Unable to run a coupled simulation with Syrthes

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CTrinca
Posts: 32
Joined: Mon Mar 30, 2015 9:19 am

Unable to run a coupled simulation with Syrthes

Post by CTrinca »

Hello everyone,

I am experiencing a problem in running my first coupled analysis using Code_Saturne and Syrthes.
I am trying to simulate the heat exchange between an internally heated rod and the surrounding flow. Both the fluid and the solid models seem to work properly when tested alone, but when I try to couple them, that's what I get:

Code: Select all

[...]

 **********************
  Starting calculation
 **********************

[fermi:03761] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 367
[fermi:03759] tcp_peer_recv_connect_ack: invalid header type: 870383616
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[13281,1],0]
  Exit code:    1
--------------------------------------------------------------------------
 solver script exited with status 1.

Error running the coupled calculation.

Either Code_Saturne or SYRTHES may have failed.

Check Code_Saturne log (listing) and SYRTHES log (syrthes.log)
for details, as well as error* files.


****************************
  Saving calculation results
 ****************************

 Error in calculation stage.

Post-processing.. 
  .syrthes (.res) --> ensight... 
     --> /home/ctrinca/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes4ensight -m "/home/ctrinca/Simulations/MeshTests/annular-conjugate/coupled-study/MESH/BLOCK7TETRAHEDRAL.syr" -r "/home/ctrinca/Simulations/MeshTests/annular-conjugate/coupled-study2/RESU_COUPLING/20150619-1013/solid/resu1.res" -o "resu1"
  .syrthes (.rdt) --> ensight... 
     --> /home/ctrinca/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes4ensight -m "/home/ctrinca/Simulations/MeshTests/annular-conjugate/coupled-study/MESH/BLOCK7TETRAHEDRAL.syr" -r "/home/ctrinca/Simulations/MeshTests/annular-conjugate/coupled-study2/RESU_COUPLING/20150619-1013/solid/resu1.rdt" -o "resu1_rdt"
However, syrthes.log does not report any problem and saturne does not generate any listing at all, except for the preprocessor's log, which looks OK. I am attaching my meshes, my input files and the logs I got.

I have had a lot of trouble trying to run this simulation, but most of them were trivial mistakes I found out looking less superficially at the documentation and I am sorry if this is the case again. This time, though, I have not a clue about where to look.

Thanks a lot in advance and best regards,

Cosimo
Attachments
coupling_problem.zip
(4.22 MiB) Downloaded 214 times
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: Unable to run a coupled simulation with Syrthes

Post by Yvan Fournier »

Hello,

Are you sure you are using the same MPI library version and build for both codes ?

The error you have is typically the sort of error you can get when mixing MPI implmentations/versions...

Regards,

Yvan
CTrinca
Posts: 32
Joined: Mon Mar 30, 2015 9:19 am

Re: Unable to run a coupled simulation with Syrthes

Post by CTrinca »

Hello,

Thanks for your reply. No, I cannot say I am sure. How can I check if this is the problem and, in case it is, how can I fix it? It's a novice question, I know, but this is what I am...
Many thanks again and best regards,

Cosimo
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: Unable to run a coupled simulation with Syrthes

Post by Yvan Fournier »

Hello,

You can run "ldd" on the Code_Saturne (cs_solver) and Syrthes (syrthes) executables in the fluid and solid subdirectories of the case that failed.

In your Syrthes installation (setup.ini), you can also make sure the "mpicc" value for the compiler is the same as that for the Code_Saturne install (if you used a binary-only install, the library is probably different, explaining the crash).

Regards,

Yvan
CTrinca
Posts: 32
Joined: Mon Mar 30, 2015 9:19 am

Re: Unable to run a coupled simulation with Syrthes

Post by CTrinca »

Hello,

Thank you a lot for your time. As you suggested, the error was due to the fact that Saturne and Syrthes were using two different mpicc compiler. I reinstalled both and the simulation eventually started. However, my sorrows are not over yet...

At the first iteration the analysis crashed, giving this message:

Code: Select all

[...]
MPI_ABORT was invoked on rank -2 in communicator MPI_COMM_NULL 
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec noticed that process rank 0 with PID 30192 on node fermi exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
 solver script exited with status 139.

Error running the coupled calculation.

Either Code_Saturne or SYRTHES may have failed.

Check Code_Saturne log (listing) and SYRTHES log (syrthes.log)
for details, as well as error* files.
On syrthes.log I found these lines:

Code: Select all

[fermi:30192] *** Process received signal ***
[fermi:30192] Signal: Segmentation fault (11)
[fermi:30192] Signal code: Address not mapped (1)
[fermi:30192] Failing at address: (nil)
[fermi:30192] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340)[0x7f4a7c6fe340]
[fermi:30192] [ 1] /lib/x86_64-linux-gnu/libc.so.6(fclose+0x4)[0x7f4a7c3967d4]
[fermi:30192] [ 2] ./syrthes[0x40768f]
[fermi:30192] [ 3] ./syrthes[0x402ccf]
[fermi:30192] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f4a7c349ec5]
[fermi:30192] [ 5] ./syrthes[0x402ef5]
[fermi:30192] *** End of error message ***
Any idea about what else I have done wrong?
Thank you very much for your help anyway.
Best regards,

Cosimo
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: Unable to run a coupled simulation with Syrthes

Post by Yvan Fournier »

Hello,

How far does your computation run before the crash ?

There is a Syrthes bug which sometimes causes a crash at the end of the computation. If this is where you crash, I can post a patch, at least until the Syrthes team releases a bug-fix release.

Si could you check or post a larger portion of the Code_Saturne listing or Syrthes syrthes.log file ?

Regards,

Yvan
CTrinca
Posts: 32
Joined: Mon Mar 30, 2015 9:19 am

Re: Unable to run a coupled simulation with Syrthes

Post by CTrinca »

Hello,

Unfortunately, the crash occurs at the very first iteration: I am uploading the complete log, as well as the listing from Code_Saturne. I can't see any problem in the latter, except for the line:

Code: Select all

Application "solid" (SYRTHES 4) requested calculation stop.
Meanwhile, I also noticed that the file stderr.txt output by syrthes is not empty, but reports:

Code: Select all

 
Cannot run syrthes in code coupling mode with this function.

  Error while running syrthes
Stop Syrthes execution.
Sorry I haven't noticed it before, this must be due to something wrong I did in the case definition. I can't tell which function is causing problem though... I am posting the .syd file in case you wish to check it.

Thanks as always, and regards,

Cosimo
Attachments
ctrinca_logs.zip
(15.18 KiB) Downloaded 210 times
JeremyA
Posts: 31
Joined: Fri Jul 26, 2019 10:33 am

Re: Unable to run a coupled simulation with Syrthes

Post by JeremyA »

Hello,

I got the same error

Do we have a solution for CTrinca 's problem ?

Code: Select all

Cannot run syrthes in code coupling mode with this function.

  Error while running syrthes
Stop Syrthes execution.
Best regards,

Jérémy
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: Unable to run a coupled simulation with Syrthes

Post by Yvan Fournier »

Hello,

I don't know, it was a SIGSEGV, and on an old version.

What logs do you have ?

Regards,

Yvan
JeremyA
Posts: 31
Joined: Fri Jul 26, 2019 10:33 am

Re: Unable to run a coupled simulation with Syrthes

Post by JeremyA »

Here's log files
Attachments
summary.log
(41.57 KiB) Downloaded 167 times
listingSOLID.log
(10.92 KiB) Downloaded 187 times
listing.log
(20.22 KiB) Downloaded 174 times
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