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ID  Project  Category  View Status  Date Submitted  Last Update 

0003983  OpenFOAM  Bug  public  20230522 17:41  20230523 17:15 
Reporter  EmilyManchester  Assigned To  will  
Priority  normal  Severity  minor  Reproducibility  always 
Status  closed  Resolution  fixed  
Summary  0003983: Using csv file types as boundary condition results in strange error  
Description  Using the following custom boundary condition and running decomposePar causes a strange rewrite which causes the solver to crash: boundaryField { INLET { type turbulentInletSEM; meanVelocity tableFile; meanVelocityCoeffs { file "inlet_meanVelocity.csv"; format csv; nHeaderLine 0; // number of header lines refColumn 0; // time column index componentColumns (1 2 3); // data column index mergeSeparators no; } } } decomposePar rewrites the line: componentColumns (1 2 3); to: componentColumns List<label> 3(1 2 3); The leading '3' ahead of '(1 2 3)' causes the following error when running pimpleFoam: [66] > FOAM FATAL IO ERROR: [66] Expected a ')' while reading binaryBlock, found on line 52 the word 'separator' [66] [66] file: /mnt/lustre/indy2lfs/work/.../T001_TI1_L1mm/processor66/1.48/U at line 52. [66] [66] From function Foam::Istream& Foam::Istream::readEnd(const char*) [66] in file db/IOstreams/IOstreams/Istream.C at line 109. [66] FOAM parallel run exiting Once decomposed, any of pimpleFoam, reconstructPar, changeDictionary or foamDictionary crash producing the same error message. I cannot use changeDictionary or foamDictionary to overwrite the problem line 'componentColumns List<label> 3(1 2 3);' without it failing. Running the case in serial works fine. I believe this is the same issue as reported in '0003651: Using csv files together with binary file format results in error if run in parallel'. I installed OpenFOAM 8.0 in October 2022 after the bug was reported as fixed in March 2021.  
Tags  No tags attached.  

@EmilyManchester Quick questions/requests: 1. A test case with which developers can test this issue, would speed up things by a lot. Preferably if it was based on one of OpenFOAM's own tutorial cases for the same version you are using. 2. Which version of OpenFOAM are you using? Is it really version 8? How was it built/installed exactly? 3. Have you tested this with OpenFOAM 10 or dev? 

On point 2, more specifically, what is the build hash? There should be a line right at the top of the output that looks like this: Build : 89603c2377861 

1. I have provided a test case adapted from the pitzDailyPulse tutorial which includes changing the 'inlet' BC in 0/U to read from a .csv file. I have included my log files from running in both serial; which works, and in parallel; which crashes. 2. The build on my laptop is Build : 81c9b5879390b I primarily use OpenFOAM on Cirrus, which simply says Build : 8 I have encountered the problem both on my laptop and Cirrus HPC 3. I have not tested this on newer versions 

I am unable to reproduce the problem, the case runs fine with OpenFOAM8 and OpenFOAMdev in serial and parallel. 

