Package to read from ADIOS, including staging.
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README.md

pbdADIOS

pbdADIOS is a package to connect R with ADIOS parallel middleware for IO. Staging and in situ capability.

pbdADIOS requires:

More information about pbdADIOS can be found in the ADIOS User's Manual.

Usage

# load pbdADIOS lib
library(pbdADIOS, quiet = TRUE)

# print variables and attributes
bpls("attributes.bp")

# dump all variables
bp.dump("attributes.bp")

# read a variable
bp.read("attributes.bp", "temperature")

finalize() # pbdMPI final

More examples in demo directory.

Installation

This file is for a Linux, Mac OS X and Solaris

  1. 'pbdMPI' Installation:

    See 'pbdMPI/INSTALL' for the details.
    
  2. MXML installation:

    Install MXML. Download MXML from : http://www.msweet.org/projects.php?Z3

    ./configure --prefix=SpecifyInstallPath  
    make
    make install 
    
  3. ADIOS Installation:

    Install ADIOS. Download from : https://www.olcf.ornl.gov/center-projects/adios/

    ./configure CFLAGS="-w -fpic" --prefix=SpecifyInstallPath  
          --disable-fortran
          --without-hdf5
          --without-phdf5
          --without-netcdf
          --without-nc4par
          --without-dataspaces 
          --without-flexpath
          --without-lustre 
          --enable-shared=yes 
          --with-mxml=Specify_MXML_InstallPath 
          --with-pic
    make
    make install
    
  4. 'pbdADIOS' Installation:

    Download and install 'pbdADIOS'

    R CMD INSTALL pbdADIOS_0.1-0.tar.gz --configure-args="--with-adios-home=Specify_ADIOS_InstallPath"