View Issue Details
| ID | Project | Category | View Status | Date Submitted | Last Update |
|---|---|---|---|---|---|
| 0003983 | OpenFOAM | Bug | public | 2023-05-22 17:41 | 2023-05-23 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 : 8-9603c2377861 |
|
|
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 : 8-1c9b5879390b 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 OpenFOAM-8 and OpenFOAM-dev 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 : 8-1c9b5879390b
Exec : pimpleFoam -parallel
Date : May 23 2023
Time : 16:51:41
Host : "E-10LXXD2299V6V"
PID : 2260
I/O : uncollated
Case : /mnt/m/CodeDevelopment/TestCases/SEM_paraboloid_pulsatile/T008/TestCase/pitzDailyPulse
nProcs : 4
Slaves :
3
(
"E-10LXXD2299V6V.2261"
"E-10LXXD2299V6V.2262"
"E-10LXXD2299V6V.2263"
)
Pstream initialized with:
floatTransfer : 0
nProcsSimpleSum : 0
commsType : nonBlocking
polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied 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 OpenFOAM-8 beyond what you have, and we're not about to start creating them almost three years after OpenFOAM-8's release. Your options are to pull version 8 from github and build it yourself, or update to a pack of OpenFOAM-9 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 : 8-e0f23cae73e0
Exec : pimpleFoam -parallel
Date : May 23 2023
Time : 17:14:53
Host : "dm"
PID : 21927
I/O : uncollated
Case : /home/dm2/henry/OpenFOAM/henry-dev/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 run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied 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: 3.47235e-05 max: 0.0125372
Starting time loop
Courant Number mean: 3.47235e-05 max: 0.0125372
deltaT = 0.00119048
Time = 0.00119048
smoothSolver: Solving for Ux, Initial residual = 1, Final residual = 5.47558e-06, No Iterations 9
smoothSolver: Solving for Uy, Initial residual = 0.0244401, Final residual = 4.6274e-06, No Iterations 5
GAMG: Solving for p, Initial residual = 1, Final residual = 0.00492784, No Iterations 10
time step continuity errors : sum local = 4.46176e-07, global = -2.73624e-08, cumulative = -2.73624e-08
GAMG: Solving for p, Initial residual = 0.023069, Final residual = 4.8959e-08, No Iterations 17
time step continuity errors : sum local = 4.48754e-10, global = -3.98478e-11, cumulative = -2.74023e-08
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 = 4.33887e-06, No Iterations 9
smoothSolver: Solving for Uy, Initial residual = 0.284202, Final residual = 7.34735e-06, No Iterations 9
GAMG: Solving for p, Initial residual = 0.0368593, Final residual = 0.000213222, No Iterations 9
time step continuity errors : sum local = 1.8174e-06, global = -2.2638e-07, cumulative = -2.53783e-07
GAMG: Solving for p, Initial residual = 0.0785227, Final residual = 9.46742e-08, No Iterations 18
time step continuity errors : sum local = 3.20115e-10, global = -2.22408e-11, cumulative = -2.53805e-07
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 = 6.00843e-06, No Iterations 8
smoothSolver: Solving for Uy, Initial residual = 0.168027, Final residual = 5.59485e-06, No Iterations 9
GAMG: Solving for p, Initial residual = 0.275252, Final residual = 0.00221582, No Iterations 4
time step continuity errors : sum local = 2.64634e-06, global = -1.03474e-06, cumulative = -1.28854e-06
GAMG: Solving for p, Initial residual = 0.121411, Final residual = 6.09646e-08, No Iterations 19
time step continuity errors : sum local = 8.44788e-11, global = -1.81652e-11, cumulative = -1.28856e-06
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 = 5.14668e-06, No Iterations 9
smoothSolver: Solving for Uy, Initial residual = 0.0542629, Final residual = 6.35587e-06, No Iterations 9
GAMG: Solving for p, Initial residual = 0.0419176, Final residual = 0.000191396, No Iterations 5
time step continuity errors : sum local = 2.93437e-07, global = 1.16879e-07, cumulative = -1.17168e-06
