Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.CaOscillations.Cytosol.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 0.001408/0.001408, allocations: 113.9 kB / 18.94 MB, free: 2.93 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 0.001481/0.001481, allocations: 186.3 kB / 22.22 MB, free: 5.105 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 1.414/1.414, allocations: 225.6 MB / 251 MB, free: 13.02 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 0.0709/0.0709, allocations: 12.42 MB / 318.7 MB, free: 12.94 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.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol") [Timeout 660]
"Warning: Ignoring unknown experiment annotation option: Algorithm = \"dassl\"
Notification: Performance of FrontEnd - loaded program: time 0.001951/0.001951, allocations: 69.95 kB / 445.3 MB, free: 3.969 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.128/0.13, allocations: 54.96 MB / 0.4885 GB, free: 12.94 MB / 366.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.004884/0.1348, allocations: 2.868 MB / 0.4913 GB, free: 10.05 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003254/0.1352, allocations: 195.1 kB / 0.4915 GB, free: 9.863 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 8.89e-05/0.1353, allocations: 12 kB / 0.4915 GB, free: 9.852 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 8.333e-05/0.1353, allocations: 31.73 kB / 0.4916 GB, free: 9.82 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001558/0.1355, allocations: 43.56 kB / 0.4916 GB, free: 9.777 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002259/0.1357, allocations: 43.89 kB / 0.4916 GB, free: 9.734 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002458/0.136, allocations: 187.2 kB / 0.4918 GB, free: 9.551 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002278/0.1362, allocations: 76.84 kB / 0.4919 GB, free: 9.477 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001116/0.1363, allocations: 87.7 kB / 0.492 GB, free: 9.391 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001633/0.1365, allocations: 91.55 kB / 0.4921 GB, free: 9.301 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.142e-05/0.1365, allocations: 28 kB / 0.4921 GB, free: 9.273 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.405e-05/0.1365, allocations: 20 kB / 0.4921 GB, free: 9.254 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 6.54e-05/0.1366, allocations: 51.78 kB / 0.4922 GB, free: 9.203 MB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001104/0.1367, allocations: 107.4 kB / 0.4923 GB, free: 9.098 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0003113/0.137, allocations: 231 kB / 0.4925 GB, free: 8.871 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.354e-06/0.137, allocations: 4 kB / 0.4925 GB, free: 8.867 MB / 366.1 MB
Notification: Performance of FrontEnd: time 1.774e-06/0.137, allocations: 0 / 0.4925 GB, free: 8.867 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 9.017e-06/0.137, allocations: 0 / 0.4925 GB, free: 8.867 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: 60
 * Number of variables: 60
Notification: Performance of Generate backend data structure: time 0.0008009/0.1378, allocations: 437.9 kB / 0.4929 GB, free: 8.402 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.219e-05/0.1379, allocations: 8.031 kB / 0.4929 GB, free: 8.395 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.914e-05/0.138, allocations: 28.75 kB / 0.4929 GB, free: 8.367 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001591/0.1381, allocations: 138.2 kB / 0.4931 GB, free: 8.207 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.946e-05/0.1381, allocations: 20.88 kB / 0.4931 GB, free: 8.188 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.184e-05/0.1382, allocations: 24.38 kB / 0.4931 GB, free: 8.164 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003843/0.1386, allocations: 196.6 kB / 0.4933 GB, free: 7.965 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.712e-05/0.1386, allocations: 8.188 kB / 0.4933 GB, free: 7.957 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.653e-05/0.1386, allocations: 11.94 kB / 0.4933 GB, free: 7.945 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.078e-05/0.1386, allocations: 8 kB / 0.4933 GB, free: 7.938 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002793/0.1389, allocations: 137.9 kB / 0.4935 GB, free: 7.805 MB / 366.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001371/0.1403, allocations: 0.7245 MB / 0.4942 GB, free: 7.023 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002337/0.1405, allocations: 98.48 kB / 0.4943 GB, free: 6.918 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002367/0.1408, allocations: 84.8 kB / 0.4943 GB, free: 6.832 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.193e-05/0.1408, allocations: 4 kB / 0.4943 GB, free: 6.828 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.786e-05/0.1408, allocations: 38.55 kB / 0.4944 GB, free: 6.781 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=15): time 1.102e-06/0.1408, allocations: 0 / 0.4944 GB, free: 6.781 MB / 366.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001275/0.1421, allocations: 0.5032 MB / 0.4949 GB, free: 6.246 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.289e-05/0.1421, allocations: 59.34 kB / 0.4949 GB, free: 6.176 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001551/0.1423, allocations: 156.4 kB / 0.4951 GB, free: 6.008 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.582e-05/0.1423, allocations: 29.7 kB / 0.4951 GB, free: 5.973 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001064/0.1424, allocations: 152.2 kB / 0.4953 GB, free: 5.82 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 6.028e-05/0.1425, allocations: 71.42 kB / 0.4953 GB, free: 5.75 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.206e-05/0.1426, allocations: 45.66 kB / 0.4954 GB, free: 5.699 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001724/0.1427, allocations: 330.8 kB / 0.4957 GB, free: 5.367 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.354e-05/0.1428, allocations: 36.22 kB / 0.4957 GB, free: 5.332 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001279/0.1429, allocations: 97.91 kB / 0.4958 GB, free: 5.219 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001386/0.1443, allocations: 395.4 kB / 0.4962 GB, free: 4.812 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.182e-06/0.1443, allocations: 0 / 0.4962 GB, free: 4.812 MB / 366.