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 0.001372/0.001372, allocations: 104.3 kB / 16.45 MB, free: 6.445 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 0.001579/0.001579, allocations: 188.6 kB / 19.4 MB, free: 3.66 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 1.519/1.519, allocations: 225.6 MB / 247.8 MB, free: 3.738 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 0.07024/0.07024, allocations: 12.41 MB / 315.1 MB, free: 280 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: "" <> buildModelFMU(BioChem.Examples.GMO.cell,fileNamePrefix="BioChem_BioChem_Examples_GMO_cell",fmuType="me",version="2.0",platforms={"static"})
"" <> buildModelFMU(BioChem.Examples.GMO.cell,fileNamePrefix="BioChem_BioChem_Examples_GMO_cell",fmuType="me",version="2.0",platforms={"static"}) [Timeout 660]
"Warning: Ignoring unknown experiment annotation option: Algorithm = \"dassl\"
Notification: Performance of FrontEnd - loaded program: time 0.001886/0.001886, allocations: 63.89 kB / 439.5 MB, free: 6.184 MB / 366.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3132/0.3151, allocations: 54.91 MB / 494.4 MB, free: 22.84 MB / 366.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.006496/0.3216, allocations: 4.336 MB / 498.8 MB, free: 20.03 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0005806/0.3222, allocations: 303.3 kB / 499.1 MB, free: 19.8 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001556/0.3223, allocations: 15.62 kB / 499.1 MB, free: 19.8 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001296/0.3225, allocations: 50.7 kB / 499.1 MB, free: 19.77 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001964/0.3227, allocations: 76.39 kB / 499.2 MB, free: 19.71 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002443/0.3229, allocations: 68.98 kB / 499.3 MB, free: 19.67 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0003096/0.3232, allocations: 302 kB / 499.6 MB, free: 19.52 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002502/0.3235, allocations: 117.4 kB / 499.7 MB, free: 19.46 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001331/0.3236, allocations: 127.5 kB / 499.8 MB, free: 19.4 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001922/0.3238, allocations: 156.7 kB / 500 MB, free: 19.32 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 5.577e-05/0.3238, allocations: 33.06 kB / 0.4883 GB, free: 19.32 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 5.821e-05/0.3239, allocations: 32.84 kB / 0.4883 GB, free: 19.32 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 6.285e-05/0.324, allocations: 74.25 kB / 0.4884 GB, free: 19.27 MB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.000133/0.3241, allocations: 163.9 kB / 0.4885 GB, free: 19.16 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0004281/0.3245, allocations: 367.5 kB / 0.4889 GB, free: 19.01 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.831e-06/0.3245, allocations: 0 / 0.4889 GB, free: 19.01 MB / 366.1 MB
Notification: Performance of FrontEnd: time 1.382e-06/0.3245, allocations: 1.875 kB / 0.4889 GB, free: 19.01 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 9.107e-06/0.3245, allocations: 0 / 0.4889 GB, free: 19.01 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 0.0008962/0.3254, allocations: 0.6109 MB / 0.4895 GB, free: 18.5 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.558e-05/0.3255, allocations: 8.875 kB / 0.4895 GB, free: 18.5 MB / 366.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 9.136e-05/0.3256, allocations: 77.25 kB / 0.4896 GB, free: 18.44 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.143e-05/0.3256, allocations: 37.45 kB / 0.4896 GB, free: 18.42 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001104/0.3258, allocations: 206.8 kB / 0.4898 GB, free: 18.19 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.704e-05/0.3258, allocations: 29.53 kB / 0.4898 GB, free: 18.18 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.623e-05/0.3258, allocations: 37.47 kB / 0.4899 GB, free: 18.17 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.00048/0.3263, allocations: 313.2 kB / 0.4902 GB, free: 18.03 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.858e-05/0.3263, allocations: 9.156 kB / 0.4902 GB, free: 18.02 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.705e-05/0.3264, allocations: 15.31 kB / 0.4902 GB, free: 18.01 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.191e-05/0.3264, allocations: 8.75 kB / 0.4902 GB, free: 18.01 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0004125/0.3268, allocations: 238.9 kB / 0.4904 GB, free: 17.93 MB / 366.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001798/0.3286, allocations: 1.041 MB / 0.4914 GB, free: 17.32 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003428/0.3289, allocations: 168.8 kB / 0.4916 GB, free: 17.24 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.000185/0.3291, allocations: 106.4 kB / 0.4917 GB, free: 17.2 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.373e-05/0.3291, allocations: 2.156 kB / 0.4917 GB, free: 17.2 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.374e-05/0.3292, allocations: 37.89 kB / 0.4917 GB, free: 17.15 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=22): time 2.144e-06/0.3292, allocations: 0 / 0.4917 GB, free: 17.15 MB / 366.1 MB
