View source for Using Nek5000 with ICE

<div style="border-style:dashed;border-width:2px;border-color:black;text-align:center;font-size:24px;font-weight:bold;color:red;">This is a legacy tutorial and may contain outdated information.</div>

This document is designed to outline the basic steps of setting up and using the Nek5000 plugins in ICE. There are two different tasks for the input generation and launching of Nek5000 within ICE: 

* '''Nek5000 Model Builder''' - Using selected parameters, generates a set of input files necessary to launch the Nek5000 neutronics codes. 
* '''Nek5000 Launcher''' - Initiates the Nek5000 codes to run on a local or remote system using the files generated from the ''Nek5000 Model Builder''. 

== Background ==

Part of our work in the 2013 fiscal year included a detailed analysis of Nek5000's existing graphical input generator, PreNek. We worked closely with the Nek5000 team to determine how it works and discover any painful points related to its use. The ICE and Nek5000 teams decided that the best course of action was to slowly reproduce the capabilities that exist in PreNek in ICE during the 2014 fiscal year, focusing on usability first, and inclusion of advanced features second. The goal is to produce a tool that will allow users to work with all of Nek5000's examples and, eventually, allow users to create entirely new Nek5000 problems from scratch. 

We started by creating a new set of tools in ICE that can read and write Nek5000's .rea files. The first example that we targeted was Nek's conjugate heat transfer example, conj_ht, which includes a number of different options, a mesh, and some boundary conditions. ICE will support more examples in the very near future.

== Getting Started == 

=== Installation & Configuration ===

Follow the instructions in the [[Getting ICE]] article to download and install the latest version of ICE on your system. 

=== Prerequisites ===

You should have [https://nek5000.mcs.anl.gov/download/ Nek5000 installed] on a machine, either your local machine or a remote machine. ICE should work with either the current version or legacy repo, but only the legacy version includes the example problems which ICE will run. 

Additionally, ICE's support for input creation is limited to loading and modifying existing ''two-dimensional'' problems. This means that ICE requires a <tt>*.rea</tt> example file from Nek5000 to get the information it needs to generate input. Below is a list of <tt>*.rea</tt> files that have been tested with ICE:

* <tt>conj_ht.rea</tt>
* <tt>eddy_uv.rea</tt>
* <tt>kov.rea</tt>
* <tt>ray_dd.rea</tt>
* <tt>ray_dn.rea</tt>
* <tt>ray_nn.rea</tt>
* <tt>shear4.rea</tt>
* <tt>v2d.rea</tt>

These files can be found in the <code>/nek5/examples</code> directory of the legacy Nek5000 installation, or downloaded individually from the [https://svn.mcs.anl.gov/repos/nek5/examples/ Nek5000 SVN repository]. Once you've obtained a <tt>*.rea</tt> file, create a directory named <tt>Nek5000_Model_Builder</tt> in your local file system your workspace's itemDB folder.

Place the <tt>*.rea</tt> file here before launching ICE. If you have never launched ICE on your system before, you will also have to open it to create a workspace and place the file in the new itemDB folder which ICE will automatically create inside the workspace.

In the following tutorial, we'll be modifying the <tt>conj_ht.rea</tt> problem.

== Building Nek ==

ICE will require that you have already built Nek5000 for your sample problem on the machine which will run the job. To do this, first find the example code you wish to run. They are located in the <tt>/examples</tt> folder of the legacy repo, and most be downloaded from [https://svn.mcs.anl.gov/repos/nek5/examples/ the repo] and placed in an <tt>/examples</tt> folder inside the current repo. Next find the makenek script. In the current repo, this is located at <tt>bin/makenek</tt> and in the legacy repo it is at <tt>trunk/nek/makenek</tt>. Copy it into the folder of the example problem you wish to use and run <code>./makenek problemName</code>, where problemName is the name of the <tt>.usr</tt> file in the directory. For example, to run the conj_ht problem you will need to copy makenek into <tt>/examples/conj_ht</tt> and run <code>./makenek conj_ht</code>.

If everything was done correctly, this will produce an executable named nek5000. 

== Creating a Nek5000 <tt>*.rea</tt> Input File ==

Once ICE is properly installed and you have placed the <tt>*.rea</tt> file (<tt>conj_ht.rea</tt> in this example) in your <code>itemDB/Nek5000_Model_Builder</code> directory, you can begin creating input for Nek5000. 

To begin, launch ICE (if it isn't already running), and you should be presented with an empty workbench. 

