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Hi all,

I am a telemac beginner and I am trying to do a 3D model using a BINARY BOUNDARY DATA FILE. For this, I have used the python script ConvertToBND.py applied on a selafin output file from a previous simple 3D simulation. This was conceived as an initial simple test to see how this worked.

The problem is that I get the error below.

I have checked that the compilation options are ok.
I send my configuration files in case anyone can help me. Unfortunately, the boundary data file is too big, so I cannot include it.





Thanks in advance for your time!!
Luz


... splitting / copying other input files
partitioning: T3DBND
+> /gpfs/software/opentelemac/v7p2r2/builds/subpar/bin/partel < PARTEL.PAR >> partel_T3DBND.log
copyPartition:
|runPARTEL: Could not split your file T3DBND (runcode=139) with the error as follows:
|
|... The following command failed for the reason above (or below)
|/gpfs/software/opentelemac/v7p2r2/builds/subpar/bin/partel < PARTEL.PAR >> partel_T3DBND.log
|
| You may have forgotten to compile PARTEL with the appropriate compiler directive
| (add -DHAVE_MPI to your cmd_obj in your configuration file).
|
|Here is the log:

Hello Luz,

Can you please try to add the keyword "BINARY BOUNDARY DATA FILE FORMAT = SERAFIN" in your steering file, and tell us what happens.
If the error message remains, can you also post the partel_T3DBND.log file, and if possible a subset of your binary boundary file (the 2 first time steps for instance).

Hope this helps,
Laurent

Hi Laurent,

Thanks for your reply. I have added the suggested keyword and I get the same error.

The partel_T3DBND.log file is empty.

This is the BINARY BOUNDARY DATA FILE with just a couple or time steps:




Just in case it helps, I get a file called PARTEL.PAR that contains this:

T3DBND
SERAFIN
T3DCLI
24
1



T3DGEO
SERAFIN

and I get a Core dump, which has some legible parts, I think related to the partition of the bnd file (but I am not sure). I attach it in case it helps.





Thanks a lot!
Luz

Hi, I have the same problem .
From the output of PARTEL log , seems BND file shoule be a 3D file,but convertToBND.py generate a 2D file with each element have 4 nodes.
My question is how to build the 3D BND file. Hope there is an example.
From my personal view ,the BND file might be a 2D file like vertical slice.or there is a dimension "time" to become a 3D file ? the dimension are (bndnode,nplan,time).
thanks.

liuy

Hi,

Could you re-run the following command from your temporary folder:
And post the result here because it looks like we are missing the actual error.

Hope it helps.

Hi,

The error message is a segmentation fault in the subroutine parres.f, maybe an array index out of bounds exception.
After some investigations, it seems that the error occurs between lines 276 and 291 (v7p2r1 of parres.f), during the building of the 3D connectivity table, in the first iteration of the double loops (I=1 for NPLAN_INP, and J=1 for NELEM_GEO).
I didn't have more time to look any further, but I wonder about the allocation of IKLE3D above:
ALLOCATE (IKLE3D(NELEM_GEO*(NPLAN_INP-1)*NDP_INP),STAT=IERR)
should not that be
ALLOCATE (IKLE3D(NELEM_INP*(NPLAN_INP-1)*NDP_INP),STAT=IERR)

First, can you reproduce the error?

Regards,
Laurent

Hello,

First of all I think you should check that your boundary file is in the correct coordinate system: it seems to me that this is not the case. You can use the runSELAFIN script, with
--ll2sph to convert from longitude-latitude to spherical for example.
Cheers,
Agnès

What I mean is that T3DBND is partitionned using PARRES, which means the same partitionning is applied to T3DBND than to T3DGEO. If T3DBND is not in the same coordinates system, the partitionning of T3DBND should fail. This may be the cause of your issue.

Agnès

Hi all,

Both my geometry and boundary files are in lat/lon, so I would think this is not the problem.

