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July 13, 2013, 05:32 |
decomposePar 4-core warning/error?
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#1 |
Member
Anand Lobo
Join Date: Jun 2013
Posts: 56
Rep Power: 13 |
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. |
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July 13, 2013, 15:00 |
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#2 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
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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:
Best regards, Bruno
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July 15, 2013, 05:21 |
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#3 | |
Member
Anand Lobo
Join Date: Jun 2013
Posts: 56
Rep Power: 13 |
Quote:
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" ); 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. Last edited by Boloar; July 15, 2013 at 06:35. |
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July 15, 2013, 05:37 |
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#4 |
Member
Anand Lobo
Join Date: Jun 2013
Posts: 56
Rep Power: 13 |
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! Last edited by Boloar; July 15, 2013 at 07:38. |
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July 16, 2013, 17:06 |
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#5 |
Retired Super Moderator
Bruno Santos
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Hi Anand,
I'll try to look at this as soon as I can, possibly only in the coming weekend Best regards, Bruno
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July 16, 2013, 23:17 |
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#6 |
Senior Member
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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); } );
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July 21, 2013, 11:53 |
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#7 |
Retired Super Moderator
Bruno Santos
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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 $FOAM_SRC/turbulenceModels/incompressible/RAS/lnInclude/alphatJayatillekeWallFunctionFvPatchScalarField.H In theory, you should only have problems if you eventually do need this wall function "alphatJayatillekeWallFunction" in either "incompressible" or "compressible", because only the first one registered is the most likely to be used. If this is the case, you'll have to switch to OpenFOAM 2.2.x or apply manually the commit I mentioned above and rebuild only the library "$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
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July 22, 2013, 03:58 |
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#8 | |
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Anand Lobo
Join Date: Jun 2013
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Quote:
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. |
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August 21, 2013, 11:33 |
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#9 |
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laurentL
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hello,
just to confirme that the solution from Bruno works find for me thanks again Bruno! |
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August 21, 2013, 23:59 |
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#10 |
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Anand Lobo
Join Date: Jun 2013
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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
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August 28, 2013, 10:20 |
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#11 | |
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musaddeque hossein
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Quote:
Please let me know, thanks! |
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August 28, 2013, 11:32 |
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#12 |
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laurentL
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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 |
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August 28, 2013, 17:05 |
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#13 |
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musaddeque hossein
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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 |
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August 29, 2013, 00:32 |
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#14 |
Senior Member
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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
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August 29, 2013, 08:19 |
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#15 |
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musaddeque hossein
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August 30, 2013, 23:17 |
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#16 |
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Robert
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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. |
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August 31, 2013, 09:42 |
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#17 |
Senior Member
musaddeque hossein
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Robert:
Thankyou very much. Much appreciated!! |
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February 6, 2014, 11:34 |
swak4foam patch give the same error
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#18 |
Member
Emeline Noel
Join Date: Dec 2013
Location: Paris
Posts: 31
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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 |
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February 6, 2014, 17:08 |
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#19 |
Retired Super Moderator
Bruno Santos
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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:
Bruno
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March 27, 2014, 10:34 |
Informations
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#20 | |
Member
Emeline Noel
Join Date: Dec 2013
Location: Paris
Posts: 31
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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:
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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