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-   -   Application sample with glibc error (http://www.cfd-online.com/Forums/openfoam-post-processing/61400-application-sample-glibc-error.html)

matthias March 28, 2008 18:21

Hi, I have a strange proble
 
Hi,

I have a strange problem with sample, after I run it I'm getting always this error:

*** glibc detected *** sample: corrupted double-linked list: 0x0000000000772d10 ***
======= Backtrace: =========
/lib64/libc.so.6[0x371b46e583]
/lib64/libc.so.6[0x371b47015d]
/lib64/libc.so.6(cfree+0x8c)[0x371b473b1c]
.../OpenFOAM/OpenFOAM-1.4.1-dev/lib/linux64GccDPOpt/libOpenFOAM.so(_ZN4Foam8ITst reamD2Ev+0x273)[0x2aaaac1b4153]
.../OpenFOAM/OpenFOAM-1.4.1-dev/lib/linux64GccDPOpt/libOpenFOAM.so(_ZN4Foam14pri mitiveEntryD0Ev+0x30)[0x2aaaac1b4440]
.../OpenFOAM/OpenFOAM-1.4.1-dev/lib/linux64GccDPOpt/libOpenFOAM.so(_ZN4Foam10dic tionaryD2Ev+0x6d)[0x2aaaac1af0ad]
.../OpenFOAM/OpenFOAM-1.4.1-dev/lib/linux64GccDPOpt/libOpenFOAM.so(_ZN4Foam15dic tionaryEntryD0Ev+0x28)[0x2aaaac1b74b8]
.../OpenFOAM/OpenFOAM-1.4.1-dev/lib/linux64GccDPOpt/libOpenFOAM.so(_ZN4Foam10dic tionaryD1Ev+0x6d)[0x2aaaac1ae9ad]
.../OpenFOAM/OpenFOAM-1.4.1-dev/lib/linux64GccDPOpt/libOpenFOAM.so[0x2aaaac16560 8]
/lib64/libc.so.6(__cxa_finalize+0x9d)[0x371b43374d]
.../OpenFOAM/OpenFOAM-1.4.1-dev/lib/linux64GccDPOpt/libOpenFOAM.so[0x2aaaac1591e 6]
======= Memory map: ========
00400000-004a1000 r-xp 00000000 00:12 491143200 .../OpenFOAM/OpenFOAM-1.4.1-dev/applications/bin/linux64GccDPOpt/sample
006a1000-006a5000 rw-p 000a1000 00:12 491143200 .../OpenFOAM/OpenFOAM-1.4.1-dev/applications/bin/linux64GccDPOpt/sample
006a5000-08c82000 rw-p 006a5000 00:00 0 [heap]
3614a00000-3614a2f000 r-xp 00000000 08:01 28838812 /usr/lib64/libgslcblas.so.0.0.0
3614a2f000-3614c2f000 ---p 0002f000 08:01 28838812 /usr/lib64/libgslcblas.so.0.0.0
3614c2f000-3614c30000 rw-p 0002f000 08:01 28838812 /usr/lib64/libgslcblas.so.0.0.0
3614e00000-3614f9c000 r-xp 00000000 08:01 28837421 /usr/lib64/libgsl.so.0.9.0
3614f9c000-361519c000 ---p 0019c000 08:01 28837421 /usr/lib64/libgsl.so.0.9.0
361519c000-36151a9000 rw-p 0019c000 08:01 28837421 /usr/lib64/libgsl.so.0.9.0
371b000000-371b01a000 r-xp 00000000 08:01 54100302 /lib64/ld-2.6.so
371b21a000-371b21b000 r--p 0001a000 08:01 54100302 /lib64/ld-2.6.so
371b21b000-371b21c000 rw-p 0001b000 08:01 54100302 /lib64/ld-2.6.so
371b400000-371b547000 r-xp 00000000 08:01 54100303 /lib64/libc-2.6.so
371b547000-371b747000 ---p 00147000 08:01 54100303 /lib64/libc-2.6.so
371b747000-371b74b000 r--p 00147000 08:01 54100303 /lib64/libc-2.6.so
371b74b000-371b74c000 rw-p 0014b000 08:01 54100303 /lib64/libc-2.6.so
371b74c000-371b751000 rw-p 371b74c000 00:00 0
371b800000-371b882000 r-xp 00000000 08:01 54100315 /lib64/libm-2.6.so
371b882000-371ba81000 ---p 00082000 08:01 54100315 /lib64/libm-2.6.so
371ba81000-371ba82000 r--p 00081000 08:01 54100315 /lib64/libm-2.6.so
371ba82000-371ba83000 rw-p 00082000 08:01 54100315 /lib64/libm-2.6.so
371bc00000-371bc02000 r-xp 00000000 08:01 54100307 /lib64/libdl-2.6.so
371bc02000-371be02000 ---p 00002000 08:01 54100307 /lib64/libdl-2.6.so
371be02000-371be03000 r--p 00002000 08:01 54100307 /lib64/libdl-2.6.so
371be03000-371be04000 rw-p 00003000 08:01 54100307 /lib64/libdl-2.6.so
371d000000-371d015000 r-xp 00000000 08:01 54100311 /lib64/libpthread-2.6.so
