Main Page/faq

This is the resource listing page for NekCEM.

Resource Links

• Parallel I/O of NekCEM

• Hybrid programming (proposed work)

• Sync/Async Blocking/non-blocking I/O

• Blue Gene/Q and Mira

• Meeting Notes

Implementation

I/O code

• I/O functions were initiated from cem_out function of cem_dg.F (and cem_dg2.F).
• Implementation of parallel I/O routine were defined in vtkbin.c and rbIO_nekcem.c
• vtkcommon.c and vtkcommon.h serve as a place to hold common functions as well as global variables.
  

• cem_out_fields3 (in cem_dg.F)
  • openfile3(dumpno, nid) !vtkbin.c
  • vtk_dump_header3
    • writeheader3() !vtkbin.c
    • writenodes3() !vtkbin.c
    • write2dcells3 !vtkbin.c
      or write3dcells3 !vtkbin.c
  • vtk_dump_field3
    • writefield3 !vtkbin.c
  • close_file3 !vtkbin.c

• Binary file → ASCII file: transfer double/float/int/read to chars then write out
  • float (4 bytes) → %18.8E
  • int (4 bytes) → %10d
  • long long (8 bytes) → %18lld
  • elemType → %4d

NekCEM notes

• compile and run NekCEM
  • in a specific case, ../../bin/cleanall, ../../bin/makenek, ../../bin/nek "case_name" #proc
  • e.g., in cylwave, ../../bin/nek cylwave 4

• scaling
  • strong scaling: defined as how the solution time varies with the number of processors for a fixed total problem size.
  • weak scaling: defined as how the solution time varies with the number of processors for a fixed problem size per processor.
• pre-compute file size
  • #grid point = nx * ny * nz * nelt; size = #grid point * 3 * float
  • cell type: 2d → 4 * #cell * int + 1* #cell * int (3d → 9)
  • #field = nfields * 3 * #grid point; size = #field * float;

• .box → num elements in x,y,z
• .rea → input data
• SIZEu → SIZE parameters:
  • lxi ?
  • lp = #proc
  • lelx = 20 each dimension
  • lelv = alloc max # of element per proc
• .usr → subuser.F
• cem() in cem_dg.F is the main solver and application entry point

• only CELL and point data need to be re-computed

To-do List

• More tests on BG/P for config with ng = M and 1< nf < M
• Tests on Kraken and Jaguar
• Pthread + MPI for I/O
• OpenMP/Pthread + MPI for NekCEM computation
• Parallel I/O for reading .rea file

Miscellaneous notes

• Fortran generated binary file may not be correctly read in C.
• -lstdc++ for link
• libF77 and libI77
• common.h and common_c.h
• write() in Fortran: 6 refer to screen, * is to screen as well ..