[MOAB-dev] Fwd: About reading vtk in parallel mode.

Fri Sep 6 00:01:21 CDT 2013

 I found some information about iZoltan 
http://lists.mcs.anl.gov/pipermail/moab-dev/2012/004439.html

Maybe I should use this way for loading vtk files? 

_______________________________
Best regards, Ilya Romero
Nuclear  Safety Institute
Russian Academy of Sciences

-------- Пересылаемое сообщение --------
От кого: Иля <ilacai at mail.ru>
Кому: MOAB-dev at mcs.anl.gov
Дата: Пятница,  6 сентября 2013, 8:53 +04:00
Тема: About reading vtk in parallel mode.

I am new in MOAB and don't have enough experience in your program product. And I'm sorry for my maybe silly questions.

Could you please help me with the following situation. The main idea is using solution coupling in my research. I found workable example in MOAB package: {$MOAB_dir}/tools/mbcoupler/mbcoupler_test.cpp. So at the first, I decided just to change meshes in this example. And I tryed to understand how to use meshes in parallel mode.

1) I had the geometry of both new meshes in vtk format: geom1.vtk, geom2.vtk. Using MBConverter I converted them into vtk format, supporting by MOAB
./mbconvert -f vtk geom1.vtk geom1_c.vtk
2)Using MBZoltan I converted new vtk files into h5m format, dividing in 4 parts
./ mbpart 4 - T  geom 1_c. vtk  geom 1_ p . h 5 m
3) I read geom1_p.h5m with Tecplot and checked PARALLEL_PARTITION tag existance (according MOAB_UG.doc). There are values: 0,1,2,3, that is correct. So I tryed to use 2 variants of reading parameters:
«PARALLEL=READ_PART; PARTITION=PARALLEL_PARTITION; PARTITION_DISTRIBUTE;CPUTIME»
and
«PARALLEL=READ_PART; PARTITION=PARALLEL_PARTITION; PARTITION_VAL=0,1,2,3;CPUTIME»
4) Then I used these meshes with mbcoupler_test 
mpirun -as intel -np 2 -q test ./mbcoupler_test -meshes geom1_p.h5m geom2_p.h5m -itag vertex_field -outfile test.h5m
But these meshes weren't read with program. The listing file has the following information:

Parallel Read times: 
0.030983 PARALLEL READ PART
0.030983 PARALLEL TOTAL
Parallel Read times: 
0.00436592 PARALLEL READ PART
0.00436592 PARALLEL TOTAL
Proc 0 iface entities: 
0 0d iface entities.
0 1d iface entities.
0 2d iface entities.
0 3d iface entities.
(0 verts adj to other iface ents)
Proc 1 iface entities: 
0 0d iface entities.
0 1d iface entities.
0 2d iface entities.
0 3d iface entities.
(0 verts adj to other iface ents)
Failure; message:
No tag value for root set
Failure; message:
No tag value for root set
application called MPI_Abort(MPI_COMM_WORLD, 6) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 6) - process 1
rank 1 in job 1 t60-2.parallel.ru_43452 caused collective abort of all ranks
exit status of rank 1: return code 6
5) If I set readOpts = "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION;PARTITION_DISTRIBUTE;PARALLEL_RESOLVE_SHARED_ENTS;PARALLEL_GHOSTS=3.0.1;CPUTIME"; the meshes are read, but option PARALLEL_RESOLVE_SHARED_ENTS gives errror

Parallel Read times:
0.198586 PARALLEL READ PART
0.026906 PARALLEL RESOLVE_SHARED_ENTS
0.00115585 PARALLEL EXCHANGE_GHOSTS
9.60827e-05 PARALLEL RESOLVE_SHARED_SETS
0.226157 PARALLEL TOTAL
Parallel Read times:
0.00666714 PARALLEL READ PART
0.00862002 PARALLEL RESOLVE_SHARED_ENTS
0.00228691 PARALLEL EXCHANGE_GHOSTS
4.41074e-05 PARALLEL RESOLVE_SHARED_SETS
0.0157781 PARALLEL TOTAL
Proc 0 iface entities:
96 0d iface entities.
154 1d iface entities.
60 2d iface entities.
0 3d iface entities.
(96 verts adj to other iface ents)
Proc 1 iface entities:
96 0d iface entities.
154 1d iface entities.
60 2d iface entities.
0 3d iface entities.
(96 verts adj to other iface ents)
application called MPI_Abort(MPI_COMM_WORLD, 6) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 6) - process 1
Failure; message:
No sparse tag __PARALLEL_SHARED_PROCS value for Vertex 969
Failure; message:
No sparse tag __PARALLEL_SHARED_PROCS value for Vertex 800
rank 1 in job 1 t60-2.parallel.ru_41693 caused collective abort of all ranks
exit status of rank 1: return code 6

5) Using  this information I checked my h5m files with MBconverter
mpirun -np 2 -q test -as intel ./mbconvert -O PARALLEL=READ_PART -O PARTITION=PARALLEL_PARTITION -O PARALLEL_RESOLVE_SHARED_ENTS -O PARALLEL_GHOSTS=3.0.1 -o PARALLEL=WRITE_PART geom1_p.h5m geom1_last.h5m
The result is successful:
Read "geom1_p.h5m"
Wrote "geom1_last.h5m" 6) So could you please explain how I should correct read meshes in parallel? Form vtk to h5m parallel mesh (I would like to use  READ_PART method ). What do I do wrong? (All using files are applied with this letter)

Thank you.

_______________________________
Best regards, Ilya Romero
Nuclear  Safety Institute
Russian Academy of Sciences

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