xgrid.run: Remote execution of user-specified R functions on Apple Xgrid...

In ashiklom/runjags: Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS

Description

Allows arbitrary R code to be executed on Apple Xgrid distributed computing clusters and the results returned to the R session of the user. Jobs can either be run synchronously (the process will wait for the model to complete before returning the results) or asynchronously (the process will terminate on submission of the job and results are retrieved at a later time). Access to an Xgrid cluster with R (along with all packages required by the function) installed is required. Due to the dependance on Xgrid software to perform the underlying submission and retrieval of jobs, these functions can only be used on machines running Mac OS X.

The two utility functions xgrid.jobs and xgrid.delete allow the currently running jobs to be examined and deleted from inside R.

*Note* Apple has discontinued Xgrid from Mac OS 10.8 onwards, and these functions are deprecated as of runjags version 2.

Usage

xgrid.run(f=function(iteration){}, niters=1, object.list=list(),
	file.list=character(0), max.threads=100, arguments=as.list(1:niters),
	Rversion="", packages=list(), artfun=function() writeLines("1"),
	email=NA, profiling=TRUE, cpuarch=NA, minosversion=NA,
	queueforserver=FALSE, hostnode=NA, forcehost=FALSE, ramrequired=10,
	jobname=NA, cleanup=TRUE, showprofiles=FALSE, Rpath='/usr/bin/R',
	Rbuild='64', max.filesize="1GB", 
	mgridpath=system.file("xgrid", "mgrid.sh", package="runjags"),
	hostname=Sys.getenv("XGRID_CONTROLLER_HOSTNAME"),
	password=Sys.getenv("XGRID_CONTROLLER_PASSWORD"), tempdir=FALSE,
	keep.files=FALSE, show.output=TRUE, threads=min(niters, max.threads), ...)

xgrid.submit(f=function(iteration){}, niters=1, object.list=list(),
	file.list=character(0), max.threads=100, arguments=as.list(1:niters),
	Rversion="", packages=list(), artfun=function() writeLines("1"),
	email=NA, profiling=TRUE, cpuarch=NA, minosversion=NA,
	queueforserver=FALSE, hostnode=NA, forcehost=FALSE, ramrequired=10,
	jobname=NA, Rpath='/usr/bin/R', Rbuild='64', max.filesize="1GB",
	mgridpath=system.file("xgrid", "mgrid.sh", package="runjags"),
	hostname=Sys.getenv("XGRID_CONTROLLER_HOSTNAME"),
	password=Sys.getenv("XGRID_CONTROLLER_PASSWORD"), show.output=TRUE,
	separate.jobs=FALSE, threads=min(niters, max.threads), ...)

xgrid.results(jobinfo, wait=TRUE, partial.retrieve=!wait,
	cleanup=!partial.retrieve, show.output=TRUE)

xgrid.jobs(comment=FALSE, user=FALSE, jobs=10,
	mgridpath=system.file("xgrid", "mgrid.sh", package="runjags"),
	hostname=Sys.getenv("XGRID_CONTROLLER_HOSTNAME"),
	password=Sys.getenv("XGRID_CONTROLLER_PASSWORD"))

xgrid.delete(jobinfo, keep.files=FALSE)

xapply(X, FUN, method.options=list(), ...)