errorlog.pimpleFoam_parallel (3,557 bytes)
/**\ =========  \\ / F ield  OpenFOAM: The Open Source CFD Toolbox \\ / O peration  Website: https://openfoam.org \\ / A nd  Version: 8 \\/ M anipulation  \**/ Build : 81c9b5879390b Exec : pimpleFoam parallel Date : May 23 2023 Time : 16:51:41 Host : "E10LXXD2299V6V" PID : 2260 I/O : uncollated Case : /mnt/m/CodeDevelopment/TestCases/SEM_paraboloid_pulsatile/T008/TestCase/pitzDailyPulse nProcs : 4 Slaves : 3 ( "E10LXXD2299V6V.2261" "E10LXXD2299V6V.2262" "E10LXXD2299V6V.2263" ) Pstream initialized with: floatTransfer : 0 nProcsSimpleSum : 0 commsType : nonBlocking polling iterations : 0 sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). fileModificationChecking : Monitoring runtime modified files using timeStampMaster (fileModificationSkew 10) allowSystemOperations : Allowing usersupplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 PIMPLE: No convergence criteria found PIMPLE: Operating solver in transient mode with 1 outer corrector PIMPLE: Operating solver in PISO mode Reading field p Reading field U [1] [1] [1] > FOAM FATAL IO ERROR: [1] Expected a ')' while reading binaryBlock, found on line 34 the word 'separator' [1] [1] file: /mnt/m/CodeDevelopment/TestCases/SEM_paraboloid_pulsatile/T008/TestCase/pitzDailyPulse/processor1/0/U at line 34. [1] [1] From function Foam::Istream& Foam::Istream::readEnd(const char*) [1] in file db/IOstreams/IOstreams/Istream.C at line 109. [1] FOAM parallel run exiting [1] [0] [0] [0] > FOAM FATAL IO ERROR: [0] Expected a ')' while reading binaryBlock, found on line 34 the word 'separator' [0] [0] file: /mnt/m/CodeDevelopment/TestCases/SEM_paraboloid_pulsatile/T008/TestCase/pitzDailyPulse/processor0/0/U at line 34. [0] [0] From function Foam::Istream& Foam::Istream::readEnd(const char*) [0] in file db/IOstreams/IOstreams/Istream.C at line 109. [0] FOAM parallel run exiting [0]  MPI_ABORT was invoked on rank 1 in communicator MPI COMMUNICATOR 3 SPLIT FROM 0 with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.  [2] [2] [2] > FOAM FATAL IO ERROR: [2] Expected a ')' while reading binaryBlock, found on line 34 the word 'separator' [2] [2] file: /mnt/m/CodeDevelopment/TestCases/SEM_paraboloid_pulsatile/T008/TestCase/pitzDailyPulse/processor2/0/U at line 34. [2] [2] From function Foam::Istream& Foam::Istream::readEnd(const char*) [2] in file db/IOstreams/IOstreams/Istream.C at line 109. [2] FOAM parallel run exiting [2] [3] [3] [3] > FOAM FATAL IO ERROR: [3] Expected a ')' while reading binaryBlock, found on line 34 the word 'separator' [3] [3] file: /mnt/m/CodeDevelopment/TestCases/SEM_paraboloid_pulsatile/T008/TestCase/pitzDailyPulse/processor3/0/U at line 34. [3] [3] From function Foam::Istream& Foam::Istream::readEnd(const char*) [3] in file db/IOstreams/IOstreams/Istream.C at line 109. [3] FOAM parallel run exiting 

"Build : 8" implies it was built from a source pack, which will have been created at the point of release before any bug fixes. Your laptop version is two commits before the relevant fix. In both cases, you just need to update, but there are no packaged (deb, docker, etc...) versions of OpenFOAM8 beyond what you have, and we're not about to start creating them almost three years after OpenFOAM8's release. Your options are to pull version 8 from github and build it yourself, or update to a pack of OpenFOAM9 or above. 

