README.md

In gschnabel/clusterTALYS: TALYS Calculations in Parallel on Cluster

clusterTALYS - R package

The package cluserTALYS enables launching calculations in parallel over an SSH connection on computers with multiple processors, clusters of work stations, or scientific computing clusters.

Requirements

This package makes use of the functionality of the R package clusterSSH to communicate with the cluster, which must therefore be installed together with its dependencies. Some of the required packages currently use the commands rsync, ssh, ps, mkpipe and pipes. This means that clusterSSH due to its dependencies can only be used under UNIX-like systems. Further, the package TALYSeval must be installed on the computing nodes of the cluster and a shared network file system availabe used for communication.

Installation

In order to install the package with all its dependencies, execute the following commands in a terminal:

mkdir inst
cd inst

git clone https://github.com/gschnabel/interactiveSSH.git
git clone https://github.com/gschnabel/rsyncFacility.git
git clone https://github.com/gschnabel/remoteFunctionSSH.git
git clone https://github.com/gschnabel/clusterSSH.git
git clone https://github.com/gschnabel/clusterTALYS.git
git clone https://github.com/gschnabel/TALYSeval.git

R CMD INSTALL interactiveSSH
R CMD INSTALL rsyncFacility.git
R CMD INSTALL remoteFunctionSSH
R CMD INSTALL clusterSSH
R CMD INSTALL clusterTALYS
R CMD INSTALL TALYSeval

Further, R must be installed on the cluster and the package TALYSeval installed there. Depending on the cluster configuration, the following on the login node may do the job:

mkdir inst
cd inst

git clone https://github.com/gschnabel/TALYSeval.git
R CMD INSTALL TALYSeval

Basic usage

First, we need to initialize the functionality of package remoteFunctionSSH to lauch R functions on a remote computer (e.g., the login node):

remObj <- initSSH(ssh_login, ssh_pw,
                  tempdir.loc = calcdir_loc,
                  tempdir.rem = calcdir_rem)

The variables ssh_login and ssh_pw have to be initialized by the SSH credentials of the user. The variable calcdir_loc must contain an existing path on the local machine, preferably empty. The variable calcdir_rem contains an existing path on the remote machine, whose content mirrors that of calcdir_loc.

Next, we need to set up the functionality of the package clusterSSH to launch code given as an R function in parallel:

clustObj <- initCluster(functions_multinode, remObj)

The first variable functions_multinode is part of the clusterSSH package and contains functions to manage parallel computations on a cluster of worker nodes with a shared network filesystem but without a task scheduler, such as the Sun Grid Engine (SGE).

In addition, a script must be manually started on the worker nodes that should participate in computations.

startNodeController_<- remObj$createRemoteFunction(
    clustObj$startNodeController,
    fun.name = "startNodeController"
)
startNodeController()

The last command will print out a command string, say cmdstr, that you should launch on the worker nodes. It may be convenient idea to execute nohup cmdstr & instead of just cmdstr to install the controller scripts on the worker nodes permanently.

Finally, the functionality of the clusterTALYS package needs to be initialized. This can be done via the command

talysClustObj <- initClusterTALYS(clustObj, "talys")

The second argument is for the situation where the talys executable is in of the directories specified in the environment variable PATH. Otherwise, the full path to the executable must be specified.

A calculation can be now launched in the following way (here with 56Fe and the neutron-induced total cross section as an example):

library(data.table)

paramList1 <- list(projectile = "n",
                   element = "Fe",
                   mass = 56,
                   energy = c(1,2,3))

paramList2 <- list(projectile = "p",
                   element = "Fe",
                   mass = 56,
                   energy = c(1,2,3))

outSpec <- data.table(REAC = "CS/TOT",
                      L1 = seq(1, 3, length = 10),
                      L2 = 0, L3 = 0) 

severalParamLists <- list(paramList1, paramList2)

runObj <- talysClustObj$run(severalParamLists, outSpec)

In this example two calculations are launched in parallel. The latter function talysClustObj$run returns immediately without waiting for the termination of the calculations. A function that does wait is talysClustObj$eval.

The termination of the calculations can be checked with talysClustObj$isRunning and in case this function returns FALSE, results retrieved by

result <- talysClustObj$result(runObj)

gschnabel/clusterTALYS documentation built on July 25, 2020, 5:11 p.m.