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undefined symbol Error After Modifying Turbulence Model |
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#1 |
New Member
Kuzey Can Derman
Join Date: Oct 2022
Posts: 12
Rep Power: 3 ![]() |
Hello,
I was learning to modify and compile turbulence models from a youtube (can't post link) tutorial. It is trying modify kOmega model My options file inside Make directory is as Code:
EXE_INC = \ -I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \ -I$(LIB_SRC)/TurbulenceModels/incompressible/lnInclude \ -I$(LIB_SRC)/transportModels \ -I$(LIB_SRC)/finiteVolume/lnInclude \ -I$(LIB_SRC)/meshTools/lnInclude LIB_LIBS = \ -lincompressibleTransportModels \ -lturbulenceModels \ -lfiniteVolume \ -lmeshTools Code:
--> FOAM Warning : From void* Foam::dlLibraryTable::openLibrary(const Foam::fileName&, bool) in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 65 Could not load "$FOAM_USER_LIBBIN/myturbulentTransportModels.so" /home/myname/OpenFOAM/myname-v2006/platforms/linux64GccDPInt32Opt/lib/myturbulentTransportModels.so: undefined symbol: _ZNK4Foam29incompressibleTurbulenceModel2muEl My first consideration was some local file issue with cluster but I don't know. I can supply other materials. Please help, thank you. |
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#2 |
New Member
Kuzey Can Derman
Join Date: Oct 2022
Posts: 12
Rep Power: 3 ![]() |
Somewhat it is solved. I can see the name of my turbulence model. But now some other thing is broken.
As a last resort I copied libraries I need to the user lib directory. Then after compilation and running simpleFoam it started giving me duplicate entry errors. Then I deleted those libraries from user lib and compiled again but error didn't disappear. I don't know whether I broke something by doing this. Error is: Code:
Duplicate entry laminar in runtime selection table TurbulenceModel #0 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam5error14safePrintStackERSo+0x27) [0x7fadfa88cb57] #1 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libincompressibleTurbulenceModels.so(_ZN4Foam15TurbulenceModelINS_17geometricOneFieldES1_NS_29incompressibleTurbulenceModelENS_14transportModelEE31adddictionaryConstructorToTableINS_12laminarModelINS_29IncompressibleTurbulenceModelIS3_EEEEEC1ERKNS_4wordE+0xd6) [0x7fadfb4010b6] #2 /home/myname/OpenFOAM/myname-v2006/platforms/linux64GccDPInt32Opt/lib/myturbulentTransportModels.so(+0x35fc7) [0x7fadf1731fc7] #3 /lib64/ld-linux-x86-64.so.2(+0xfac3) [0x7fadff387ac3] #4 /lib64/ld-linux-x86-64.so.2(+0x1469e) [0x7fadff38c69e] #5 /lib64/ld-linux-x86-64.so.2(+0xf8d4) [0x7fadff3878d4] #6 /lib64/ld-linux-x86-64.so.2(+0x13c8b) [0x7fadff38bc8b] #7 /lib64/libdl.so.2(+0xeeb) [0x7fadf9e5eeeb] #8 /lib64/ld-linux-x86-64.so.2(+0xf8d4) [0x7fadff3878d4] #9 /lib64/libdl.so.2(+0x14ed) [0x7fadf9e5f4ed] #10 /lib64/libdl.so.2(dlopen+0x31) [0x7fadf9e5ef81] #11 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam6dlOpenERKNS_8fileNameEb+0x39) [0x7fadfa87e789] #12 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam6dlOpenERKNS_8fileNameERSs+0xe) [0x7fadfa87fb0e] #13 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable11openLibraryERKNS_8fileNameEb+0x77) [0x7fadfa58c617] #14 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable4openERKNS_8fileNameEb+0x16) [0x7fadfa58d806] #15 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable4openERKNS_10dictionaryERKNS_4wordE+0x68) [0x7fadfa58dab8] #16 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam4TimeC2ERKNS_4wordERKNS_7argListES3_S3_bb+0x4af) [0x7fadfa5b9b2f] #17 