GAMG: Solving for p, Initial residual = 0.0206295, Final residual = 9.6817e-08, No Iterations 15
time step continuity errors : sum local = 1.44334e-10, global = -2.58226e-11, cumulative = -1.17171e-06
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 = 9.87343e-06, No Iterations 9
smoothSolver: Solving for Uy, Initial residual = 0.033307, Final residual = 5.35931e-06, No Iterations 10
GAMG: Solving for p, Initial residual = 0.00834394, Final residual = 3.69134e-05, No Iterations 8
time step continuity errors : sum local = 6.74476e-08, global = -6.29748e-09, cumulative = -1.178e-06
GAMG: Solving for p, Initial residual = 0.00530647, Final residual = 8.42068e-08, No Iterations 14
time step continuity errors : sum local = 1.7069e-10, global = 1.34942e-11, cumulative = -1.17799e-06
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 = 6.95769e-06, No Iterations 11
smoothSolver: Solving for Uy, Initial residual = 0.0374957, Final residual = 7.53473e-06, No Iterations 11
GAMG: Solving for p, Initial residual = 0.00704514, Final residual = 3.54147e-05, No Iterations 8
time step continuity errors : sum local = 8.85748e-08, global = -1.0318e-08, cumulative = -1.18831e-06
GAMG: Solving for p, Initial residual = 0.00541429, Final residual = 8.52065e-08, No Iterations 14
time step continuity errors : sum local = 2.34366e-10, global = 1.91364e-11, cumulative = -1.18829e-06
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 = 8.49563e-06, No Iterations 12
smoothSolver: Solving for Uy, Initial residual = 0.0386809, Final residual = 9.39543e-06, No Iterations 12
GAMG: Solving for p, Initial residual = 0.00699236, Final residual = 4.48133e-05, No Iterations 8
time step continuity errors : sum local = 1.44917e-07, global = -1.78496e-08, cumulative = -1.20614e-06
GAMG: Solving for p, Initial residual = 0.00561656, Final residual = 5.40502e-08, No Iterations 15
time step continuity errors : sum local = 1.9472e-10, global = -1.94988e-11, cumulative = -1.20616e-06
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 = 8.43489e-06, No Iterations 14
smoothSolver: Solving for Uy, Initial residual = 0.0417478, Final residual = 6.46956e-06, No Iterations 15
GAMG: Solving for p, Initial residual = 0.0084841, Final residual = 4.64554e-05, No Iterations 8
time step continuity errors : sum local = 2.04803e-07, global = -2.55381e-08, cumulative = -1.2317e-06
GAMG: Solving for p, Initial residual = 0.00674411, Final residual = 5.00084e-08, No Iterations 15
time step continuity errors : sum local = 2.46109e-10, global = -2.51078e-11, cumulative = -1.23172e-06
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 = 6.72712e-06, No Iterations 16
smoothSolver: Solving for Uy, Initial residual = 0.0416194, Final residual = 8.23109e-06, No Iterations 16
GAMG: Solving for p, Initial residual = 0.00974356, Final residual = 9.66558e-05, No Iterations 7
time step continuity errors : sum local = 5.25974e-07, global = 9.67635e-08, cumulative = -1.13496e-06
GAMG: Solving for p, Initial residual = 0.00758843, Final residual = 7.84621e-08, No Iterations 14
time step continuity errors : sum local = 4.68991e-10, global = 3.71463e-11, cumulative = -1.13492e-06
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 = 7.39866e-06, No Iterations 18
smoothSolver: Solving for Uy, Initial residual = 0.0421904, Final residual = 9.19042e-06, No Iterations 18
GAMG: Solving for p, Initial residual = 0.0107398, Final residual = 4.30291e-05, No Iterations 7
time step continuity errors : sum local = 2.98824e-07, global = -8.25902e-08, cumulative = -1.21751e-06
GAMG: Solving for p, Initial residual = 0.00807351, Final residual = 8.52643e-08, No Iterations 14
time step continuity errors : sum local = 6.28222e-10, global = -7.83348e-11, cumulative = -1.21759e-06
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 = 7.29686e-06, No Iterations 18
