Elmer Runtime Environment Homepage

Elmer is a Finite Element Software for Multiphysical Problems. This page describes the use and installaton of Elmer in Grid environments based on NorduGrid ARC middleware. For a complete description of the Resource Specification Language, Information System, User Interface and the Grid Manager, see the NorduGrid documentation. The full documentation of Elmer can be found from http://www.csc.fi/elmer/.

Version information

Current stable version

none

Development version

Old versions

none

Interface definition

In the remote computing resources Elmer RE provides a command ElmerSolver_grid, which is found in the path. The same command supports both serial and parallel jobs. The selection of the appropriate parallel environment is done transparently, so the user does not need to run mpirun or other similar commands to initialize the environment. However, the following things need to be done by the user to run a parallel job:

• Split the data set into a suitable format for the parallel version of Elmer.
• Request a desired number of processors by adding parameter count=N to the xRSL file (see the examples section for details).

For more information about input and output file formats and splitting the data, see the Elmer homepage.

Examples

In these examples, we use a small wrapper script runElmer.sh which reads the input files from a tar package, runs ElmerSolver_grid and then creates another tar package of the output files.

runElmer.sh:

#!/bin/sh
tar xfz inputfiles.tar.gz
rm -f inputfiles.tar.gz
ElmerSolver_grid
tar cfz outputfiles.tar.gz *

Serial job

Sample xRSL job description for a serial job:

&
(executable="runElmer.sh")
(stdout="std.out")
(stderr="std.err")
(inputfiles=("inputfiles.tar.gz" "inputfiles_serial.tar.gz"))
(outputfiles=("outputfiles.tar.gz" ""))
(gmlog="gridlog")
(jobname="My serial Elmer job")
(cputime=5)
(memory=200)
(runtimeenvironment >= "APPS/MATH/ELMER-5.0.2")

inputfiles_serial.tar.gz contains an example input dataset for a serial job.

Parallel job

Sample xRSL job description for a parallel job using 4 processors:

&
(executable="runElmer.sh")
(count=4)
(stdout="std.out")
(stderr="std.err")
(inputfiles=("inputfiles.tar.gz" "inputfiles_parallel.tar.gz"))
(outputfiles=("outputfiles.tar.gz" ""))
(gmlog="gridlog")
(jobname="My parallel Elmer job")
(cputime=5)
(memory=200)
(runtimeenvironment >= "APPS/MATH/ELMER-5.0.2")

inputfiles_parallel.tar.gz contains an example input dataset for a parallel job.

Please note that the script runElmer.sh is the same for both serial and parallel jobs, but the parallel jobs require a set of input files where the data is split for a parallel run.

System administrator guide for installing the RE

Installation instructions for the ElmerSolver software itself can be found from Elmer homepage.

The runtime environment script needs to initialize the MPI environment and provide the command ElmerSolver_grid, which calls either the serial solver ElmerSolver or the parallel solver ElmerSolver_mpi depending on whether the user requests one or more processors for the job.

Here's a sample initialization script to be installed into the NorduGrid RE directory ($RUNTIME_CONFIG_DIR) and a sample ElmerSolver_grid wrapper script:

• ELMER-5.0.2
• ElmerSolver_grid

Please note that the MPI environment initialization and paths where the software is installed often differ between systems, so it is probable that at least some paths in the scripts require modifications during the installation.

Verification of the RE

Installation can be verified by running the example script.

Contact information

Please contact Elmer developers at http://www.csc.fi/elmer/ directly in matters concerning the Elmer application.

Questions related to RE itself, such as questions about installing RE, feature requests and improvement suggestions, can be mailed to Elmer RE maintainers grid-support@csc.fi.