simpleFoam() [0x421737] #18 simpleFoam() [0x41bca6] #19 /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fadf90783d5] #20 simpleFoam() [0x41f10d] Duplicate entry RAS in runtime selection table TurbulenceModel #0 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam5error14safePrintStackERSo+0x27) [0x7fadfa88cb57] #1 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libincompressibleTurbulenceModels.so(_ZN4Foam15TurbulenceModelINS_17geometricOneFieldES1_NS_29incompressibleTurbulenceModelENS_14transportModelEE31adddictionaryConstructorToTableINS_8RASModelINS_29IncompressibleTurbulenceModelIS3_EEEEEC1ERKNS_4wordE+0xd6) [0x7fadfb4011b6] #2 /home/myname/OpenFOAM/myname-v2006/platforms/linux64GccDPInt32Opt/lib/myturbulentTransportModels.so(+0x36072) [0x7fadf1732072] #3 /lib64/ld-linux-x86-64.so.2(+0xfac3) [0x7fadff387ac3] #4 /lib64/ld-linux-x86-64.so.2(+0x1469e) [0x7fadff38c69e] #5 /lib64/ld-linux-x86-64.so.2(+0xf8d4) [0x7fadff3878d4] #6 /lib64/ld-linux-x86-64.so.2(+0x13c8b) [0x7fadff38bc8b] #7 /lib64/libdl.so.2(+0xeeb) [0x7fadf9e5eeeb] #8 /lib64/ld-linux-x86-64.so.2(+0xf8d4) [0x7fadff3878d4] #9 /lib64/libdl.so.2(+0x14ed) [0x7fadf9e5f4ed] #10 /lib64/libdl.so.2(dlopen+0x31) [0x7fadf9e5ef81] #11 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam6dlOpenERKNS_8fileNameEb+0x39) [0x7fadfa87e789] #12 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam6dlOpenERKNS_8fileNameERSs+0xe) [0x7fadfa87fb0e] #13 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable11openLibraryERKNS_8fileNameEb+0x77) [0x7fadfa58c617] #14 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable4openERKNS_8fileNameEb+0x16) [0x7fadfa58d806] #15 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable4openERKNS_10dictionaryERKNS_4wordE+0x68) [0x7fadfa58dab8] #16 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam4TimeC2ERKNS_4wordERKNS_7argListES3_S3_bb+0x4af) [0x7fadfa5b9b2f] #17 simpleFoam() [0x421737] #18 simpleFoam() [0x41bca6] #19 /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fadf90783d5] #20 simpleFoam() [0x41f10d] Duplicate entry LES in runtime selection table TurbulenceModel #0 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam5error14safePrintStackERSo+0x27) [0x7fadfa88cb57] #1 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libincompressibleTurbulenceModels.so(_ZN4Foam15TurbulenceModelINS_17geometricOneFieldES1_NS_29incompressibleTurbulenceModelENS_14transportModelEE31adddictionaryConstructorToTableINS_8LESModelINS_29IncompressibleTurbulenceModelIS3_EEEEEC2ERKNS_4wordE+0xd6) [0x7fadfb4012b6] #2 /home/myname/OpenFOAM/myname-v2006/platforms/linux64GccDPInt32Opt/lib/myturbulentTransportModels.so(+0x3611d) [0x7fadf173211d] #3 /lib64/ld-linux-x86-64.so.2(+0xfac3) [0x7fadff387ac3] #4 /lib64/ld-linux-x86-64.so.2(+0x1469e) [0x7fadff38c69e] #5 /lib64/ld-linux-x86-64.so.2(+0xf8d4) [0x7fadff3878d4] #6 /lib64/ld-linux-x86-64.so.2(+0x13c8b) [0x7fadff38bc8b] #7 /lib64/libdl.so.2(+0xeeb) [0x7fadf9e5eeeb] #8 /lib64/ld-linux-x86-64.so.2(+0xf8d4) [0x7fadff3878d4] #9 /lib64/libdl.so.2(+0x14ed) [0x7fadf9e5f4ed] #10 /lib64/libdl.so.2(dlopen+0x31) [0x7fadf9e5ef81] #11 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam6dlOpenERKNS_8fileNameEb+0x39) [0x7fadfa87e789] #12 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam6dlOpenERKNS_8fileNameERSs+0xe) [0x7fadfa87fb0e] #13 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable11openLibraryERKNS_8fileNameEb+0x77) [0x7fadfa58c617] #14 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable4openERKNS_8fileNameEb+0x16) [0x7fadfa58d806] #15 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam14dlLibraryTable4openERKNS_10dictionaryERKNS_4wordE+0x68) [0x7fadfa58dab8] #16 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam4TimeC2ERKNS_4wordERKNS_7argListES3_S3_bb+0x4af) [0x7fadfa5b9b2f] #17 simpleFoam() [0x421737] #18 simpleFoam() [0x41bca6] #19 /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fadf90783d5] #20 simpleFoam() [0x41f10d] Any help is appreciated, thank you. |