smoothSolver: Solving for Uy, Initial residual = 0.036476, Final residual = 8.48955e-06, No Iterations 18
GAMG: Solving for p, Initial residual = 0.00984132, Final residual = 7.28346e-05, No Iterations 5
time step continuity errors : sum local = 5.16084e-07, global = 4.53598e-08, cumulative = -1.17223e-06
GAMG: Solving for p, Initial residual = 0.00680361, Final residual = 5.22537e-08, No Iterations 16
time step continuity errors : sum local = 3.66576e-10, global = -7.31249e-11, cumulative = -1.1723e-06
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 = 7.07156e-06, No Iterations 18
smoothSolver: Solving for Uy, Initial residual = 0.0312272, Final residual = 7.73722e-06, No Iterations 18
GAMG: Solving for p, Initial residual = 0.00874256, Final residual = 4.40883e-05, No Iterations 7
time step continuity errors : sum local = 3.1006e-07, global = 5.19179e-08, cumulative = -1.12039e-06
GAMG: Solving for p, Initial residual = 0.00852431, Final residual = 5.96332e-08, No Iterations 15
time step continuity errors : sum local = 3.83327e-10, global = -4.58498e-11, cumulative = -1.12043e-06
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 = 9.59999e-06, No Iterations 17
smoothSolver: Solving for Uy, Initial residual = 0.0268009, Final residual = 9.95387e-06, No Iterations 17
GAMG: Solving for p, Initial residual = 0.0127583, Final residual = 0.000106596, No Iterations 7
time step continuity errors : sum local = 7.23585e-07, global = -1.33255e-07, cumulative = -1.25369e-06
GAMG: Solving for p, Initial residual = 0.0152239, Final residual = 7.57264e-08, No Iterations 16
time step continuity errors : sum local = 4.29747e-10, global = -3.20484e-11, cumulative = -1.25372e-06
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 = 8.8609e-06, No Iterations 17
smoothSolver: Solving for Uy, Initial residual = 0.0228145, Final residual = 8.70941e-06, No Iterations 17
GAMG: Solving for p, Initial residual = 0.0180435, Final residual = 6.93997e-05, No Iterations 8
time step continuity errors : sum local = 4.41971e-07, global = 5.21092e-08, cumulative = -1.20161e-06
GAMG: Solving for p, Initial residual = 0.0239871, Final residual = 5.46559e-08, No Iterations 17
time step continuity errors : sum local = 2.64241e-10, global = 2.78088e-11, cumulative = -1.20158e-06
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 = 7.92436e-06, No Iterations 17
smoothSolver: Solving for Uy, Initial residual = 0.0193969, Final residual = 7.38931e-06, No Iterations 17
GAMG: Solving for p, Initial residual = 0.0235672, Final residual = 9.52278e-05, No Iterations 8
time step continuity errors : sum local = 5.52774e-07, global = 6.71122e-08, cumulative = -1.13447e-06
GAMG: Solving for p, Initial residual = 0.0349452, Final residual = 7.7662e-08, No Iterations 17
time step continuity errors : sum local = 3.07951e-10, global = 3.24414e-11, cumulative = -1.13444e-06
ExecutionTime = 0.56 s ClockTime = 1 s
.
.
.
|
| Date Modified | Username | Field | Change |
|---|---|---|---|
| 2023-05-22 17:41 | EmilyManchester | New Issue | |
| 2023-05-22 18:36 | wyldckat | Note Added: 0013022 | |
| 2023-05-23 11:41 | will | Note Added: 0013023 | |
| 2023-05-23 15:44 | EmilyManchester | Note Added: 0013024 | |
| 2023-05-23 15:44 | EmilyManchester | File Added: pitzDailyPulse.zip | |
| 2023-05-23 16:35 | henry | Note Added: 0013025 | |
| 2023-05-23 16:54 | EmilyManchester | Note Added: 0013027 | |
| 2023-05-23 16:54 | EmilyManchester | File Added: errorlog.pimpleFoam_parallel | |
| 2023-05-23 17:14 | will | Assigned To | => will |
| 2023-05-23 17:14 | will | Status | new => closed |
| 2023-05-23 17:14 | will | Resolution | open => fixed |
| 2023-05-23 17:14 | will | Note Added: 0013028 | |
| 2023-05-23 17:14 | will | Note Edited: 0013028 | |
| 2023-05-23 17:15 | henry | Note Added: 0013029 | |
| 2023-05-23 17:15 | henry | File Added: log |
