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-   -   decomposePar 4-core warning/error? (http://www.cfd-online.com/Forums/openfoam-bugs/120728-decomposepar-4-core-warning-error.html)

Boloar July 13, 2013 05:32

decomposePar 4-core warning/error?
 
Hi guys.
I've got a 2D VAWT simulation running on a 6-year-old dual-Xeon processor with hyperthreading (so effectively quad-core) computer.
I've run the very same simulation on my 5-year-old Core 2 Duo laptop, with no hitches. But on the quad-core, I got this weird error in my log.decomposePar file. Any advice as to what it might mean?

I'm not even sure if it's really an error, since decomposePar finishes without a problem and pimpleDyMFoam runs afterward without crashing ...

Code:

/*---------------------------------------------------------------------------*\
| =========                |                                                |
| \\      /  F ield        | OpenFOAM: The Open Source CFD Toolbox          |
|  \\    /  O peration    | Version:  2.2.1                                |
|  \\  /    A nd          | Web:      www.OpenFOAM.org                      |
|    \\/    M anipulation  |                                                |
\*---------------------------------------------------------------------------*/
Build  : 2.2.1-57f3c3617a2d
Exec  : decomposePar
Date  : Jul 13 2013
Time  : 12:23:57
Host  : "Ubuntu"
PID    : 2796
Case  : vawt_sim_4cores
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Duplicate entry alphatJayatillekeWallFunction in runtime selection table fvPatchField
#0        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam5error14safePrintStackERSo+0x29) [0xb6134fc9]
#1        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libincompressibleRASModels.so(_ZN4Foam12fvPatchFieldIdE26addpatchConstructorToTableINS_14incompressible47alphatJayatillekeWallFunctionFvPatchScalarFieldEEC2ERKNS_4wordE+0x111) [0xb5269d11]
#2        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libincompressibleRASModels.so(+0xb6952) [0xb5121952]
#3        /lib/ld-linux.so.2(+0xf216) [0xb77b9216]
#4        /lib/ld-linux.so.2(+0xf2fc) [0xb77b92fc]
#5        /lib/ld-linux.so.2(+0x132b6) [0xb77bd2b6]
#6        /lib/ld-linux.so.2(+0xf05e) [0xb77b905e]
#7        /lib/ld-linux.so.2(+0x12af4) [0xb77bcaf4]
#8        /lib/i386-linux-gnu/libdl.so.2(+0x19ed) [0xb5bd59ed]
#9        /lib/ld-linux.so.2(+0xf05e) [0xb77b905e]
#10        /lib/i386-linux-gnu/libdl.so.2(+0x1422) [0xb5bd5422]
#11        /lib/i386-linux-gnu/libdl.so.2(dlopen+0x4c) [0xb5bd5a7c]
#12        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam6dlOpenERKNS_8fileNameEb+0x48) [0xb612edf8]
#13        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable4openERKNS_8fileNameEb+0x61) [0xb5ea5991]
#14        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable4openERKNS_10dictionaryERKNS_4wordE+0xb7) [0xb5ea5cf7]
#15        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam4TimeC1ERKNS_4wordERKNS_7argListES3_S3_+0x366) [0xb5ebfb06]
#16        decomposePar() [0x80ad0a7]
#17        /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0xb58f1935]
#18        decomposePar() [0x80b5591]
Duplicate entry alphatJayatillekeWallFunction in runtime selection table fvPatchField
#0        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam5error14safePrintStackERSo+0x29) [0xb6134fc9]
#1        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libincompressibleRASModels.so(_ZN4Foam12fvPatchFieldIdE32addpatchMapperConstructorToTableINS_14incompressible47alphatJayatillekeWallFunctionFvPatchScalarFieldEEC2ERKNS_4wordE+0xd0) [0xb5269e10]
#2        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libincompressibleRASModels.so(+0xb697a) [0xb512197a]
#3        /lib/ld-linux.so.2(+0xf216) [0xb77b9216]
#4        /lib/ld-linux.so.2(+0xf2fc) [0xb77b92fc]
#5        /lib/ld-linux.so.2(+0x132b6) [0xb77bd2b6]
#6        /lib/ld-linux.so.2(+0xf05e) [0xb77b905e]
#7        /lib/ld-linux.so.2(+0x12af4) [0xb77bcaf4]
#8        /lib/i386-linux-gnu/libdl.so.2(+0x19ed) [0xb5bd59ed]
#9        /lib/ld-linux.so.2(+0xf05e) [0xb77b905e]
#10        /lib/i386-linux-gnu/libdl.so.2(+0x1422) [0xb5bd5422]
#11        /lib/i386-linux-gnu/libdl.so.2(dlopen+0x4c) [0xb5bd5a7c]
#12        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam6dlOpenERKNS_8fileNameEb+0x48) [0xb612edf8]
#13        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable4openERKNS_8fileNameEb+0x61) [0xb5ea5991]
#14        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable4openERKNS_10dictionaryERKNS_4wordE+0xb7) [0xb5ea5cf7]
#15        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam4TimeC1ERKNS_4wordERKNS_7argListES3_S3_+0x366) [0xb5ebfb06]
#16        decomposePar() [0x80ad0a7]
#17        /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0xb58f1935]
#18        decomposePar() [0x80b5591]
Duplicate entry alphatJayatillekeWallFunction in runtime selection table fvPatchField
#0        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam5error14safePrintStackERSo+0x29) [0xb6134fc9]
#1        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libincompressibleRASModels.so(_ZN4Foam12fvPatchFieldIdE31adddictionaryConstructorToTableINS_14incompressible47alphatJayatillekeWallFunctionFvPatchScalarFieldEEC2ERKNS_4wordE+0xd0) [0xb5269ef0]
#2        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libincompressibleRASModels.so(+0xb69a2) [0xb51219a2]
#3        /lib/ld-linux.so.2(+0xf216) [0xb77b9216]
#4        /lib/ld-linux.so.2(+0xf2fc) [0xb77b92fc]
#5        /lib/ld-linux.so.2(+0x132b6) [0xb77bd2b6]
#6        /lib/ld-linux.so.2(+0xf05e) [0xb77b905e]
#7        /lib/ld-linux.so.2(+0x12af4) [0xb77bcaf4]
#8        /lib/i386-linux-gnu/libdl.so.2(+0x19ed) [0xb5bd59ed]
#9        /lib/ld-linux.so.2(+0xf05e) [0xb77b905e]
#10        /lib/i386-linux-gnu/libdl.so.2(+0x1422) [0xb5bd5422]
#11        /lib/i386-linux-gnu/libdl.so.2(dlopen+0x4c) [0xb5bd5a7c]
#12        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam6dlOpenERKNS_8fileNameEb+0x48) [0xb612edf8]
#13        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable4openERKNS_8fileNameEb+0x61) [0xb5ea5991]
#14        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable4openERKNS_10dictionaryERKNS_4wordE+0xb7) [0xb5ea5cf7]
#15        /opt/openfoam221/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam4TimeC1ERKNS_4wordERKNS_7argListES3_S3_+0x366) [0xb5ebfb06]
#16        decomposePar() [0x80ad0a7]
#17        /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0xb58f1935]
#18        decomposePar() [0x80b5591]