log (12,817 bytes)
/**\ =========  \\ / F ield  OpenFOAM: The Open Source CFD Toolbox \\ / O peration  Website: https://openfoam.org \\ / A nd  Version: 8 \\/ M anipulation  \**/ Build : 8e0f23cae73e0 Exec : pimpleFoam parallel Date : May 23 2023 Time : 17:14:53 Host : "dm" PID : 21927 I/O : uncollated Case : /home/dm2/henry/OpenFOAM/henrydev/run/Bugs/pimpleFoam/pitzDailyPulse nProcs : 4 Slaves : 3 ( "dm.21928" "dm.21929" "dm.21930" ) Pstream initialized with: floatTransfer : 0 nProcsSimpleSum : 0 commsType : nonBlocking polling iterations : 0 sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). SetNaN : Initialising allocated memory to NaN (FOAM_SETNAN). fileModificationChecking : Monitoring runtime modified files using timeStampMaster (fileModificationSkew 10) allowSystemOperations : Allowing usersupplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 PIMPLE: No convergence criteria found PIMPLE: Operating solver in transient mode with 1 outer corrector PIMPLE: Operating solver in PISO mode Reading field p Reading field U Reading/calculating face flux field phi Selecting incompressible transport model Newtonian Selecting turbulence model type laminar Selecting laminar stress model Stokes No MRF models present No finite volume options present Courant Number mean: 3.47235e05 max: 0.0125372 Starting time loop Courant Number mean: 3.47235e05 max: 0.0125372 deltaT = 0.00119048 Time = 0.00119048 smoothSolver: Solving for Ux, Initial residual = 1, Final residual = 5.47558e06, No Iterations 9 smoothSolver: Solving for Uy, Initial residual = 0.0244401, Final residual = 4.6274e06, No Iterations 5 GAMG: Solving for p, Initial residual = 1, Final residual = 0.00492784, No Iterations 10 time step continuity errors : sum local = 4.46176e07, global = 2.73624e08, cumulative = 2.73624e08 GAMG: Solving for p, Initial residual = 0.023069, Final residual = 4.8959e08, No Iterations 17 time step continuity errors : sum local = 4.48754e10, global = 3.98478e11, cumulative = 2.74023e08 ExecutionTime = 0.07 s ClockTime = 1 s Courant Number mean: 0.0220936 max: 0.331472 deltaT = 0.00139456 Time = 0.00258503 smoothSolver: Solving for Ux, Initial residual = 0.833578, Final residual = 4.33887e06, No Iterations 9 smoothSolver: Solving for Uy, Initial residual = 0.284202, Final residual = 7.34735e06, No Iterations 9 GAMG: Solving for p, Initial residual = 0.0368593, Final residual = 0.000213222, No Iterations 9 time step continuity errors : sum local = 1.8174e06, global = 2.2638e07, cumulative = 2.53783e07 GAMG: Solving for p, Initial residual = 0.0785227, Final residual = 9.46742e08, No Iterations 18 time step continuity errors : sum local = 3.20115e10, global = 2.22408e11, cumulative = 2.53805e07 ExecutionTime = 0.11 s ClockTime = 1 s Courant Number mean: 0.0284474 max: 0.395325 deltaT = 0.001635 Time = 0.00422003 smoothSolver: Solving for Ux, Initial residual = 0.265665, Final residual = 6.00843e06, No Iterations 8 smoothSolver: Solving for Uy, Initial residual = 0.168027, Final residual = 5.59485e06, No Iterations 9 GAMG: Solving for p, Initial residual = 0.275252, Final residual = 0.00221582, No Iterations 4 time step continuity errors : sum local = 2.64634e06, global = 1.03474e06, cumulative = 1.28854e06 GAMG: Solving for p, Initial residual = 0.121411, Final residual = 6.09646e08, No Iterations 19 time step continuity errors : sum local = 8.44788e11, global = 1.81652e11, cumulative = 1.28856e06 ExecutionTime = 0.15 s ClockTime = 1 s Courant Number mean: 0.0373334 max: 0.473919 deltaT = 0.0019075 Time = 0.00612753 smoothSolver: Solving for Ux, Initial residual = 0.293811, Final residual = 5.14668e06, No Iterations 9 smoothSolver: Solving for Uy, Initial residual = 0.0542629, Final residual = 6.35587e06, No Iterations 9 GAMG: Solving for p, Initial residual = 0.0419176, Final residual = 0.000191396, No Iterations 5 time step continuity errors : sum local = 2.93437e07, global = 1.16879e07, cumulative = 1.17168e06 GAMG: Solving for p, Initial residual = 0.0206295, Final residual = 9.6817e08, No Iterations 15 time step continuity errors : sum local = 1.44334e10, global = 2.58226e11, cumulative = 1.17171e06 ExecutionTime = 0.18 s ClockTime = 1 s Courant Number mean: 0.0492226 max: 0.581813 deltaT = 0.00219362 Time = 0.00832115 smoothSolver: Solving