[sebastian]

Hello Everybody,

I have installed the latest version of OpenFOAM-2.1.x (download from git) on our SGI Altix UV 1000.
The compilation run without any error message using the compiler version gcc 4.3.4.
After the installation I tried to run a tutorial to see if the solver are working. However I got an error message and I dont have a clue whats wrong. This is what I got when running the pitzDaily tutorial of simpleFoam:

Build  : 2.1.x
Exec   : simpleFoam
Date   : Oct 31 2012
Time   : 09:08:50
Host   : "altix-uv"
PID    : 172905
Case   : /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/tutorials/incompressible/simpleFoam/pitzDaily
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

Create mesh for time = 0

Reading field p

Reading field U

Reading/calculating face flux field phi

Selecting incompressible transport model Newtonian
Selecting RAS turbulence model kEpsilon
*** glibc detected *** simpleFoam: double free or corruption (top): 0x0000000000a92ca0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x75218)[0x7f4b44ee5218]
/lib64/libc.so.6(cfree+0x6c)[0x7f4b44eea1ec]
simpleFoam(_ZN4Foam16DimensionedFieldIdNS_7volMeshEED2Ev+0x20)[0x41b070]
simpleFoam(_ZN4Foam14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEED0Ev+0xa6)[0x41bd06]
/scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libincompressibleRASModels.so(_ZN4Foam14incompressible9RASModels8kEpsilonC1ERKNS_14GeometricFieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshEEERKNS3_IdNS_13fvsPatchFieldENS_11surfaceMeshEEERNS_14transportModelERKNS_4wordESK_+0x98e)[0x7f4b47b0f3be]
/scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libincompressibleRASModels.so(_ZN4Foam14incompressible8RASModel31adddictionaryConstructorToTableINS0_9RASModels8kEpsilonEE3NewERKNS_14GeometricFieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshEEERKNS6_IdNS_13fvsPatchFieldENS_11surfaceMeshEEERNS_14transportModelERKNS_4wordE+0x59)[0x7f4b47b33949]
/scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libincompressibleRASModels.so(_ZN4Foam14incompressible8RASModel3NewERKNS_14GeometricFieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshEEERKNS2_IdNS_13fvsPatchFieldENS_11surfaceMeshEEERNS_14transportModelERKNS_4wordE+0x322)[0x7f4b47ad6902]
simpleFoam[0x41751a]
/lib64/libc.so.6(__libc_start_main+0xe6)[0x7f4b44e8ebc6]
simpleFoam[0x416d99]
======= Memory map: ========
00400000-00463000 r-xp 00000000 00:19 317537                             /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/bin/simpleFoam
00663000-00665000 r--p 00063000 00:19 317537                             /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/bin/simpleFoam
00665000-00666000 rw-p 00065000 00:19 317537                             /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/bin/simpleFoam
00666000-00aaf000 rw-p 00000000 00:00 0                                  [heap]
7f4b3c000000-7f4b3c021000 rw-p 00000000 00:00 0 
7f4b3c021000-7f4b40000000 ---p 00000000 00:00 0 
7f4b43768000-7f4b43a6b000 rw-p 00000000 00:00 0 
7f4b43a6b000-7f4b43a6e000 r-xp 00000000 41:83 3817503                    /usr/lib64/libbitmask.so.1.0.1
7f4b43a6e000-7f4b43c6d000 ---p 00003000 41:83 3817503                    /usr/lib64/libbitmask.so.1.0.1
7f4b43c6d000-7f4b43c6e000 r--p 00002000 41:83 3817503                    /usr/lib64/libbitmask.so.1.0.1
7f4b43c6e000-7f4b43c6f000 rw-p 00003000 41:83 3817503                    /usr/lib64/libbitmask.so.1.0.1
7f4b43c6f000-7f4b43c7b000 r-xp 00000000 41:83 3817531                    /usr/lib64/libcpuset.so.1.1.0
7f4b43c7b000-7f4b43e7a000 ---p 0000c000 41:83 3817531                    /usr/lib64/libcpuset.so.1.1.0
7f4b43e7a000-7f4b43e7b000 r--p 0000b000 41:83 3817531                    /usr/lib64/libcpuset.so.1.1.0
7f4b43e7b000-7f4b43e7c000 rw-p 0000c000 41:83 3817531                    /usr/lib64/libcpuset.so.1.1.0
7f4b43e7c000-7f4b43e84000 r-xp 00000000 41:83 4710677                    /lib64/librt-2.11.1.so
7f4b43e84000-7f4b44083000 ---p 00008000 41:83 4710677                    /lib64/librt-2.11.1.so
7f4b44083000-7f4b44084000 r--p 00007000 41:83 4710677                    /lib64/librt-2.11.1.so
7f4b44084000-7f4b44085000 rw-p 00008000 41:83 4710677                    /lib64/librt-2.11.1.so
7f4b44085000-7f4b4408b000 r-xp 00000000 00:19 273913                     /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libfileFormats.so
7f4b4408b000-7f4b4428a000 ---p 00006000 00:19 273913                     /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libfileFormats.so
7f4b4428a000-7f4b4428b000 r--p 00005000 00:19 273913                     /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libfileFormats.so
7f4b4428b000-7f4b4428c000 rw-p 00006000 00:19 273913                     /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libfileFormats.so
7f4b4428c000-7f4b443ae000 r-xp 00000000 41:83 1934228                    /opt/sgi/mpt/mpt-2.04/lib/libmpi.so
7f4b443ae000-7f4b445ad000 ---p 00122000 41:83 1934228                    /opt/sgi/mpt/mpt-2.04/lib/libmpi.so
7f4b445ad000-7f4b445af000 r--p 00121000 41:83 1934228                    /opt/sgi/mpt/mpt-2.04/lib/libmpi.so
7f4b445af000-7f4b445b4000 rw-p 00123000 41:83 1934228                    /opt/sgi/mpt/mpt-2.04/lib/libmpi.so
7f4b445b4000-7f4b445c5000 rw-p 00000000 00:00 0 
7f4b445c5000-7f4b445da000 r-xp 00000000 41:83 4710664                    /lib64/libz.so.1.2.3
7f4b445da000-7f4b447d9000 ---p 00015000 41:83 4710664                    /lib64/libz.so.1.2.3
7f4b447d9000-7f4b447da000 r--p 00014000 41:83 4710664                    /lib64/libz.so.1.2.3
7f4b447da000-7f4b447db000 rw-p 00015000 41:83 4710664                    /lib64/libz.so.1.2.3
7f4b447db000-7f4b44847000 r-xp 00000000 00:19 273914                     /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libtriSurface.so
7f4b44847000-7f4b44a47000 ---p 0006c000 00:19 273914                     /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libtriSurface.so
7f4b44a47000-7f4b44a48000 r--p 0006c000 00:19 273914                     /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libtriSurface.so
7f4b44a48000-7f4b44a49000 rw-p 0006d000 00:19 273914                     /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libtriSurface.so
7f4b44a49000-7f4b44a60000 r-xp 00000000 41:83 4710586                    /lib64/libpthread-2.11.1.so
7f4b44a60000-7f4b44c60000 ---p 00017000 41:83 4710586                    /lib64/libpthread-2.11.1.so
7f4b44c60000-7f4b44c61000 r--p 00017000 41:83 4710586                    /lib64/libpthread-2.11.1.so
7f4b44c61000-7f4b44c62000 rw-p 00018000 41:83 4710586                    /lib64/libpthread-2.11.1.so
7f4b44c62000-7f4b44c66000 rw-p 00000000 00:00 0 
7f4b44c66000-7f4b44c6f000 r-xp 00000000 00:19 273910                     /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/mpi/libPstream.soAborted