Decomposing mesh region0

Create mesh

Calculating distribution of cells
Selecting decompositionMethod simple

Finished decomposition in 0.01 s

Calculating original mesh data

Distributing cells to processors

Distributing faces to processors

Distributing points to processors

Constructing processor meshes

Processor 0
    Number of cells = 3056
    Number of faces shared with processor 1 = 67
    Number of faces shared with processor 2 = 81
    Number of processor patches = 2
    Number of processor faces = 148
    Number of boundary faces = 6513

Processor 1
    Number of cells = 3109
    Number of faces shared with processor 0 = 67
    Number of faces shared with processor 3 = 64
    Number of processor patches = 2
    Number of processor faces = 131
    Number of boundary faces = 6668

Processor 2
    Number of cells = 3109
    Number of faces shared with processor 0 = 81
    Number of faces shared with processor 3 = 72
    Number of processor patches = 2
    Number of processor faces = 153
    Number of boundary faces = 6611

Processor 3
    Number of cells = 3055
    Number of faces shared with processor 1 = 64
    Number of faces shared with processor 2 = 72
    Number of processor patches = 2
    Number of processor faces = 136
    Number of boundary faces = 6548

Number of processor faces = 284
Max number of cells = 3109 (0.8678724957% above average 3082.25)
Max number of processor patches = 2 (0% above average 2)
Max number of faces between processors = 153 (7.746478873% above average 142)

Time = 0

Processor 0: field transfer
Processor 1: field transfer
Processor 2: field transfer
Processor 3: field transfer

End.


wyldckat July 13, 2013 15:00

Greetings Anand,

This is indeed an intriguing warning message... it seems to have loaded the library "libincompressibleRASModels.so" 4 times, where it complains 3 times when it finds the repeated object "alphatJayatillekeWallFunction".

