ergm (version 3.6.1)

ergm-parallel: Parallel Processing in the ergm Package

Description

For estimation that require MCMC, ergm can take advantage of multiple CPUs or CPU cores on the system on which it runs, as well as computing clusters. It uses package parallel and snow to facilitate this, and supports all cluster types that they does.

The number of nodes used and the parallel API are controlled using the parallel and parallel.type arguments passed to the control functions, such as control.ergm. The ergm.getCluster function is usually called internally by the ergm process (in ergm.getMCMCsample) and will attempt to start the appropriate type of cluster indicated by the control.ergm settings. The ergm.stopCluster is helpful if the user has directly created a cluster. Further details on the various cluster types are included below.

Usage

ergm.getCluster(control, verbose=FALSE)
ergm.stopCluster(object, ...)

Arguments

control

a control.ergm list of parameter values from which the parallel settings should be read

object

an object, probably of class "cluster"

verbose

logical, should detailed status info be printed to console

...

not currently used

PSOCK clusters

The parallel package is used with PSOCK clusters by default, to utilize multiple cores on a system. The number of cores on a system can be determined with the detectCores function. This method works with the base installation of R on all platforms, and does not require additional software. For more advanced applications, such as clusters that span multiple machines on a network, the clusters can be initialized manually, and passed into ergm using the parallel control argument. See the second example below.

MPI clusters

To use MPI to accelerate ERGM sampling, pass the control parameter parallel.type="MPI". ergm requires the snow and Rmpi packages to communicate with an MPI cluster. Using MPI clusters requires the system to have an existing MPI installation. See the MPI documentation for your particular platform for instructions. To use ergm across multiple machines in a high performance computing environment, see the section "User initiated clusters" below.

User initiated clusters

A cluster can be passed into ergm with the parallel control parameter. ergm will detect the number of nodes in the cluster, and use all of them for MCMC sampling. This method is flexible: it will accept any cluster type that is compatible with snow or parallel packages. Usage examples for a multiple-machine high performance MPI cluster can be found at the statnet wiki: https://statnet.csde.washington.edu/trac/wiki/ergmParallel

Examples

# Uses 2 SOCK clusters for MCMLE estimation
data(faux.mesa.high)
nw <- faux.mesa.high
fauxmodel.01 <- ergm(nw ~ edges + isolates + gwesp(0.2, fixed=TRUE), 
                     control=control.ergm(parallel=2, parallel.type="PSOCK"))
summary(fauxmodel.01)