blockMesh and checkMesh works without any error. Its the same problem for any other solver I tried.
So far I have used OpenFOAM-1.6-ext and this works. I am not sure about the environmental variables, 2.1.x has changed a little bit, but I have set them as I did for 1.6-ext. However as long as I don't get any error message while compiling, the variables should be set right?

I found an old thread about OF-1.5 which seems to be somehow similar:
http://www.cfd-online.com/Forums/ope...ofoam-run.html
However this didn't really help.

I hope that anybody has an idea.
Thanks!
Sebastian

[wyldckat]

Hi Sebastian,

Mmm, interesting... OK, there is a couple of linking options that might be disrupting things, namely:

-Xlinker --no-as-needed

These were added because of the latest ld binaries present in modern Linux Distributions.

Therefore, try this:

1. Edit OpenFOAM's "etc/bashrc" file and change this entry:
   

   export WM_COMPILER=Gcc

   To this:
   

   export WM_COMPILER=Gcc43

   This way it will use the specific configurations for the Gcc 4.3.x series.
2. If you edited anything in the rules files at "wmake/rules/linux64Gcc", then you better edit once again at "wmake/rules/linux64Gcc43".
3. Build OpenFOAM once again with an updated shell environment (when in doubt, start a new terminal ).

Hopefully this will avoid the issue that Mattijs wrote on that other thread:

Originally Posted by mattijs

1) double corruption means that some allocated memory gets deleted twice. You can investigate these problems with e.g. valgrind. It usually happens from having an OpenFOAM debug symbol twice in your executable or libraries.

Yet another possibility is to even take out another one the options present in files "wmake/rules/linux64Gcc43/c" and "wmake/rules/linux64Gcc43/c++", namely these two options:

-Xlinker --add-needed

Best regards,
Bruno

[sebastian]

Hello Bruno,

thank you for your advices.
I did what you have told me and changed

export WM_COMPILER=Gcc

to

export WM_COMPILER=Gcc43

(and also changed the rules in "wmake/rules/linux64Gcc43").