OK, a few questions:
  1. How did you install OpenFOAM 2.2.1? Did you use the official Deb packs for Ubuntu?
  2. Do you also have OpenFOAM 2.2.0 installed? And if you do, how are you keeping them apart?
  3. Does your case have the entry "libs" in the file "system/controlDict"? And if it does, what does it contain?
  4. Do any of the boundary conditions in your case use the incompressible "alphatJayatillekeWallFunction"? Possibly 4 boundary conditions?
  5. Do you have any customized boundary conditions in binary form? If you do, is there any named "alphatJayatillekeWallFunction"?
  6. Have you modified the global or personal "controlDict" files? For more on this topic: http://openfoamwiki.net/index.php/Ho...in_debug_flags
Either way, at first glance, it doesn't seem to be too problematic, but if the solver complains about the same, then it might be a good reason for concern.

Best regards,
Bruno

Boloar July 15, 2013 05:21

Quote:

Originally Posted by wyldckat (Post 439569)
  1. How did you install OpenFOAM 2.2.1? Did you use the official Deb packs for Ubuntu?
  2. Do you also have OpenFOAM 2.2.0 installed? And if you do, how are you keeping them apart?
  3. Does your case have the entry "libs" in the file "system/controlDict"? And if it does, what does it contain?
  4. Do any of the boundary conditions in your case use the incompressible "alphatJayatillekeWallFunction"? Possibly 4 boundary conditions?
  5. Do you have any customized boundary conditions in binary form? If you do, is there any named "alphatJayatillekeWallFunction"?
  6. Have you modified the global or personal "controlDict" files? For more on this topic: http://openfoamwiki.net/index.php/Ho...in_debug_flags
Either way, at first glance, it doesn't seem to be too problematic, but if the solver complains about the same, then it might be a good reason for concern.

I'm using Lubuntu 13.04 (raring) (dual-booting with Windows).

Looks like the solver had the same error in the beginning, but it still continued solving. I had stopped the simulation myself after about two hours or so since I had to switch to Windows for a while. After about 2 hours of simulation it had got to approximately 0.8s of simulated time, and I had set it to simulate 8 seconds.

Background information on the case: I basically used the AMI mesh from the tutorial incompressible/pimpleDyMFoam/propeller, converted into a 2D mesh using my own STL files, and basically dumped that mesh into the tutorial incompressible/pimpleDyMFoam/wingmotion2D/pimpleDyMFoam. After a lot of work and a lot of help, I got it solving.
This worked fine on my dual core. The only change I made was in decomposeParDict and the Allrun bash script to break it into 4 instead of 2.

1) Yes, I installed OpenFOAM 2.2.1 using the deb packs.
2) I don't have 2.2.0 installed.

3) The libs entry in controlDict contains:
Code:

libs
(
    "libOpenFOAM.so"
    "libforces.so"
);

This should be exactly the same as the wingMotion tutorial.

4), 5), and 6) I'm not familiar enough with OpenFOAM to try any major customizations, I stuck with using the boundary conditions from the wingMotion tutorial with no changes. The only change I made to the controlDict file was the maxCo parameter, from 0.9 to 0.5.

Boloar July 15, 2013 05:37

https://www.dropbox.com/s/ip7zqpslwz1zass/VAWT_sim.zip

There's my (cleaned) case files, with the log files from the previous run included. Looks like the error's in all of the files. I'm not sure why it would call it multiple times ... And I have no memory of ever typing in any different wallFunction except what was in the wingMotion tutorial.
Thanks for your advice!

wyldckat July 16, 2013 17:06

Hi Anand,

I'll try to look at this as soon as I can, possibly only in the coming weekend :(

Best regards,
Bruno

julien.decharentenay July 16, 2013 23:17

Hi, I have encountered the same issue and narrowed it down to the following (in my case):

forces function in the controlDict:

Code:

functions
(
  forces
  {
    type forces;
    functionObjectLibs ( "libforces.so" );
    outputControl timeStep;
    outputInterval 1;
    patches ( Volume_0 );
    rhoName  rhoInf;
    rhoInf  1.205;
    pName    p;
    UName    U;
    log      true;
    CofR    (4.999999999999449e-05 0.0 0.0);
  }
);

If you comment the section, the error disappear - but in all likelyhood the forces output disappear as well...

wyldckat July 21, 2013 11:53

Greetings to all!