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#3 |
New Member
Yueyun Xi
Join Date: Nov 2022
Posts: 14
Rep Power: 3 ![]() |
Hi Kuzey,
I have met the "duplicate entry in runtime selection table" warning before, and I think that's because I have two versions of source code of my custom class, and during the compilation, different parts of OpenFOAM used different versions. So, my custom class register with the runtime selection table twice. From my personal experience, I didn't find that it will effect the functionality of the solver (except from raising this warning). Hope this would help, Yueyun Last edited by yueyun; November 13, 2023 at 07:57. Reason: Fix typo |
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#4 |
New Member
Kuzey Can Derman
Join Date: Oct 2022
Posts: 12
Rep Power: 3 ![]() |
Thanks for the answer Yueyun.
Can you describe more about "I have two versions of source code". And while solver works and goes few hundred iterations, it crashes before finishing. Thanks, Kuzey. |
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#5 |
New Member
Kuzey Can Derman
Join Date: Oct 2022
Posts: 12
Rep Power: 3 ![]() |
simpleFoam starts with above error, works normally and can solve turbulence. But at the end it gives this.
Code:
*** Error in `simpleFoam': corrupted size vs. prev_size: 0x0000000000cb31d0 *** ======= Backtrace: ========= /lib64/libc.so.6(+0x80d37)[0x7f0af84c2d37] /lib64/libc.so.6(+0x8130e)[0x7f0af84c330e] /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam14primitiveEntryD0Ev+0x12f)[0x7f0af9943e5f] /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam10dictionaryD1Ev+0x1fd)[0x7f0af993071d] /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam15dictionaryEntryD0Ev+0x29)[0x7f0af9946a29] /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam10dictionaryD1Ev+0x1fd)[0x7f0af993071d] /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam10dictionaryD0Ev+0x9)[0x7f0af99307f9] /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam5debug20deleteControlDictPtrD1Ev+0x2d2)[0x7f0af97a40c2] /lib64/libc.so.6(__cxa_finalize+0x9a)[0x7f0af847beda] /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(+0x348a13)[0x7f0af9796a13] ======= Memory map: ======== 00400000-0046b000 r-xp 00000000 7af:9233a 144115963216868157 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/bin/simpleFoam 0066a000-0066c000 r--p 0006a000 7af:9233a 144115963216868157 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/bin/simpleFoam 0066c000-0066d000 rw-p 0006c000 7af:9233a 144115963216868157 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/bin/simpleFoam 00a74000-01163000 rw-p 00000000 00:00 0 [heap] 7f0aee940000-7f0aee975000 r-xp 00000000 7af:9233a 144115963216868423 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libODE.so 7f0aee975000-7f0aeeb74000 ---p 00035000 7af:9233a 144115963216868423 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libODE.so 7f0aeeb74000-7f0aeeb76000 r--p 00034000 7af:9233a 144115963216868423 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libODE.so 7f0aeeb76000-7f0aeeb77000 rw-p 00036000 7af:9233a 