Then I have rebuilt OpenFOAM. Again, compilation was without any error message, however there is still this failure when running a solver.

Your additional suggestion was concerning -Xlinker- in the files "wmake/rules/linux64Gcc43/c" and "wmake/rules/linux64Gcc43/c++".
The current default settings are

LINKEXE     = $(cc) -Xlinker --add-needed -Xlinker -z -Xlinker nodefs

in the file c. And

LINKEXE     = $(CC) $(c++FLAGS) -Xlinker --add-needed

in the file c++. You mean that in both files

-Xlinker --add-needed

should be replaced by

-Xlinker --no-as-needed

, is that correct?

Best regards,
Sebastian

[wyldckat]

Hi Sebastian,

Originally Posted by sebastian

You mean that in both files

-Xlinker  --add-needed

should be replaced by

-Xlinker  --no-as-needed

, is that correct?

In reference to this sentence:

Originally Posted by wyldckat

Yet another possibility is to even take out another one the options present in files (...)

I meant "take out" in the sense of "remove it as well"

To better explain myself: I suspect that "-Xlinker --add-needed" is also contaminating the build process, leading to duplicate symbols in memory!
It could be a build option that is not yet fully supported in the binutils version (http://www.gnu.org/software/binutils/) used in your machine.

Best regards,
Bruno

[sebastian]

Dear Bruno,

I have deleted the lines

LINKEXE     = $(cc) -Xlinker --add-needed -Xlinker -z -Xlinker nodefs

and

LINKEXE     = $(CC) $(c++FLAGS) -Xlinker --add-needed

in both files "wmake/rules/linux64Gcc43/c" and "wmake/rules/linux64Gcc43/c++".
However now the compiler gives me an error now. I have stopped compilation after I realised that somethings going wrong. Would you mind to have a look on my log-file?

Update:
Ah, or did you mean only deleting the parts -Xlinker --add-needed in those lines? Sorry

Thank you a lot.
Sebastian

[wyldckat]

Hi Sebastian,

Originally Posted by sebastian

Update:
Ah, or did you mean only deleting the parts -Xlinker --add-needed in those lines? Sorry

Yes, the idea is to only remove those two options from both files!

Best regards,
Bruno

[sebastian]

Hello Bruno,

the new build of OpenFOAM still does not give me a working solver, same problem. I have removed the options -Xinker --add-needed in the c and c++ file in wmake/rules/linux64Gcc43/ :

LINKEXE     = $(cc) -Xlinker -z -Xlinker nodefs

LINKEXE     = $(CC) $(c++FLAGS)

Furthermore I noticed that there is one error when building the third-party. The error shows up at the very end of compilation, and I am not sure how concerning this is (attached log-file). When running third-party Allwmake once again its not complaing anymore (see top of the log-file in my very first post).

Best regards,
Sebastian

[wyldckat]

Hi Sebastian,

If you're talking about this error:

make: [install] Error 1 (ignored)

Then it can be ignored.

If you're talking about this one:

Build Tecio
    optional component was not found

It's not a problem, since it's optional.

Other than all of this... I have no more ideas
I'm only able to either suggest that you contact the respective section of SGI; or contact OpenCFD directly through their support form: http://www.openfoam.com/support/software.php - at the very least, they could/should indicate who you can contact at SGI.

Good luck!
Bruno

[sebastian]

Hello Bruno,

okay, thank you very much. I will post it here once I have solved this problem.
Please, let me know if you think of anything else.

Best regards,
Sebastian

[wyldckat]

Hi Sebastian,

I'm remembered something from some of the latest forum threads I've seen... try the following command:

ldd $(which simpleFoam)

And confirm whether there are duplicate libraries or wrong libraries being loaded... for example, libraries from 1.6-ext being picked up by simpleFoam 2.1.x!

Best regards,
Bruno

[sebastian]

Originally Posted by wyldckat

I'm remembered something from some of the latest forum threads I've seen... try the following command:

ldd $(which simpleFoam)

