Nek5000_Notes

Introduction

This page concerns the ongoing development of the Nek5000 plugins for NiCE.

Disclaimer: This is a rough draft page for development of the plugins with Nek5000 for NiCE. The number of items, the item's descriptions, parameters, and profiling may change.

Types of Plugins

Currently there are 3 types of "Items" planned for:

• Nek5000 Model Builder Plugin
• Nek5000 Launcher Plugin
• Nek5000 Output Analyzer

Notes

The items listed below are uncatagorized notes. These should be put in their proper place eventually. For now, these will be visible for the time being.

Nek5000 is a incompressible fluid flow solver written by Argonne Labs. It is an open source code that handles both c and fortran77 codes.

For NiCE to utilize this code, there are several vital components to the execution of the program. Nek5000 default directory is /home/user/nek5_svn/.... This directory is vital for the building and execution of the nek5000 code. There are also many different types of files that need to be in it's own folder (separate from the source directory (rea, re2, usr, SIZE, SESSION.NAME) to handle the build and execution. Thankfully, Nek5000 utilizes OUT OF SOURCE builds. Nevertheless, in order to execute specific jobs each job must be built from source along with the various input files. Also, there are several tools required to fully utilize the mapping methods in nek5000. These can be found in tools (Especially for genmap). Make sure to make all tools.

Here is a list of required input files and their basic descriptions. <file> is interchangeable, but they should MATCH:

• <file>.usr - declares subroutines and customized codes
• <file>.rea
• <file>.re2 - supplement file to rea?
• SIZE
• makenek - a customized bash "make file" with parameters. It is in trunk/nek. MPI is automatically enabled here.
• SESSION.NAME - A direct path to the folder that contains the inputfiles. Utilized during execution (not required for build).
• genmap - Not required in the directory, but once built in nek5000 tools, it should be able to be accessed by the command line with genmap.
• <file>.f - generated from the compiler.

Once all these files are in the directory and everything is installed correctly (See nek5000 home page for details), then the following steps must be undertaken in order to get a working execution of nek5000:

• Copy the makenek into the job's directory.
• Indicate the location of the job's directory with the SESSION.NAME. Make sure all files (usr, rea, re2, SIZE, and makenek exist in this directory).
• Run genmap. Pipe the required rea file. This will produce a map/box.
• Run the build with makenek. **Make sure to specify whether or not MPI is used. MPI enabled by default! **
• Execute nek5000 with the appropriate nek5000 executable.

And that's it. Once the process finishes, it will list fld or fl0? files. FLD files can be used by VisIT (with the appropriate metadata file).

More to come!