371d015000-371d214000 ---p 00015000 08:01 54100311 /lib64/libpthread-2.6.so
371d214000-371d215000 r--p 00014000 08:01 54100311 /lib64/libpthread-2.6.so
371d215000-371d216000 rw-p 00015000 08:01 54100311 /lib64/libpthread-2.6.so
371d216000-371d21a000 rw-p 371d216000 00:00 0
3725200000-3725202000 r-xp 00000000 08:01 54100323 /lib64/libutil-2.6.so
3725202000-3725401000 ---p 00002000 08:01 54100323 /lib64/libutil-2.6.so
3725401000-3725402000 r--p 00001000 08:01 54100323 /lib64/libutil-2.6.so
3725402000-3725403000 rw-p 00002000 08:01 54100323 /lib64/libutil-2.6.so
3725e00000-3725e15000 r-xp 00000000 08:01 54100309 /lib64/libnsl-2.6.so
3725e15000-3726014000 ---p 00015000 08:01 54100309 /lib64/libnsl-2.6.so
3726014000-3726015000 r--p 00014000 08:01 54100309 /lib64/libnsl-2.6.so
3726015000-3726016000 rw-p 00015000 08:01 54100309 /lib64/libnsl-2.6.so
3726016000-3726018000 rw-p 3726016000 00:00 0
389b000000-389b00d000 r-xp 00000000 08:01 54099983 /lib64/libgcc_s-4.1.2-20070925.so.1
389b00d000-389b20d000 ---p 0000d000 08:01 54099983 /lib64/libgcc_s-4.1.2-20070925.so.1
389b20d000-389b20e000 rw-p 0000d000 08:01 54099983 /lib64/libgcc_s-4.1.2-20070925.so.1
389bc00000-389bce5000 r-xp 00000000 08:01 21004479 /usr/lib64/libstdc++.so.6.0.8
389bce5000-389bee5000 ---p 000e5000 08:01 21004479 /usr/lib64/libstdc++.so.6.0.8
389bee5000-389beeb000 r--p 000e5000 08:01 21004479 /usr/lib64/libstdc++.so.6.0.8
389beeb000-389beee000 rw-p 000eb000 08:01 21004479 /usr/lib64/libstdc++.so.6.0.8
389beee000-389bf00000 rw-p 389beee000 00:00 0
2aaaaaaab000-2aaaaaaad000 rw-p 2aaaaaaab000 00:00 0
2aaaaaaad000-2aaaaaaf5000 r-xp 00000000 00:12 508875021 .../OpenFOAM/OpenFOAM-1.4.1-dev/lib/linux64GccDPOpt/libsampling.so
2aaaaaaf5000-2aaaaacf5000 ---p 00048000 00:12 508875021 .../OpenFOAM/OpenFOAM-1.4.1-dev/lib/linux64GccDPOpt/libsampling.so
2aaaaacf5000-2aaaaacf7000 rw-p 00048000 00:12 508875021 .../OpenFOAM/OpenFOAM-1.4.1-dev/lib/linux64GccDPOpt/libsampling.so
2aaaaacf7000-2aaaaae5f000 r-xp 00000000 00:12 508874957

...


2aaab0021000-2aaab4000000 ---p 2aaab0021000 00:00 0
7fff0e0c4000-7fff0e0da000 rw-p 7ffffffe9000 00:00 0 [stack]
7fff0e172000-7fff0e175000 r-xp 7fff0e172000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Abgebrochen



If I run sample on a different case (another mesh and geometry) then it works without any error. CheckMesh shows also no errors. Furthermore sample writes out the "sample files" so that I can use them.
I tried to trace back the error in sample.C and I found out that the following code lines are responsible for the output above.

PtrList<sampleset> sampleSets
(
sampleDict.lookup("sampleSets"),
sampleSet::iNew(mesh, searchEngine)
);


So, does anyone have an idea? Maybe my case is broken (mesh)?
If I copy the case to another machine and run sample there the error doesn't occur.
I must say, that I did an update from sourceforge a few days ago.


mfg
Matthias

mbeaudoin March 29, 2008 16:24

Hello Matthias, Does your o
 
Hello Matthias,

Does your other machine run the updated version of OF-1.4.1-dev too?

Have you tried forcing a complete recompilation of sample (wclean, wmake)?

Is is possible for you to share this case so I could take a look with my installation?

Martin


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