Hi Bruno,

good idea. However I think everything looks correct:

la2bsesa@altix-uv:/scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x> ldd $(which simpleFoam)
        linux-vdso.so.1 =>  (0x00007fff82dff000)
        libincompressibleTurbulenceModel.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libincompressibleTurbulenceModel.so (0x00007f19815dc000)
        libincompressibleRASModels.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libincompressibleRASModels.so (0x00007f19810e6000)
        libincompressibleTransportModels.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libincompressibleTransportModels.so (0x00007f1980e68000)
        libfiniteVolume.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libfiniteVolume.so (0x00007f197fde1000)
        libmeshTools.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libmeshTools.so (0x00007f197f946000)
        libOpenFOAM.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libOpenFOAM.so (0x00007f197f1e2000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007f197efa5000)
        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f197ec9a000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f197ea43000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f197e82c000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f197e4ce000)
        libPstream.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/mpi/libPstream.so (0x00007f197e2c3000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f197e0a6000)
        libtriSurface.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libtriSurface.so (0x00007f197de37000)
        libz.so.1 => /lib64/libz.so.1 (0x00007f197dc21000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f198183a000)
        libmpi.so => /opt/sgi/mpt/mpt-2.04/lib/libmpi.so (0x00007f197d8e7000)
        libfileFormats.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libfileFormats.so (0x00007f197d6e0000)
        librt.so.1 => /lib64/librt.so.1 (0x00007f197d4d6000)
        libcpuset.so.1 => /usr/lib64/libcpuset.so.1 (0x00007f197d2c9000)
        libbitmask.so.1 => /usr/lib64/libbitmask.so.1 (0x00007f197d0c5000)

Do you think it might be an issue with my compiler as I am using only gcc-4.3.4?

Best regards,
Sebastian

[wyldckat]

Hi Sebastian,

There are two libraries that I suspect:

• librt.so.1 - it either stands for real-time or run-time, either way, I don't think OpenFOAM will need it.
• /opt/sgi/mpt/mpt-2.04/lib/libmpi.so - this is a potential source of problems, if the incorrect build options are used, even if only running in serial mode (single-core).

OK, try this:

wmUNSET
. /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/etc/bashrc WM_MPLIB=

This will offload the OpenFOAM environment and then activate it once again, but this time with the MPI Pstream not available.

Then try again running simpleFoam and doing ldd to it, to check how things are working, if at all.
If it works this time, then it's a matter of finding the correct build options for MPT.

Best regards,
Bruno

[sebastian]

Originally Posted by wyldckat

wmUNSET
. /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/etc/bashrc WM_MPLIB=

This will offload the OpenFOAM environment and then activate it once again, but this time with the MPI Pstream not available.

Dear Bruno,

I will try, but how can I activate OF without MPI Pstream?

Sebastian

[wyldckat]

The empty "WM_MPLIB=" should do the trick!
Running those two lines of code in the command line should do the trick...

You can check your current value by running:

echo $WM_MPLIB

[sebastian]

Dear Bruno,

okay got it. But simpleFoam is still not working

This is what ldd gives back:

la2bsesa@altix-uv:/scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/tutorials/incompressible/simpleFoam/pitzDaily> ldd $(which simpleFoam)
        linux-vdso.so.1 =>  (0x00007fffaabff000)
        libincompressibleTurbulenceModel.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libincompressibleTurbulenceModel.so (0x00007fd792cdc000)
        libincompressibleRASModels.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libincompressibleRASModels.so (0x00007fd7927e6000)
        libincompressibleTransportModels.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libincompressibleTransportModels.so (0x00007fd792568000)
        libfiniteVolume.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libfiniteVolume.so (0x00007fd7914e1000)
        libmeshTools.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libmeshTools.so (0x00007fd791046000)
        libOpenFOAM.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libOpenFOAM.so (0x00007fd7908e2000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007fd7906a5000)
        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fd79039a000)
        libm.so.6 => /lib64/libm.so.6 (0x00007fd790143000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fd78ff2c000)
        libc.so.6 => /lib64/libc.so.6 (0x00007fd78fbce000)
        libPstream.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/dummy/libPstream.so (0x00007fd78f9c8000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fd78f7ab000)
        libtriSurface.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libtriSurface.so (0x00007fd78f53c000)
        libz.so.1 => /lib64/libz.so.1 (0x00007fd78f326000)
        /lib64/ld-linux-x86-64.so.2 (0x00007fd792f3a000)
        libfileFormats.so => /scratch_uv/la2bsesa/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64Gcc43DPOpt/lib/libfileFormats.so (0x00007fd78f11e000)

Best regards,
Sebastian

[wyldckat]

Hi Sebastian,

Mmm... OK, if 1.6-ext built and works without any problems and 2.1.x has problems... how about OpenFOAM 2.0.x?
The objective would be to try and isolate the version from which is started having problems, whether it's something that OpenFOAM got recently and which lead to the problem you're having.

If 2.0.x works, then try 2.1.0. If not, try 1.7.x...

Best regards,
Bruno

[sebastian]

Dear Bruno,

I already tried to install 2.0.x. Same problem. I have contacted OF-support and asked about any known problems of OF-2.x and our SGI-UV machine. Henry Weller answered me, that everything should work fine and there are no problems known. He mentioned that this looks like a library incompatibility issue, i.e. what OpenFOAM was compiled with is not the same as what it is running with...

So probably I should try to contact SGI.

Thanks for your support Bruno.

Best regards,
Sebastian