CS 2.2.1 and Syrthes 4.0.1 coupling problem

[bajsi]

Hi,

I am using CS 2.2.1 and Syrthes 4.0.1 on Ubuntu 12.04 system.

I am trying to run a simple simulation of cooling of a preheated steel slab (700°C) inside a cover (no inlet or outlet) with air convection. The temperatures of outer boundaries of are set to 0°C. There is just one boundary between slab and air. The time step (0,1 s) and duration (100 s) are identical in both cases.

Each separate code runs just fine and appears to be physically correct.

But when I run a coupled system only one time step is calculated and then the code exits - no error is given and calculation finish appears to be successful.

[bajsi]

Hi,

after some investigation I found out that the problem is not in communication between Syrthes and Code_Sature, but in postprocessing of Syrthes results.

The last lines of stdout.txt are:

***** Successful execution *****

Post-processing..
.syrthes --> med..
--> /home/niko/syrthes4.0.1/arch/Linux_x86_64/bin/syrthes4med30 -m /home/niko/Dokumenti/MECA/010_vagon_syr4/vagon_syr/MESH/s_slab_lin.syr -r /home/niko/Dokumenti/MECA/010_vagon_syr4/vagon_syr/solid/resu1.res -o resu1.med
.syrthes --> med..
--> /home/niko/syrthes4.0.1/arch/Linux_x86_64/bin/syrthes4med30 -m /home/niko/Dokumenti/MECA/010_vagon_syr4/vagon_syr/MESH/s_slab_lin.syr -r /home/niko/Dokumenti/MECA/010_vagon_syr4/vagon_syr/solid/resu1.rdt -o resu1_rdt.med

Running the last comand results in:

VAR=TEMPERATURE, type=3, nb=346
MED write: timestep=1000 time=100.000000 field=TEMPERATURE 346 values on nodes

Results conversion completed

===============================================================
SYRTHES4_TO_MED30
End of process
===============================================================