Notification: Performance of matching and sorting (n=26): time 0.002046/0.3312, allocations: 0.9047 MB / 0.4926 GB, free: 16.57 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.645e-05/0.3313, allocations: 58.78 kB / 0.4927 GB, free: 16.51 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000122/0.3314, allocations: 159.5 kB / 0.4928 GB, free: 16.37 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.546e-05/0.3314, allocations: 26.86 kB / 0.4929 GB, free: 16.34 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001066/0.3315, allocations: 222.4 kB / 0.4931 GB, free: 16.14 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 5.834e-05/0.3316, allocations: 102 kB / 0.4932 GB, free: 16.05 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.361e-05/0.3316, allocations: 62.45 kB / 0.4932 GB, free: 16 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 5.511e-05/0.3317, allocations: 335.2 kB / 0.4936 GB, free: 15.67 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001315/0.3318, allocations: 82.59 kB / 0.4936 GB, free: 15.63 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001758/0.332, allocations: 194.8 kB / 0.4938 GB, free: 15.45 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003017/0.335, allocations: 0.8183 MB / 0.4946 GB, free: 14.96 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.446e-06/0.335, allocations: 1.281 kB / 0.4946 GB, free: 14.96 MB / 366.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.000483/0.3355, allocations: 349.1 kB / 0.4949 GB, free: 14.78 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.183e-05/0.3355, allocations: 6.969 kB / 0.495 GB, free: 14.78 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.083e-05/0.3355, allocations: 11.61 kB / 0.495 GB, free: 14.77 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.388e-05/0.3356, allocations: 6.062 kB / 0.495 GB, free: 14.77 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003166/0.3359, allocations: 77.59 kB / 0.495 GB, free: 14.76 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.342e-05/0.3359, allocations: 9.938 kB / 0.4951 GB, free: 14.75 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000157/0.336, allocations: 12.84 kB / 0.4951 GB, free: 14.75 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.326e-05/0.3361, allocations: 12.19 kB / 0.4951 GB, free: 14.75 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 0.0003006/0.3364, allocations: 181.5 kB / 0.4953 GB, free: 14.58 MB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.858e-05/0.3364, allocations: 23.88 kB / 0.4953 GB, free: 14.57 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.287e-05/0.3365, allocations: 32.92 kB / 0.4953 GB, free: 14.54 MB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.488e-06/0.3365, allocations: 7.219 kB / 0.4953 GB, free: 14.53 MB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.726e-06/0.3365, allocations: 0 / 0.4953 GB, free: 14.53 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.208e-06/0.3365, allocations: 1.312 kB / 0.4953 GB, free: 14.53 MB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004343/0.3369, allocations: 360.8 kB / 0.4957 GB, free: 14.21 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.773e-06/0.3369, allocations: 0 / 0.4957 GB, free: 14.21 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000263/0.3372, allocations: 52.09 kB / 0.4957 GB, free: 14.2 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.617e-06/0.3372, allocations: 1.188 kB / 0.4957 GB, free: 14.2 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.841e-05/0.3372, allocations: 6.25 kB / 0.4957 GB, free: 14.2 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.647e-06/0.3372, allocations: 1.031 kB / 0.4957 GB, free: 14.2 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.122e-06/0.3372, allocations: 0 / 0.4957 GB, free: 14.2 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004691/0.3377, allocations: 428.2 kB / 0.4961 GB, free: 13.92 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.665e-05/0.3377, allocations: 101.4 kB / 0.4962 GB, free: 13.8 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.957e-05/0.3378, allocations: 2.062 kB / 0.4962 GB, free: 13.8 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001376/0.3379, allocations: 6.188 kB / 0.4962 GB, free: 13.8 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.304e-05/0.3379, allocations: 22.47 kB / 0.4963 GB, free: 13.79 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.3e-05/0.338, allocations: 4.594 kB / 0.4963 GB, free: 13.79 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 6.074e-05/0.338, allocations: 121.4 kB / 0.4964 GB, free: 13.69 MB / 366.1 MB
Notification: Performance of sort global known variables: time 8e-08/0.338, allocations: 0 / 0.4964 GB, free: 13.69 MB / 366.1 MB
Notification: Performance of remove unused functions: time 0.0003385/0.3384, allocations: 62.16 kB / 0.4964 GB, free: 13.68 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 0.0006204/0.339, allocations: 0.9682 MB / 0.4974 GB, free: 12.86 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003498/0.3393, allocations: 222.9 kB / 0.4976 GB, free: 12.77 MB / 366.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.255e-06/0.3393, allocations: 0.9375 kB / 0.4976 GB, free: 12.77 MB / 366.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001284/0.3395, allocations: 104.9 kB / 0.4977 GB, free: 12.72 MB / 366.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000304/0.3398, allocations: 34.92 kB / 0.4977 GB, free: 12.7 MB / 366.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002705/0.3425, allocations: 2.743 MB / 0.5004 GB, free: 10.44 MB / 366.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001768/0.3426, allocations: 0.7657 MB / 0.5012 GB, free: 9.707 MB / 366.1 MB
Notification: Performance of simCode: alias equations: time 0.0001136/0.3428, allocations: 29.22 kB / 0.5012 GB, free: 9.691 MB / 366.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001178/0.3429, allocations: 92.42 kB / 0.5013 GB, free: 9.617 MB / 366.1 MB
Notification: Performance of SimCode: time 8.81e-07/0.3429, allocations: 0 / 0.5013 GB, free: 9.617 MB / 366.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.02946/0.3723, allocations: 4.411 MB / 0.5056 GB, free: 7.383 MB / 366.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 8.129/8.501, allocations: 7.375 kB / 0.5056 GB, free: 7.379 MB / 366.1 MB
"
[Timeout remaining time 651]
(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 & /home/hudson/saved_omc/OMSimulator/install/bin/OMSimulator  --tempDir=temp_BioChem_BioChem_Examples_GMO_cell_fmu --startTime=0 --stopTime=100 --stepSize=100 --timeout=50 --tolerance=1e-06 BioChem_BioChem_Examples_GMO_cell.fmu > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1) [Timeout 52.5]
[Calling sys.exit(0), Time elapsed: 11.08772423909977]
Failed to read output from testmodel.py, exit status != 0:
8.57097121886909 8.582379732 8.254708025
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7f93f6f3e020>