Difference between revisions of "Main Page/PIO"

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:Binary (used for production, compact size), or ASCII (used for debugging, human-readable)
 
:Binary (used for production, compact size), or ASCII (used for debugging, human-readable)
  
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== Usage Introduction: ==
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== Usage Introduction ==
  
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For traditional approaches based on one file per processor, users can use #1,2,3
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Users can use #1,2,3,4,5,6,7,8 in .rea file for a specific example, by parameter 81. <br>
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in .rea file for a specific example, by parameter 81. <br>
 
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These three approaches produce one file per processor and we will refer them as ''old libraries''. <br>
 
  
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: '''param(81) = 1''': use nek5000 old_output format (ASCII, fld format, xxx-.fld). <br>
 
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: '''param(81) = 2''': use Fortran I/O library (ASCII, VTK format, ascii-xxx-.vtk). <br>
 
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: '''param(81) = 3''': use C-POSIX I/O libraries (binary, VTK format). <br>
 
  
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----
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Several '''advanced parallel I/O''' algorithms based on MPI-IO library were developed. <br>
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Several advanced parallel I/O approaches were developed. Performance for those approaches
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The analysis on the performance for those approaches are detailed in ''Parallel I/O  
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are detailed in "Jing Fu et. al, Parallel I/O performance for application-level checkpointing  
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performance for application-level checkpointing on the Blue Gene/P, by Jing Fu et. al.'' [http://www.mcs.anl.gov/~mmin]
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on the Blue Gene/P" http://www.mcs.anl.gov/~mmin/ICS2011.pdf.
 
  
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  proc=processors
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  '''param(81) = 4''': collective IO for N proc to 1 file ---> mpi-binary-N1-xxx.vtk
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  '''param(81) = 5''': collective IO for N proc to multiple M-files ---> mpi-binary-NM-xxx.vtk
 +
  '''param(81) = 6''': reduced-blocking IO for N proc to 1 file with M writers ---> mpi-binary-NM1-xxx.vtk
 +
  '''param(81) = 7''': reduced-blocking IO for N proc to 1 file with M writers ---> mpi-ascii-NM1-xxx.vtk
 +
  '''param(81) = 8''': reduced-blocking IO for N proc to multiple M-files with M writers ---> mpi-binary-NMM-xxx.vtk
  
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: '''param(81) = 4''': collective for N processors IO to 1 file (mpi-binary-N1-xxx.vtk) <br>
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'''Note''' that param(82) and param(83) need to be set correctly in *.rea file.
−
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  '''param(80)''' = ''exact'' total number of fields to be written
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: '''param(81) = 5''': collective IO for N processors to multiple M-files (mpi-binary-NM-xxx.vtk. <br>
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  '''param(82)''' = number of output files
 +
  '''param(83)''' = frequency of restart output files, 0 (no restart output), #nn (iostep*nn)
 +
  '''param(84)''' = invoked with dump_number from the name of the restarting output file
  
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: '''param(81) = 6''': reduced-blocking IO for N processors to 1 file with M writers (mpi-binary-NM1-xxx.vtk). <br>
 
  
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: '''param(81) = 6''': reduced-blocking IO for N processors to 1 file with M writers (mpi-ascii-NM1-xxx.vtk). <br>
+
----
−
 
+
For '''traditional I/O''' approaches based on one file per processor, using ''old libraries'', one can use
−
: '''param(81) = 8''': reduced-blocking IO for N processors to multiple M-files with M writers (mpi-NMM-xxx.vtk). <br>
 
  
 +
  '''param(81) = 2''': use Fortran I/O library (ASCII, VTK format) ---> ascii-xxx.vtk
 +
  '''param(81) = 3''': use C-POSIX I/O libraries (binary, VTK format) ---> binary-xxx.vtk
  
 +
  '''param(81) = 1''': use nek5000's old output format (ASCII) -> xxx.fld
  
−
Note that param(82) and param(83) need to be set correctly in *.rea file.
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== Visualization ==
  
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: '''param(82)''' = number of output files, <br>
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The output files with param(81)=2,3,4,5,6,7,8 can be visualized with '''ParaView''' and '''VisIt'''. <br>
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: '''param(83)''' = max number of fields to be written. <br>
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The output with param(81)=1 can be visualized with nek5000 visualization tool, '''postx''' <br>

Latest revision as of 22:36, 16 December 2011

This is the document page for parallel I/O library developed for NekCEM.

Background

File Format
Binary (used for production, compact size), or ASCII (used for debugging, human-readable)

Usage Introduction

Users can use #1,2,3,4,5,6,7,8 in .rea file for a specific example, by parameter 81.


Several advanced parallel I/O algorithms based on MPI-IO library were developed.
The analysis on the performance for those approaches are detailed in Parallel I/O performance for application-level checkpointing on the Blue Gene/P, by Jing Fu et. al. [1] 

 proc=processors
 param(81) = 4: collective IO for N proc to 1 file ---> mpi-binary-N1-xxx.vtk 
 param(81) = 5: collective IO for N proc to multiple M-files ---> mpi-binary-NM-xxx.vtk
 param(81) = 6: reduced-blocking IO for N proc to 1 file with M writers ---> mpi-binary-NM1-xxx.vtk
 param(81) = 7: reduced-blocking IO for N proc to 1 file with M writers ---> mpi-ascii-NM1-xxx.vtk
 param(81) = 8: reduced-blocking IO for N proc to multiple M-files with M writers ---> mpi-binary-NMM-xxx.vtk

Note that param(82) and param(83) need to be set correctly in *.rea file. 

 param(80) = exact total number of fields to be written
 param(82) = number of output files
 param(83) = frequency of restart output files, 0 (no restart output), #nn (iostep*nn) 
 param(84) = invoked with dump_number from the name of the restarting output file


For traditional I/O approaches based on one file per processor, using old libraries, one can use 

 param(81) = 2: use Fortran I/O library (ASCII, VTK format) ---> ascii-xxx.vtk
 param(81) = 3: use C-POSIX I/O libraries (binary, VTK format) ---> binary-xxx.vtk 

 param(81) = 1: use nek5000's old output format (ASCII) -> xxx.fld

Visualization

The output files with param(81)=2,3,4,5,6,7,8 can be visualized with ParaView and VisIt.
The output with param(81)=1 can be visualized with nek5000 visualization tool, postx

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