*** stack smashing detected ***: /home/niko/syrthes4.0.1/arch/Linux_x86_64/bin/syrthes4med30 terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7ff96e5e7007]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x0)[0x7ff96e5e6fd0]
/home/niko/syrthes4.0.1/arch/Linux_x86_64/bin/syrthes4med30[0x4012ac]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7ff96e4ff76d]
/home/niko/syrthes4.0.1/arch/Linux_x86_64/bin/syrthes4med30[0x401325]
======= Memory map: ========
00400000-00405000 r-xp 00000000 08:01 281353 /home/niko/syrthes4.0.1/arch/Linux_x86_64/bin/syrthes4med30
00604000-00605000 r--p 00004000 08:01 281353 /home/niko/syrthes4.0.1/arch/Linux_x86_64/bin/syrthes4med30
00605000-00606000 rw-p 00005000 08:01 281353 /home/niko/syrthes4.0.1/arch/Linux_x86_64/bin/syrthes4med30
00bd9000-018a2000 rw-p 00000000 00:00 0 [heap]
7ff96c575000-7ff96c577000 r-xp 00000000 08:01 792558 /lib/x86_64-linux-gnu/libutil-2.15.so
7ff96c577000-7ff96c776000 ---p 00002000 08:01 792558 /lib/x86_64-linux-gnu/libutil-2.15.so
7ff96c776000-7ff96c777000 r--p 00001000 08:01 792558 /lib/x86_64-linux-gnu/libutil-2.15.so
7ff96c777000-7ff96c778000 rw-p 00002000 08:01 792558 /lib/x86_64-linux-gnu/libutil-2.15.so
7ff96c778000-7ff96c77a000 r-xp 00000000 08:01 792467 /lib/x86_64-linux-gnu/libdl-2.15.so
7ff96c77a000-7ff96c97a000 ---p 00002000 08:01 792467 /lib/x86_64-linux-gnu/libdl-2.15.so
7ff96c97a000-7ff96c97b000 r--p 00002000 08:01 792467 /lib/x86_64-linux-gnu/libdl-2.15.so
7ff96c97b000-7ff96c97c000 rw-p 00003000 08:01 792467 /lib/x86_64-linux-gnu/libdl-2.15.so
7ff96c97c000-7ff96c9cc000 r-xp 00000000 08:01 680792 /usr/lib/openmpi/lib/libopen-pal.so.0.0.0
7ff96c9cc000-7ff96cbcc000 ---p 00050000 08:01 680792 /usr/lib/openmpi/lib/libopen-pal.so.0.0.0
7ff96cbcc000-7ff96cbcd000 r--p 00050000 08:01 680792 /usr/lib/openmpi/lib/libopen-pal.so.0.0.0
7ff96cbcd000-7ff96cbcf000 rw-p 00051000 08:01 680792 /usr/lib/openmpi/lib/libopen-pal.so.0.0.0
7ff96cbcf000-7ff96cbd3000 rw-p 00000000 00:00 0
7ff96cbd3000-7ff96cc1c000 r-xp 00000000 08:01 680793 /usr/lib/openmpi/lib/libopen-rte.so.0.0.0
7ff96cc1c000-7ff96ce1c000 ---p 00049000 08:01 680793 /usr/lib/openmpi/lib/libopen-rte.so.0.0.0
7ff96ce1c000-7ff96ce1d000 r--p 00049000 08:01 680793 /usr/lib/openmpi/lib/libopen-rte.so.0.0.0
7ff96ce1d000-7ff96ce1f000 rw-p 0004a000 08:01 680793 /usr/lib/openmpi/lib/libopen-rte.so.0.0.0
7ff96ce1f000-7ff96ce21000 rw-p 00000000 00:00 0
7ff96ce21000-7ff96cf1a000 r-xp 00000000 08:01 792486 /lib/x86_64-linux-gnu/libm-2.15.so
7ff96cf1a000-7ff96d119000 ---p 000f9000 08:01 792486 /lib/x86_64-linux-gnu/libm-2.15.so
7ff96d119000-7ff96d11a000 r--p 000f8000 08:01 792486 /lib/x86_64-linux-gnu/libm-2.15.so
7ff96d11a000-7ff96d11b000 rw-p 000f9000 08:01 792486 /lib/x86_64-linux-gnu/libm-2.15.so
7ff96d11b000-7ff96d131000 r-xp 00000000 08:01 792565 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7ff96d131000-7ff96d330000 ---p 00016000 08:01 792565 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7ff96d330000-7ff96d331000 r--p 00015000 08:01 792565 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7ff96d331000-7ff96d332000 rw-p 00016000 08:01 792565 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7ff96d332000-7ff96d3c7000 r-xp 00000000 08:01 680788 /usr/lib/openmpi/lib/libmpi.so.0.0.2
7ff96d3c7000-7ff96d5c7000 ---p 00095000 08:01 680788 /usr/lib/openmpi/lib/libmpi.so.0.0.2
7ff96d5c7000-7ff96d5c8000 r--p 00095000 08:01 680788 /usr/lib/openmpi/lib/libmpi.so.0.0.2
7ff96d5c8000-7ff96d5d9000 rw-p 00096000 08:01 680788 /usr/lib/openmpi/lib/libmpi.so.0.0.2
7ff96d5d9000-7ff96d5e3000 rw-p 00000000 00:00 0
7ff96d5e3000-7ff96d5f8000 r-xp 00000000 08:01 792475 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ff96d5f8000-7ff96d7f7000 ---p 00015000 08:01 792475 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ff96d7f7000-7ff96d7f8000 r--p 00014000 08:01 792475 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ff96d7f8000-7ff96d7f9000 rw-p 00015000 08:01 792475 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ff96d7f9000-7ff96d8db000 r-xp 00000000 08:01 664680 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7ff96d8db000-7ff96dada000 ---p 000e2000 08:01 664680 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7ff96dada000-7ff96dae2000 r--p 000e1000 08:01 664680 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7ff96dae2000-7ff96dae4000 rw-p 000e9000 08:01 664680 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7ff96dae4000-7ff96daf9000 rw-p 00000000 00:00 0
