README.md

In RBigData/hola: Helpful Operating Link to ADIOS

hola

• Version: 0.1-0
• License: BSL-1.0
• Project home: https://github.com/RBigData/hola
• Bug reports: https://github.com/RBigData/hola/issues

hola is the Helpful Operating Link to ADIOS, an interface to the ADIOS2 library. ADIOS2 is an I/O middleware used in some of the largest supercomputing simulations in the world. It supports several formats, including HDF5 and its native BP, as well as streaming data.

Currently we have implemented a single process (no MPI) reader and writer.

Installation

You can install the stable version from the HPCRAN using the usual install.packages():

install.packages("hola", repos=c("https://hpcran.org", "https://cran.rstudio.com"))

The development version is maintained on GitHub:

remotes::install_github("RBigData/hola")

You will need a system installation of ADIOS2; there is an example build script in hola/tools/build_adios.sh. At build time, hola needs to be able to find the file adios2/install/path/bin/adios2-config. So to build hola, you either need to add adios2/install/path/bin to your $PATH, or set configure.args e.g.

remotes::install_github("RBigData/hola", configure.args="--with-adios2-home=adios2/install/path/")

Example

Here is a basic example reading a matrix from a simple hdf5 file that was written via hdf5r and is included in the package.

dataset = system.file("datasets/example_int.h5", package="hola")
ad = hola::adios(dataset)

ad$available_variables()
## [1] "/data"

ad$read("/data")
##       [,1] [,2] [,3]
##  [1,]    1   11   21
##  [2,]    2   12   22
##  [3,]    3   13   23
##  [4,]    4   14   24
##  [5,]    5   15   25
##  [6,]    6   16   26
##  [7,]    7   17   27
##  [8,]    8   18   28
##  [9,]    9   19   29
## [10,]   10   20   30

We can also write a file and then read it back:

x = matrix(1:8, 4)
str(x)
## int [1:4, 1:2] 1 2 3 4 5 6 7 8

f = "/tmp/test.h5"
var = "/mydata"

# write 'x' to variable 'var' in file 'f'
w = hola::adios(f, mode="write")
w$write(var, x)
w$close()

# read 'var' in file 'f' to object 'y'
r = hola::adios(f)
y = r$read(var)
str(y)
## int [1:4, 1:2] 1 2 3 4 5 6 7 8

all.equal(x, y)
## [1] TRUE

RBigData/hola documentation built on Aug. 18, 2021, 4:28 p.m.