I have run the command suggested by "yugi" in my temporary folder and I get a segmentation fault as Laurent does. More specifically, I get this:

+

---

+
PARTEL/PARRES: TELEMAC METISOLOGIC PARTITIONER

REBEKKA KOPMANN & JACEK A. JANKOWSKI (BAW)
JEAN-MICHEL HERVOUET (LNHE)
CHRISTOPHE DENIS (SINETICS)
YOANN AUDOUIN (LNHE)
PARTEL (C) COPYRIGHT 2000-2002
BUNDESANSTALT FUER WASSERBAU, KARLSRUHE

METIS 5.0.2 (C) COPYRIGHT 2012
REGENTS OF THE UNIVERSITY OF MINNESOTA

BIEF V7P2R0 (C) COPYRIGHT 2012 EDF
+

---

+


MAXIMUM NUMBER OF PARTITIONS: 100000

+

---

+

--INPUT FILE NAME <INPUT_NAME>:
INPUT: T3DBND
--INPUT FILE FORMAT <INPFORMAT> [MED,SERAFIN,SERAFIND]:
INPUT: SERAFIN
--BOUNDARY CONDITIONS FILE NAME:
INPUT: T3DCLI
--NUMBER OF PARTITIONS <NPARTS> [2 -100000]:
INPUT: 24
PARTITIONING METHOD <PMETHOD> [1 (METIS) OR 2 (SCOTCH)]:
--INPUT: 1
--CONTROL SECTIONS FILE NAME (OR RETURN) :
NO SECTIONS
--CONTROL ZONES FILE NAME (OR RETURN) :
NO ZONES
--WEIR FILE NAME (OR RETURN) :
NO WEIRS
--GEOMETRY FILE NAME <INPUT_NAME>:
INPUT: T3DGEO
--GEOMETRY FILE FORMAT <GEOFORMAT> [MED,SERAFIN,SERAFIND]:
INPUT: SERAFIN
+---- PARRES: BEGINNING

---

+
+---- USING GEOMETRY FILE: T3DGEO
- FILE T3DBND OF TYPE BIG_ENDIAN
- FILE T3DBND IS SINGLE PRECISION
TREATING SUB-DOMAIN 1
- FILE T3DGEO00023-00000 OF TYPE BIG_ENDIAN
- FILE T3DGEO00023-00000 IS SINGLE PRECISION
- FILE T3DBND00023-00000 OF TYPE BIG_ENDIAN


READ_MESH_INFO: TITLE= final_bathy_preference_astrium
NUMBER OF ELEMENTS: 922
NUMBER OF POINTS: 502

FORMAT NOT INDICATED IN TITLE

NO BND ELEMENTS IN A 3D MESH


READ_MESH_INFO: TITLE=
NUMBER OF ELEMENTS: 549
NUMBER OF POINTS: 630

FORMAT NOT INDICATED IN TITLE


3D MESH DETECTED
NDP NODES PER ELEMENT: 4
ELEMENT TYPE : 30
NPLAN NUMBER OF MESH LEVELS: 10
NPOIN2 NUMBER OF 2D MESH NODES: 63
NPOIN NUMBER OF 3D MESH NODES: 630
NELEM2 NUMBER OF 2D MESH ELEMENTS: 61
NELEM NUMBER OF 3D MESH ELEMENTS: 549

THE INPUT FILE ASSUMED TO BE 3D
Segmentation fault (core dumped)


Similarly to Laurent, the error I get is this:

partitioning: T3DBND
+> /gpfs/software/opentelemac/v7p2r2/builds/intpar/bin/partel < PARTEL.PAR >> partel_T3DBND.log
At line 286 of file /gpfs/home/e088/opentelemac_72/v7p2r2/sources/utils/partel/parres.f
Fortran runtime error: Index '33193' of dimension 1 of array 'ikle3d' above upper bound of 33192


Any more ideas??? Thank you very much for your help!!

Luz

Hello,

So during the calculation you will convert the coordinates to spherical coordinates? Could you try to convert both your geometry mesh and your binary boundary file to spherical coordinates to see if you get the same issue ? I remember having similar issues when working with a lat-long T3DBND file but then my mesh had already been converted to spherical coordinates. I'm not sure it is possible to work with lat-long files directly with the binary boundary file feature.

Cheers,
Agnès