Adios2 update

[usmanriaz07]

This PR:

• modifies the writing function from omega_h mesh to adios2 file to get rid of data that does not need to be saved explicitly, and use of multi-dimensional arrays for data where needed.
• updates the corresponding read function from adios2 to omega_h.
• moves the function write_mesh () to header file.

The updated output of bpls on a mesh written to an adios2 (.bp) file is given below. In this file, mesh/planes/0 is the pre name provided to the writer function.

  int32_t  mesh/planes/0/comm_size                {1}
  int32_t  mesh/planes/0/dim                      {1}
  int32_t  mesh/planes/0/downward_adj/1_to_0      {1526, 2}
  int32_t  mesh/planes/0/downward_adj/2_to_1      {994, 3}
  int8_t   mesh/planes/0/downward_codes/2         {994, 3}
  int32_t  mesh/planes/0/family                   {1}
  int32_t  mesh/planes/0/mesh_version             {1}
  int32_t  mesh/planes/0/nghost_layers            {1}
  int32_t  mesh/planes/0/nverts                   {1}
  int32_t  mesh/planes/0/parting                  {1}
  int32_t  mesh/planes/0/rank                     {1}
  int8_t   mesh/planes/0/tags/0/class_dim/data    {533, 1}
  int32_t  mesh/planes/0/tags/0/class_id/data     {533, 1}
  double   mesh/planes/0/tags/0/coordinates/data  {533, 2}
  int8_t   mesh/planes/0/tags/1/class_dim/data    {1526, 1}
  int32_t  mesh/planes/0/tags/1/class_id/data     {1526, 1}
  int8_t   mesh/planes/0/tags/2/class_dim/data    {994, 1}
  int32_t  mesh/planes/0/tags/2/class_id/data     {994, 1}

[jacobmerson]

Looks reasonable to me. Can you post the output of bpls on a mesh file created with this?

[cwsmith]

Looks good. Thank you.

I left one comment below.

Do we have any test cases for serial/parallel adios2 read/write?

[jacobmerson]

@cwsmith I believe this is ready to merge when you return.

[cwsmith]

Looks good. A few small comments are below.

It looks like this is the current test case that writes then reads via the adios2 api:

omega_h/src/CMakeLists.txt

Lines 668 to 671 in 09a5171

	test_basefunc(adios2_io 1 ./adios2_io
	${CMAKE_SOURCE_DIR}/meshes/unitbox_cutTriCube_1k.osh
	${CMAKE_SOURCE_DIR}/meshes/plate_6elem.osh
	output.bp)

Would providing adios2osh and osh2adios converter utilities (as done for gmsh, exodus, etc.) be useful for the applications that need adios2 meshes?

[usmanriaz07]

Would providing adios2osh and osh2adios converter utilities (as done for gmsh, exodus, etc.) be useful for the applications that need adios2 meshes?

Seegyoung has already added those utilities (bp2osh and osh2bp).
https://github.com/SCOREC/omega_h/blob/master/src/CMakeLists.txt#L665-L666

[cwsmith]

/runtests

[github-actions]

Test Result: success (details)

[cwsmith]

If @jacobmerson is all set then I think this can be merged.