7ff96daf9000-7ff96de9d000 r-xp 00000000 08:01 680884 /usr/lib/libhdf5.so.6.0.3
7ff96de9d000-7ff96e09c000 ---p 003a4000 08:01 680884 /usr/lib/libhdf5.so.6.0.3
7ff96e09c000-7ff96e0a1000 r--p 003a3000 08:01 680884 /usr/lib/libhdf5.so.6.0.3
7ff96e0a1000-7ff96e0a5000 rw-p 003a8000 08:01 680884 /usr/lib/libhdf5.so.6.0.3
7ff96e0a5000-7ff96e0a7000 rw-p 00000000 00:00 0
7ff96e0a7000-7ff96e0bf000 r-xp 00000000 08:01 792534 /lib/x86_64-linux-gnu/libpthread-2.15.so
7ff96e0bf000-7ff96e2be000 ---p 00018000 08:01 792534 /lib/x86_64-linux-gnu/libpthread-2.15.so
7ff96e2be000-7ff96e2bf000 r--p 00017000 08:01 792534 /lib/x86_64-linux-gnu/libpthread-2.15.so
7ff96e2bf000-7ff96e2c0000 rw-p 00018000 08:01 792534 /lib/x86_64-linux-gnu/libpthread-2.15.so
7ff96e2c0000-7ff96e2c4000 rw-p 00000000 00:00 0
7ff96e2c4000-7ff96e2db000 r-xp 00000000 08:01 680789 /usr/lib/openmpi/lib/libmpi_cxx.so.0.0.1
7ff96e2db000-7ff96e4db000 ---p 00017000 08:01 680789 /usr/lib/openmpi/lib/libmpi_cxx.so.0.0.1
7ff96e4db000-7ff96e4dd000 r--p 00017000 08:01 680789 /usr/lib/openmpi/lib/libmpi_cxx.so.0.0.1
7ff96e4dd000-7ff96e4de000 rw-p 00019000 08:01 680789 /usr/lib/openmpi/lib/libmpi_cxx.so.0.0.1
7ff96e4de000-7ff96e691000 r-xp 00000000 08:01 792454 /lib/x86_64-linux-gnu/libc-2.15.so
7ff96e691000-7ff96e890000 ---p 001b3000 08:01 792454 /lib/x86_64-linux-gnu/libc-2.15.so
7ff96e890000-7ff96e894000 r--p 001b2000 08:01 792454 /lib/x86_64-linux-gnu/libc-2.15.so
7ff96e894000-7ff96e896000 rw-p 001b6000 08:01 792454 /lib/x86_64-linux-gnu/libc-2.15.so
7ff96e896000-7ff96e89b000 rw-p 00000000 00:00 0
7ff96e89b000-7ff96e9be000 r-xp 00000000 08:01 680952 /usr/lib/libmedC.so.1.2.4
7ff96e9be000-7ff96ebbd000 ---p 00123000 08:01 680952 /usr/lib/libmedC.so.1.2.4
7ff96ebbd000-7ff96ebbf000 r--p 00122000 08:01 680952 /usr/lib/libmedC.so.1.2.4
7ff96ebbf000-7ff96ebc0000 rw-p 00124000 08:01 680952 /usr/lib/libmedC.so.1.2.4
7ff96ebc0000-7ff96ebe2000 r-xp 00000000 08:01 792434 /lib/x86_64-linux-gnu/ld-2.15.so
7ff96ed24000-7ff96ed45000 rw-p 00000000 00:00 0
7ff96edc5000-7ff96edcf000 rw-p 00000000 00:00 0
7ff96eddf000-7ff96ede2000 rw-p 00000000 00:00 0
7ff96ede2000-7ff96ede3000 r--p 00022000 08:01 792434 /lib/x86_64-linux-gnu/ld-2.15.so
7ff96ede3000-7ff96ede5000 rw-p 00023000 08:01 792434 /lib/x86_64-linux-gnu/ld-2.15.so
7fff2a02f000-7fff2a050000 rw-p 00000000 00:00 0 [stack]
7fff2a1c3000-7fff2a1c4000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (izpis jedra)


So there appears to be a bug in syrthes4med30. Any ideas of how should I proceed - report the bug?

[Yvan Fournier]

Hello,

Thanks for your feedback.

I will report the bug to the Syrthes developers (though they are out of office this week).

If your data is very small, you could also post it here or send it to me, so that I can try to reproduce the bug (which may help fixing it faster).

Best regards,

Yvan

[bajsi]

Hi,

I attached a zip of practically all files for this mini project.
I hope this will be helpful enough.

[Yvan Fournier]

Hello,

I was not able to reproduce the bug. I re-ran your case to get a result file, and it seems to lead to less time steps than in your case, but I doubt this is the issue.

I can obtain a warning with Valgrind, but it does not lead to a crash. Even compiling Syrthes in debug mode, this executable is not itself in debug mode, so I had to re-compile it manually, but I managed to get a true "debug version" in which I can see where a potential issue might arise, but nothing definitive.

Also, stack errors are not always detectable by Valgrind, so I am not sure of anything here. I'll forward this to the Syrthes people, and let them sort this out.

Also, this might be an installation issue. I also tested on an Ubuntu 12.04 system, but with MED and a few other packages recompiled, so the difference may lie there...

Best regards,

Yvan