Arguments

f	the function to be iterated over on Xgrid. This must take at least 1 argument, the first of which represents the value of the 'arguments' list to be passed to the function for that iteration, which is the iteration number unless 'arguments' (or 'X' for xapply) is specified. Any other arguments to be passed to the function can be supplied as additional arguments to xgrid.run/xgrid.submit/xapply. The value(s) of interest should be returned by this function (an object of any class is permissable). No default.
niters	the total number of iterations over which to evaluate the function f. This can be less than the number of threads, in which case multiple iterations are evaluated serially as part of the same task. No default.
object.list	a named list of objects that will be copied to the global environment on Xgrid and so will be visible inside the function. Alternatively, this can be a character vector of objects, that will be looked for in the global environment, rather than a named list. All other objects in the current working directory will not be visible when the function is evaluated. THIS INCLUDES LIBRARIES WHICH MUST BE RE-CALLED WITHIN THE FUNCTION BEFORE USE. In order to use functions within an R library it is therefore necessary for the required library to be installed on the Xgrid nodes on which the job will be run. If not all nodes have the required libraries installed, you can use an ART script to ensure the job is sent only to machines that do (see the example provided below), or you can use mgrid to manually request certain nodes using the '-f -h <nodename>' options. Alternatively, text files containing R code can be included in the 'file.list' argument and source()d within the function. Default blank list (no objects copied).
file.list	a vector of filenames representing files in the current working directory that will be copied to the working directory of the executed function. This allows R code to be source()d, datasets to be loaded, and compiled code to be dynamically linked within the function, among other things. Default none.
max.threads	the maximum number of tasks (or jobs) to split into.
arguments	a list of values to be passed as the first argument to the function, with each element of the list specifying the value at that iteration. Default is as.list(1:niters) which passes only the iteration number to the function.
Rversion	the required R version for worker nodes to be given tasks - may include '=' or '>=' to signify exact or minimum version requirements.
packages	a list of R packages that must be installed on host nodes for them to be used.
artfun	an optional user-specified R function to determine the suitability of nodes in an ART script - must either cat() 1 (indicating suitable) or 0 (indicating unsuitable) to stdout.
email	an email address to be used to notify of job status.
profiling	option to use ART ranking to select the most suitable host nodes preferentially.
cpuarch	option to restrict the job to 'ppc' or 'intel' nodes.
minosversion	option to restrict the job to nodes running a minimum Mac OS version.
queueforserver	option to restrict the job to nodes considered to be Server machines.
hostnode	option to prefer (or restrict to if forcehost==TRUE) running the job on the specified nodes - must be provided as a single character string with the colon character (:) separating node names.
forcehost	option to restrict the job to only nodes specified by 'hostnode'.
ramrequired	the minimum amount of free RAM (obtained using an approximation) for each node to be assigned a task.
jobname	the name to give the job on Xgrid (optional).
cleanup	option to remove the job from Xgrid after completion.
showprofiles	option to show the node scores based on the ART ranking used.
Rpath	the path to the R executable on the xgrid machines. If not all machines on the xgrid cluster have R (or a required package) installed then it is possible to use an ART script to ensure the job is sent to only machines that do - see the examples section for details. Default '/usr/bin/R' (this is the default install location for R).
Rbuild	the preferred binary of R to invoke. '64' results in 'Rpath64' (if it exists), '32' in 'Rpath32' (if it exists) and ” (or either of '32' or '64' if they are not found) results in Rpath. Notice that this indicates a preference, not a certainty - if the indicated build is not avalable then another will be used. Also note that specifying '64' may be ignored for PPC nodes depending on what version of R they are running (you can ensure only intel nodes are used with mgrid using sub.options='-c intel'). Default ”.
max.filesize	the maximum total size of the objects produced by the function for each thread if xgrid.method=separatejobs, or for the entire job if xgrid.method=separatetasks. This is a failsafe designed to prevent attempted transfer of huge files bringing the xgrid controller down. If the maximum size is exceeded for a thread or job then the results are erased for all iterations within that thread or job, and the job will likely have to be re-submitted. If each chain is likely to return a large amount of information, then 'separatejobs' should be used because jobs are retrieved individually which reduces the chances of overloading the Xgrid controller. The object.list is also checked to ensure it complies with the maximum size, but the file.list and any objects saved to the working directory by the function are NOT automatically cheked. Units can be provided as either "MB" or "GB". Default "1GB".
mgridpath	the path to the local mgrid script - default uses the version installed with the runjags package.
hostname	the hostname of the Xgrid server to connect to.
password	the password for the Xgrid server given by hostname.
tempdir	for xgrid.run, option to use the temporary directory as specified by the system rather than creating files in the working directory. Any files created in the temporary directory are removed when the function exits. A temporary directory cannot be used for xgrid.submit. Default TRUE when running the job synchronously.
keep.files	option to keep the folder with files needed to run the job rather than deleting it when the job is deleted from Xgrid. This may be useful for attempting to bug fix failing jobs. Default FALSE.
show.output	option to print the output of the function (obtained using cat, writeLine or print for example) at each iteration after retrieving the job(s) from xgrid. If FALSE, the output is suppressed. Default TRUE.
separate.jobs	option to submit multiple jobs to Xgrid, to help with file size constraints (see the entry for 'threads' below).
threads	the number of threads (either jobs if separate.jobs==TRUE or tasks otherwise) to generate for the job. Each thread is sent to a separate node for execution, so the more threads there are the faster the job will finish (unless the number of threads exceeds the number of available nodes). A very large number of threads may cause problems with the Xgrid controller, hence the ability to set fewer threads than iterations. Functions that return objects of a very large size should use a large number of threads and use the xgrid.method 'separatejobs' to minimise the total size of objects returned by each xgrid job.
...	additional arguments to be passed to the function provided by f.
jobinfo	the output of a call to xgrid.submit.
wait	option to wait for the Xgrid job to complete if it has not done so already.
partial.retrieve	for xgrid.results, option to retrieve results of partially completed jobs. By default makes cleanup FALSE. Default TRUE.
comment	option to display any comments relevant to the Xgrid jobs running.
user	option to display information on the user that submitted each Xgrid job.
jobs	the number of (most recent) jobs to display information for.
X	for xapply, a vector (atomic or list) over which to apply the function provided. Equivalent to 'arguments' for xgrid.run, with niters = length(X).
FUN	for xapply, the function to be passed to xgrid.run as 'f'.
method.options	for xapply, any arguments (with the exception of 'f', 'niters' and 'arguments' which are ignored) to be passed to xgrid.run.

