pbdADIOS

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

pbdADIOS requires:

• R version 3.1.0 or higher with pbdMPI
• ADIOS 1.10.0 library

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"