bigMatrix: Load a 'bigMatrix' (deprecated)

Description Usage Arguments Details

Description

The 'bigMatrix' class is no longer implemented in the NetRep package: the shared memory approach was incompatabile with high performance compute clusters, so the parallel permutation procedure has been translated into C++ code (which is also much faster). The disk.matrix class should now be used instead when analysing large datasets.

Usage

1
load.bigMatrix(backingfile)

Arguments

backingfile

path to the backingfile for the 'bigMatrix'. The file extension must be omitted.

Details

This function will convert 'bigMatrix' data saved by previous versions of NetRep to a serialized R matrix saved in the same location and return a disk.matrix object with the associated file path. If this conversion has taken place already the function will throw a warning.

This function will also convert the 'bigMatrix' descriptor file to a big.matrix descriptor file to preserve compatability with functions in the bigmemory package. If this functionality is not required, the files with the extensions ".bin" and ".desc" may be removed.

A note for users using multi-node high performance clusters: 'big.matrix' objects are not suitable for general usage. Access to file-backed shared memory segments on multi-node systems is very slow due to consistency checks performed by the operating system. This becomes exponentially worse the more R sessions there are simultaneously accessing the shared memory segment, e.g. through parallel foreach loops.


NetRep documentation built on June 12, 2018, 5:04 p.m.