I've narrowed it down.
It's as Julien says, the "libforces.so" library helps introduce the problem. I can replicate this issue with the tutorial case "mesh/moveDynamicMesh/simpleHarmonicMotion", while using OpenFOAM 2.2.1 installed from Ubuntu Deb packages on Ubuntu 12.04, both i686 and x86_64. I only need to run blockMesh, in order to trigger the same messages.

Nonetheless, the error doesn't come from "libforces.so" itself, it's because of the following two files:
Code:

$FOAM_SRC/turbulenceModels/compressible/RAS/lnInclude/alphatJayatillekeWallFunctionFvPatchScalarField.H
$FOAM_SRC/turbulenceModels/incompressible/RAS/lnInclude/alphatJayatillekeWallFunctionFvPatchScalarField.H

In 2.2.1, they have the same exact name runtime name "alphatJayatillekeWallFunction", which is why the message is shown. But this has been fixed on the day right after the release: https://github.com/OpenFOAM/OpenFOAM...94a946c945a99b

In theory, you should only have problems if you eventually do need this wall function "alphatJayatillekeWallFunction" in either "incompressible" or "compressible", because only the first one registered is the most likely to be used. If this is the case, you'll have to switch to OpenFOAM 2.2.x or apply manually the commit I mentioned above and rebuild only the library "$FOAM_SRC/turbulenceModels/compressible/RAS/".


I've moved this thread to the bugs section, so that it will make it easier to be found in the future.

Best regards,
Bruno

Boloar July 22, 2013 03:58

Quote:

Originally Posted by wyldckat (Post 441050)
In theory, you should only have problems if you eventually do need this wall function "alphatJayatillekeWallFunction"

Much thanks, Bruno!

As far as I can tell, it doesn't affect anything during runtime since I don't actually call on that wallFunction for anything. I think I'll leave it as is since my simulation is running well for now.

laurent98 August 21, 2013 11:33

hello,
just to confirme that the solution from Bruno works find for me
thanks again Bruno!

Boloar August 21, 2013 23:59

Yeah, I haven't had this error since I upgraded to the latest GitHub release. It wasn't bothering the simulation, but it's no longer bothering me :D

musahossein August 28, 2013 10:20

Quote:

Originally Posted by wyldckat (Post 441050)
Greetings to all!

I've narrowed it down.
It's as Julien says, the "libforces.so" library helps introduce the problem. I can replicate this issue with the tutorial case "mesh/moveDynamicMesh/simpleHarmonicMotion", while using OpenFOAM 2.2.1 installed from Ubuntu Deb packages on Ubuntu 12.04, both i686 and x86_64. I only need to run blockMesh, in order to trigger the same messages.

Nonetheless, the error doesn't come from "libforces.so" itself, it's because of the following two files:
Code:

$FOAM_SRC/turbulenceModels/compressible/RAS/lnInclude/alphatJayatillekeWallFunctionFvPatchScalarField.H
$FOAM_SRC/turbulenceModels/incompressible/RAS/lnInclude/alphatJayatillekeWallFunctionFvPatchScalarField.H

In 2.2.1, they have the same exact name runtime name "alphatJayatillekeWallFunction", which is why the message is shown. But this has been fixed on the day right after the release: https://github.com/OpenFOAM/OpenFOAM...94a946c945a99b

In theory, you should only have problems if you eventually do need this wall function "alphatJayatillekeWallFunction" in either "incompressible" or "compressible", because only the first one registered is the most likely to be used. If this is the case, you'll have to switch to OpenFOAM 2.2.x or apply manually the commit I mentioned above and rebuild only the library "$FOAM_SRC/turbulenceModels/compressible/RAS/".


I've moved this thread to the bugs section, so that it will make it easier to be found in the future.

Best regards,
Bruno

I have the same problem and it appears to be triggered whenever the "libforces.so" is included in controlDict. I am running OpenFOAM 2.2.1. So how do I fix it?

Please let me know, thanks!

laurent98 August 28, 2013 11:32

very simple, just change the files
OpenFOAM-2.2.x / src / turbulenceModels / compressible / RAS / derivedFvPatchFields / wallFunctions / alphatWallFunctions / alphatJayatillekeWallFunction / alphatJayatillekeWallFunctionFvPatchScalarField.H
as describe in the link, and compile
cheers LL

musahossein August 28, 2013 17:05

Thankyou verymuch for your response. As I am a newbie when it comes to linux admin, I am not familiar with the steps involved. Are the steps described somewhere that you may know of or will you be able to provide them?