Details

These functions allow JAGS models to be run on Xgrid distributed computing clusters from within R using the same syntax as required to run the models locally. All the functionality could be replicated by saving all necessary objects to files and using the Xgrid command line utility to submit and retrieve the job manually; these functions merely provide the convenience of not having to do this manually. Xgrid support is only available on Mac OS X machines running OS X 10.5-10.7 (Xgrid support was discontinued in Mac OS X 10.8).

The xgrid controller hostname and password can also be set as environmental variables. The command line version of R knows about environmental variables set in the .profile file, but unfortunately the GUI version does not and requires them to be set from within R using:

Sys.setenv(XGRID_CONTROLLER_HOSTNAME="<hostname>")

Sys.setenv(XGRID_CONTROLLER_PASSWORD="<password>")

(These lines could be copied into your .Rprofile file for a 'set and forget' solution)

Note that the runjags package also contains a utility shell script called 'mgrid' that enhances the capabilities of Xgrid substantially - to install this from the command line navigate to the folder given by system.file("xgrid", package="runjags") and from the terminal type 'sudo cp mgrid.sh /usr/local/bin/mgrid (or similar) to make the script visible in your search path. Help on the mgrid script can then be obtained by typing 'mgrid' (with no arguments) at the command line.

Value

For xgrid.submit, a list containing the jobname (which will be required by xgrid.results to retrieve the job) and the job ID(s) for use with the xgrid command line facilities. For xgrid.run and xgrid.results, the output of the function over all iterations is returned as a list, with each element of the list representing the results at each iteration. If the function returned an error, then the error will be held in the list as the return value at the iteration that returned the error. If the function returns an object that exceeds the 'max.filesize' when combined with the results for other iterations in that job (or greater than max.filesize/threads for multi-task jobs), the results for that thread are replaced with an error message (this is to prevent the xgrid controller crashing due to transferring large files). The xapply function returns as xgrid.run (or xgrid.submit if xgrid.options=list(submitandstop=TRUE) in which case the results can be retrieved using xgrid.results).

See Also

mclapply and parLapply in the parallel package for parallel execution of code over multiple local (or remote) cores.

ashiklom/runjags documentation built on May 12, 2019, 4:42 a.m.