for Ux, Initial residual = 0.28077, Final residual = 9.87343e06, No Iterations 9 smoothSolver: Solving for Uy, Initial residual = 0.033307, Final residual = 5.35931e06, No Iterations 10 GAMG: Solving for p, Initial residual = 0.00834394, Final residual = 3.69134e05, No Iterations 8 time step continuity errors : sum local = 6.74476e08, global = 6.29748e09, cumulative = 1.178e06 GAMG: Solving for p, Initial residual = 0.00530647, Final residual = 8.42068e08, No Iterations 14 time step continuity errors : sum local = 1.7069e10, global = 1.34942e11, cumulative = 1.17799e06 ExecutionTime = 0.21 s ClockTime = 1 s Courant Number mean: 0.0645286 max: 0.720737 deltaT = 0.00260493 Time = 0.0109261 smoothSolver: Solving for Ux, Initial residual = 0.286621, Final residual = 6.95769e06, No Iterations 11 smoothSolver: Solving for Uy, Initial residual = 0.0374957, Final residual = 7.53473e06, No Iterations 11 GAMG: Solving for p, Initial residual = 0.00704514, Final residual = 3.54147e05, No Iterations 8 time step continuity errors : sum local = 8.85748e08, global = 1.0318e08, cumulative = 1.18831e06 GAMG: Solving for p, Initial residual = 0.00541429, Final residual = 8.52065e08, No Iterations 14 time step continuity errors : sum local = 2.34366e10, global = 1.91364e11, cumulative = 1.18829e06 ExecutionTime = 0.25 s ClockTime = 1 s Courant Number mean: 0.0884172 max: 0.944018 deltaT = 0.00300569 Time = 0.0139318 smoothSolver: Solving for Ux, Initial residual = 0.28492, Final residual = 8.49563e06, No Iterations 12 smoothSolver: Solving for Uy, Initial residual = 0.0386809, Final residual = 9.39543e06, No Iterations 12 GAMG: Solving for p, Initial residual = 0.00699236, Final residual = 4.48133e05, No Iterations 8 time step continuity errors : sum local = 1.44917e07, global = 1.78496e08, cumulative = 1.20614e06 GAMG: Solving for p, Initial residual = 0.00561656, Final residual = 5.40502e08, No Iterations 15 time step continuity errors : sum local = 1.9472e10, global = 1.94988e11, cumulative = 1.20616e06 ExecutionTime = 0.29 s ClockTime = 1 s Courant Number mean: 0.118592 max: 1.21123 deltaT = 0.00360682 Time = 0.0175386 smoothSolver: Solving for Ux, Initial residual = 0.287255, Final residual = 8.43489e06, No Iterations 14 smoothSolver: Solving for Uy, Initial residual = 0.0417478, Final residual = 6.46956e06, No Iterations 15 GAMG: Solving for p, Initial residual = 0.0084841, Final residual = 4.64554e05, No Iterations 8 time step continuity errors : sum local = 2.04803e07, global = 2.55381e08, cumulative = 1.2317e06 GAMG: Solving for p, Initial residual = 0.00674411, Final residual = 5.00084e08, No Iterations 15 time step continuity errors : sum local = 2.46109e10, global = 2.51078e11, cumulative = 1.23172e06 ExecutionTime = 0.32 s ClockTime = 1 s Courant Number mean: 0.167367 max: 1.63448 deltaT = 0.00405768 Time = 0.0215963 smoothSolver: Solving for Ux, Initial residual = 0.2746, Final residual = 6.72712e06, No Iterations 16 smoothSolver: Solving for Uy, Initial residual = 0.0416194, Final residual = 8.23109e06, No Iterations 16 GAMG: Solving for p, Initial residual = 0.00974356, Final residual = 9.66558e05, No Iterations 7 time step continuity errors : sum local = 5.25974e07, global = 9.67635e08, cumulative = 1.13496e06 GAMG: Solving for p, Initial residual = 0.00758843, Final residual = 7.84621e08, No Iterations 14 time step continuity errors : sum local = 4.68991e10, global = 3.71463e11, cumulative = 1.13492e06 ExecutionTime = 0.36 s ClockTime = 1 s Courant Number mean: 0.221166 max: 2.08655 deltaT = 0.00473396 Time = 0.0263302 smoothSolver: Solving for Ux, Initial residual = 0.264245, Final residual = 7.39866e06, No Iterations 18 smoothSolver: Solving for Uy, Initial residual = 0.0421904, Final residual = 9.19042e06, No Iterations 18 GAMG: Solving for p, Initial residual = 0.0107398, Final residual = 4.30291e05, No Iterations 7 time step continuity errors : sum local = 2.98824e07, global = 8.25902e08, cumulative = 1.21751e06 GAMG: Solving for p, Initial residual = 0.00807351, Final residual = 8.52643e08, No Iterations 14 time step continuity errors : sum local = 6.28222e10, global = 7.83348e11, cumulative = 1.21759e06 ExecutionTime = 0.39 s ClockTime = 1 s Courant Number mean: 0.303499 max: 2.75858 deltaT = 0.00473396 Time = 0.0310642 