Sorry for the trouble.

Thanks
Musa

julien.decharentenay August 29, 2013 00:32

Hi Musa,

I have personally gone the way of not trying to fix it. I am just waiting for the next oF version to be released. The issue is "cosmetic" for me as it only affect the screen output.

Julien

musahossein August 29, 2013 08:19

Quote:

Originally Posted by julien.decharentenay (Post 448642)
Hi Musa,

I have personally gone the way of not trying to fix it. I am just waiting for the next oF version to be released. The issue is "cosmetic" for me as it only affect the screen output.

Julien

Understood. Thankyou for your response.

lordvon August 30, 2013 23:17

In case you still wanted to know, these are the steps I took to recompile:

1. 'sudo bash' and login

2. Replace the 'alphatJayatillekeWallFunctionFvPatchScalarField.H ' file linked above with yours in opt/openfoam221/src/turbulenceModels/... etc (same path); you can get to 'opt/openfoam221/src' by 'cd $FOAM_SRC'

3. Go to '/opt/openfoam221/src/turbulenceModels/compressible/RAS'

4. 'wmake'

5. It will compile in a few minutes or so, and then the errors should be gone.

musahossein August 31, 2013 09:42

Robert:

Thankyou very much. Much appreciated!!

zarox February 6, 2014 12:34

swak4foam patch give the same error
 
Hi everyone,

I have a problem similar than you. But the issue appeared after I applied a patch for swak4foam given by one post in this forum. The patch make ale to have libsimpleSwakFunctionObjects.so and libswakFunctionObjects.so. Now, I didn't have error message concerning that lib but error message similar than you : Duplicate entry .......

If, I don't use libs ( libswakFunctionObjects.so .. No problem ...

Just to inform all of us. Also, I use LES, and all Duplicate entry have a matter with LES ... I don't know what is the problem

wyldckat February 6, 2014 18:08

Greetings zarox,

Sorry, but I could not understand what is the specific problem you're having, since you did not provided any specific information. For example:
  1. Quote:

    Originally Posted by zarox (Post 473778)
    But the issue appeared after I applied a patch for swak4foam given by one post in this forum. The patch make ale to have libsimpleSwakFunctionObjects.so and libswakFunctionObjects.so.

    What specific patch are you referring to and which specific version of swak4Foam are you using?
  2. Quote:

    Originally Posted by zarox (Post 473778)
    Also, I use LES, and all Duplicate entry have a matter with LES ... I don't know what is the problem

    If you don't provide the output given by the solver, we cannot ascertain what exactly is wrong.
  3. What specific version of OpenFOAM are you using?
Best regards,
Bruno

zarox March 27, 2014 11:34

Informations
 
1 Attachment(s)
Hi Wyldckat,

I have read many post from you, your are a master! In order to try to give you some information, the patch was given by you in that post :

Quote:

Originally Posted by wyldckat (Post 434217)
Greetings to all!

@Daniel: Many thanks for the report! I've submitted this issue to swak4Foam's bug tracker: https://sourceforge.net/apps/mantisbt/openfoam-extend/view.php?id=174 - along with the bug fix.

In addition, two notes:
  1. swak4Foam 0.2.4 is already available: http://www.cfd-online.com/Forums/openfoam-news-announcements-other/93090-swak4foam-new-release-2.html#post433484 post #29
  2. Attached is a patch for this version 0.2.4, for compiling with the latest OpenFOAM 2.2.x.
    • Additionally, for those who don't have Git nor SVN ready to be used for getting the latest swak4Foam 0.2.4, feel free to use the ZIP button at the upper left corner of this page: https://github.com/wyldckat/swak4foam/tree/OF22X - it's already patched for building with OpenFOAM 2.2.x.
For applying the attached patch, do the following steps:

  1. Place the attached file inside the main swak4Foam source code folder (version 0.2.4).
  2. Run the following commands:
    Code:

    gunzip patch_swak2Foam_024_OF22x_49808a1c.gz
    patch -p1 < patch_swak2Foam_024_OF22x_49808a1c

  3. And finally, build swak4Foam:
    Code:

    ./Allwmake > make.log 2>&1
Best regards,


Bruno


Before using this patch libsimpleSwakFunctionObjects.so and libswakFunctionObjects.so were not in the lib directory if memory serves well!

In addition the swak4foam version is 0.2.4 and the OpenFOAM version 2.2.2


Concerning the output log, I give a part in the attached file.

Thanks to your reply.

Best Regards


Emeline


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