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0003328/0.1447, allocations: 209.4 kB / 0.4964 GB, free: 4.602 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.627e-05/0.1447, allocations: 7.938 kB / 0.4964 GB, free: 4.594 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.091e-06/0.1447, allocations: 4 kB / 0.4964 GB, free: 4.59 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.234e-05/0.1447, allocations: 7.938 kB / 0.4964 GB, free: 4.582 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002026/0.1449, allocations: 51.91 kB / 0.4965 GB, free: 4.531 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.094e-05/0.1449, allocations: 4 kB / 0.4965 GB, free: 4.527 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.474e-05/0.145, allocations: 8 kB / 0.4965 GB, free: 4.52 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.633e-05/0.145, allocations: 12.19 kB / 0.4965 GB, free: 4.508 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
         endoplasmicReticulum.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         p3_sbml:VARIABLE(start = 0.95 fixed = true )  type: Real
         Ca_Cyt.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         endoplasmicReticulum.CaER.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: 7
 * 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 (28):
 * Single equations (assignments): 28
 * 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 0.0002853/0.1453, allocations: 151.3 kB / 0.4966 GB, free: 4.352 MB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.662e-05/0.1453, allocations: 11.91 kB / 0.4966 GB, free: 4.34 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0003172/0.1457, allocations: 178.5 kB / 0.4968 GB, free: 4.156 MB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.883e-06/0.1457, allocations: 4 kB / 0.4968 GB, free: 4.152 MB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.917e-06/0.1457, allocations: 0 / 0.4968 GB, free: 4.152 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.122e-06/0.1457, allocations: 3.984 kB / 0.4968 GB, free: 4.148 MB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007863/0.1465, allocations: 0.4888 MB / 0.4973 GB, free: 3.613 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.754e-06/0.1465, allocations: 0 / 0.4973 GB, free: 3.613 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002097/0.1467, allocations: 39.91 kB / 0.4973 GB, free: 3.574 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.905e-06/0.1467, allocations: 0 / 0.4973 GB, free: 3.574 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.7e-05/0.1467, allocations: 4 kB / 0.4973 GB, free: 3.57 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.4e-06/0.1467, allocations: 8 kB / 0.4973 GB, free: 3.562 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 6.62e-07/0.1467, allocations: 0 / 0.4973 GB, free: 3.562 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004885/0.1472, allocations: 307.8 kB / 0.4976 GB, free: 3.246 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.269e-05/0.1472, allocations: 11.91 kB / 0.4976 GB, free: 3.234 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.343e-05/0.1472, allocations: 0 / 0.4976 GB, free: 3.234 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001051/0.1473, allocations: 8.062 kB / 0.4976 GB, free: 3.227 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.63e-05/0.1474, allocations: 11.97 kB / 0.4977 GB, free: 3.215 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 9.618e-06/0.1474, allocations: 4 kB / 0.4977 GB, free: 3.211 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 8.632e-05/0.1475, allocations: 122.6 kB / 0.4978 GB, free: 3.094 MB / 366.1 MB
Notification: Performance of sort global known variables: time 6e-08/0.1475, allocations: 0 / 0.4978 GB, free: 3.094 MB / 366.1 MB
Notification: Performance of remove unused functions: time 0.0002712/0.1478, allocations: 36 kB / 0.4978 GB, free: 3.059 MB / 366.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (V,endoplasmicReticulum.V,endoplasmicReticulum.CaER.n,Ca_Cyt.n,p3_sbml)
 * 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 (18):
 * Single equations (assignments): 18
 * 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 0.0001247/0.1479, allocations: 95.25 kB / 0.4979 GB, free: 2.957 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002691/0.1481, allocations: 131.8 kB / 0.498 GB, free: 2.828 MB / 366.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.966e-06/0.1481, allocations: 0 / 0.498 GB, free: 2.828 MB / 366.1 MB
Notification: Performance of simCode: created simulation system equations: time 9.861e-05/0.1482, allocations: 64.28 kB / 0.4981 GB, free: 2.766 MB / 366.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003034/0.1486, allocations: 36.53 kB / 0.4981 GB, free: 2.738 MB / 366.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0009545/0.1495, allocations: 0.5009 MB / 0.4986 GB, free: 2.211 MB / 366.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004198/0.1499, allocations: 0.7397 MB / 0.4993 GB, free: 1.445 MB / 366.1 MB
Notification: Performance of simCode: alias equations: time 6.752e-05/0.15, allocations: 13.42 kB / 0.4994 GB, free: 1.43 MB / 366.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.087e-05/0.15, allocations: 19.44 kB / 0.4994 GB, free: 1.414 MB / 366.1 MB
Notification: Performance of SimCode: time 3.11e-07/0.15, allocations: 3.938 kB / 0.4994 GB, free: 1.41 MB / 366.1 MB
Notification: Performance of Templates: time 0.004795/0.1548, allocations: 1.535 MB / 0.5009 GB, free: 15.88 MB / 382.1 MB
"
[Timeout remaining time 660]
make -j1 -f BioChem_BioChem.Examples.CaOscillations.Cytosol.makefile [Timeout 660]
(rm -f BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe ; mkfifo BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe ; head -c 1048576 < BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe >> ../files/BioChem_BioChem.Examples.CaOscillations.Cytosol.sim & ./BioChem_BioChem.Examples.CaOscillations.Cytosol  -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 4.5383025873452425]
Failed to read output from testmodel.py, exit status != 0:
0.1622284585610032 0.17695301900000002 0.036899435
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7fd7e32697b0>