638]
Failed to read output from testmodel.py, exit status != 0:
0.17148113530129194 0.415298625 0.272797912
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7ff27eebd7b0>