144115963216868423 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libODE.so 7f0aeeb77000-7f0aeeb8f000 r-xp 00000000 7af:9233a 144115963216868383 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libpairPatchAgglomeration.so 7f0aeeb8f000-7f0aeed8e000 ---p 00018000 7af:9233a 144115963216868383 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libpairPatchAgglomeration.so 7f0aeed8e000-7f0aeed8f000 r--p 00017000 7af:9233a 144115963216868383 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libpairPatchAgglomeration.so 7f0aeed8f000-7f0aeed90000 rw-p 00018000 7af:9233a 144115963216868383 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libpairPatchAgglomeration.so 7f0aeed90000-7f0aefae8000 r-xp 00000000 7af:9233a 144115963216868479 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libchemistryModel.so 7f0aefae8000-7f0aefce7000 ---p 00d58000 7af:9233a 144115963216868479 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libchemistryModel.so 7f0aefce7000-7f0aefd2a000 r--p 00d57000 7af:9233a 144115963216868479 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libchemistryModel.so 7f0aefd2a000-7f0aefd30000 rw-p 00d9a000 7af:9233a 144115963216868479 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libchemistryModel.so 7f0aefd30000-7f0aefd37000 rw-p 00000000 00:00 0 7f0aefd37000-7f0aefd64000 r-xp 00000000 7af:9233a 144115963216868381 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libdistributionModels.so 7f0aefd64000-7f0aeff63000 ---p 0002d000 7af:9233a 144115963216868381 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libdistributionModels.so 7f0aeff63000-7f0aeff65000 r--p 0002c000 7af:9233a 144115963216868381 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libdistributionModels.so 7f0aeff65000-7f0aeff66000 rw-p 0002e000 7af:9233a 144115963216868381 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libdistributionModels.so 7f0aeff66000-7f0af0687000 r-xp 00000000 7af:9233a 144115963216868432 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libfieldFunctionObjects.so 7f0af0687000-7f0af0886000 ---p 00721000 7af:9233a 144115963216868432 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libfieldFunctionObjects.so 7f0af0886000-7f0af0899000 r--p 00720000 7af:9233a 144115963216868432 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libfieldFunctionObjects.so 7f0af0899000-7f0af08a2000 rw-p 00733000 7af:9233a 144115963216868432 /lustre/apps/openfoam/2006/OpenFOAM-v2006/platforms/linux64GccDPInt32Opt/lib/libfieldFunctionObjects.so 7f0af08a2000-7f0af08a4000 rw-p 00000000 00:00 0 7f0af0d95000-7f0af159a000 r--s 00000000 08:04 1564719 /var/lib/sss/mc/passwd 7f0af159a000-7f0af15a2000 r-xp 00000000 08:04 14455 /usr/lib64/libnss_sss.so.2 7f0af15a2000-7f0af17a1000 ---p 00008000 08:04 14455 /usr/lib64/libnss_sss.so.2 7f0af17a1000-7f0af17a2000 r--p 00007000 08:04 14455 /usr/lib64/libnss_sss.so.2 7f0af17a2000-7f0af17a3000 rw-p 00008000 08:04 14455 /usr/lib64/libnss_sss.so.2Aborted Code:
Create time --> FOAM Warning : From void* Foam::dlLibraryTable::openLibrary(const Foam::fileName&, bool) in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 65 Could not load "$FOAM_USER_LIBBIN/myturbulentTransportModels.so" /home/myname/OpenFOAM/myname-v2006/platforms/linux64GccDPInt32Opt/lib/myturbulentTransportModels.so: undefined symbol: _ZTIN4Foam29incompressibleTurbulenceModelE Create mesh for time = 0 Thanks for any help |
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Tags |
development, library compilation, modifying model |
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