smoothSolver: Solving for Ux, Initial residual = 0.230933, Final residual = 7.29686e06, No Iterations 18 smoothSolver: Solving for Uy, Initial residual = 0.036476, Final residual = 8.48955e06, No Iterations 18 GAMG: Solving for p, Initial residual = 0.00984132, Final residual = 7.28346e05, No Iterations 5 time step continuity errors : sum local = 5.16084e07, global = 4.53598e08, cumulative = 1.17223e06 GAMG: Solving for p, Initial residual = 0.00680361, Final residual = 5.22537e08, No Iterations 16 time step continuity errors : sum local = 3.66576e10, global = 7.31249e11, cumulative = 1.1723e06 ExecutionTime = 0.43 s ClockTime = 1 s Courant Number mean: 0.348371 max: 3.07293 deltaT = 0.00473396 Time = 0.0357981 smoothSolver: Solving for Ux, Initial residual = 0.200044, Final residual = 7.07156e06, No Iterations 18 smoothSolver: Solving for Uy, Initial residual = 0.0312272, Final residual = 7.73722e06, No Iterations 18 GAMG: Solving for p, Initial residual = 0.00874256, Final residual = 4.40883e05, No Iterations 7 time step continuity errors : sum local = 3.1006e07, global = 5.19179e08, cumulative = 1.12039e06 GAMG: Solving for p, Initial residual = 0.00852431, Final residual = 5.96332e08, No Iterations 15 time step continuity errors : sum local = 3.83327e10, global = 4.58498e11, cumulative = 1.12043e06 ExecutionTime = 0.47 s ClockTime = 1 s Courant Number mean: 0.39122 max: 3.35311 deltaT = 0.00473396 Time = 0.0405321 smoothSolver: Solving for Ux, Initial residual = 0.171147, Final residual = 9.59999e06, No Iterations 17 smoothSolver: Solving for Uy, Initial residual = 0.0268009, Final residual = 9.95387e06, No Iterations 17 GAMG: Solving for p, Initial residual = 0.0127583, Final residual = 0.000106596, No Iterations 7 time step continuity errors : sum local = 7.23585e07, global = 1.33255e07, cumulative = 1.25369e06 GAMG: Solving for p, Initial residual = 0.0152239, Final residual = 7.57264e08, No Iterations 16 time step continuity errors : sum local = 4.29747e10, global = 3.20484e11, cumulative = 1.25372e06 ExecutionTime = 0.5 s ClockTime = 1 s Courant Number mean: 0.43079 max: 3.60442 deltaT = 0.00473396 Time = 0.045266 smoothSolver: Solving for Ux, Initial residual = 0.144087, Final residual = 8.8609e06, No Iterations 17 smoothSolver: Solving for Uy, Initial residual = 0.0228145, Final residual = 8.70941e06, No Iterations 17 GAMG: Solving for p, Initial residual = 0.0180435, Final residual = 6.93997e05, No Iterations 8 time step continuity errors : sum local = 4.41971e07, global = 5.21092e08, cumulative = 1.20161e06 GAMG: Solving for p, Initial residual = 0.0239871, Final residual = 5.46559e08, No Iterations 17 time step continuity errors : sum local = 2.64241e10, global = 2.78088e11, cumulative = 1.20158e06 ExecutionTime = 0.53 s ClockTime = 1 s Courant Number mean: 0.466074 max: 3.80437 deltaT = 0.00473396 Time = 0.05 smoothSolver: Solving for Ux, Initial residual = 0.118865, Final residual = 7.92436e06, No Iterations 17 smoothSolver: Solving for Uy, Initial residual = 0.0193969, Final residual = 7.38931e06, No Iterations 17 GAMG: Solving for p, Initial residual = 0.0235672, Final residual = 9.52278e05, No Iterations 8 time step continuity errors : sum local = 5.52774e07, global = 6.71122e08, cumulative = 1.13447e06 GAMG: Solving for p, Initial residual = 0.0349452, Final residual = 7.7662e08, No Iterations 17 time step continuity errors : sum local = 3.07951e10, global = 3.24414e11, cumulative = 1.13444e06 ExecutionTime = 0.56 s ClockTime = 1 s . . . 
Date Modified  Username  Field  Change 

20230522 17:41  EmilyManchester  New Issue  
20230522 18:36  wyldckat  Note Added: 0013022  
20230523 11:41  will  Note Added: 0013023  
20230523 15:44  EmilyManchester  Note Added: 0013024  
20230523 15:44  EmilyManchester  File Added: pitzDailyPulse.zip  
20230523 16:35  henry  Note Added: 0013025  
20230523 16:54  EmilyManchester  Note Added: 0013027  
20230523 16:54  EmilyManchester  File Added: errorlog.pimpleFoam_parallel  
20230523 17:14  will  Assigned To  => will 
20230523 17:14  will  Status  new => closed 
20230523 17:14  will  Resolution  open => fixed 
20230523 17:14  will  Note Added: 0013028  
20230523 17:14  will  Note Edited: 0013028  
20230523 17:15  henry  Note Added: 0013029  
20230523 17:15  henry  File Added: log 