[[File:ICE_EmptyWorkbench.png|625px]] 

The first step to generate Nek5000 input is to create a ''Nek5000 Model Builder'' Item; switch to the ICE perspective by clicking on the ''Open Perspective'' button and selecting ICE, then (click on the green plus icon ('''<span style="color:green;">+</span>''') located at the top of the left-hand column. 

[[File:ICE_CreateItem.png]] 

This will launch a dialog prompting you to select a task (or ''Item'') to create. Find ''Nek5000 Model Builder'' in the ''Item Selector'' list (you may need to scroll down) and select ''Finish''. 

[[File:ICE_NekModelBuilderItem.png|400px]] 

=== Defining Input Parameters ===

A ''Nek5000 Model Builder'' form containing a number of tabs (near the bottom) with parameter input boxes will appear in the ICE workbench. These parameters are specific to the input required by Nek5000 and have a number of restrictions associated to them. The specifics of Nek5000 input is beyond the scope of this tutorial. However, the list below provides links to more detailed information about each parameter. Since we prepared and placed the <tt>conj_ht.rea</tt> file in the <code>itemDB/Nek5000_Model_Builder</code> directory ahead of time, you will find the parameters are already filled out with appropriate values. For some parameters, hovering over the name will display additional information about it. 

'''Input specification by section''': 

* [http://nek5000.mcs.anl.gov/index.php/Parameters Parameters]
* [http://nek5000.mcs.anl.gov/index.php/LogicalSwitches Logical switches]
* [http://nek5000.mcs.anl.gov/index.php/Restart Pre-solve/restart options]
* [http://nek5000.mcs.anl.gov/index.php/Reafile#Initial_conditions_and_drive_force_data Initial conditions, drive force data] (no longer used) 
* [http://nek5000.mcs.anl.gov/index.php/Reafile#Variable_properties Variable properties]
* [http://nek5000.mcs.anl.gov/index.php/Reafile#History_points History and integral data]
* [http://nek5000.mcs.anl.gov/index.php/Reafile#Output_specification Output specification]
* [http://nek5000.mcs.anl.gov/index.php/Reafile#Object_specification Object specification]

[[File:ICE_NekModelBuilderForm.png|625px]] 

Once you have entered all the required parameters (or have made any changes to the existing ones), save the ''Nek5000 Model Builder'' project by clicking the floppy disk icon located in the top left-hand corner of ICE (or ''Ctrl''+''S''/''⌘''+''S'').

[[File:ICE_SaveButton.png]]

Clicking on the last tab in the ''Nek5000 Model Builder'' form will open the ''Mesh Editor'' with the current mesh for this problem displayed. More information on editing the mesh is available in [[Editing Meshes|Editing Meshes]].

=== Generating Nek5000 Input Files ===

The last step in creating input is to actually generate the <tt>*.rea</tt> file that will be used to launch Nek5000 in the next section. To do this, select the ''Process'' drop-down menu located in the upper right corner of your ''Nek5000 Model Builder'' window, select ''Write Nek5000 input'', and click ''Go!''. This will convert the parameters entered on your ''Nek5000 Model Builder'' form into a text-based format that is compatible with Nek5000; this process should only take a few seconds at most. The phrase "Done!" should appear next to the title of your ''Nek5000 Model Builder'' workspace. 

[[File:ICE_WriteNekInput.png]] 

This file will be created in your <code>itemDB</code> directory and will have the file name <tt>Nek5000_Model_Builder_{num}.rea</tt>, where <tt>{num}</tt> is your model builder Item number (i.e. ''Nek5000 Model Builder'' '''''1''''', ''Nek5000 Model Builder'' '''''2''''', etc.). It's important to note, that if you have a previously generated Nek5000 input file in your default directory, generating another input file with the same Item number will overwrite your existing file without warning. 

This concludes the Nek5000 input file generation; the <tt>*.rea</tt> input file created here will be used to launch Nek5000 in the next section. If you would like to review the generated input file before moving onto the next step, you can do so by selecting the ''File > Open File...'' menu in ICE, and navigating to your <tt>Nek5000_Model_Builder_{num}.rea</tt> file. This will display the input file in your ICE workbench. You may make modifications and save changes to the <tt>*.rea</tt> file from within ICE, however, this is not recommended for users unfamiliar with Nek5000. 

[[File:ICE_NekReaInputFile.png|625px]]

== Launching a Nek5000 Problem ==

The process for launching Nek5000 from within ICE is not entirely different from creating an input file. ICE abstracts activities in such a way that they are not so different mechanically, even if the information exchanged is significantly different. 

=== Creating the Launcher ===

To begin creating a job launcher, click on the green plus icon ('''<span style="color:green;">+</span>''') at the top of the ''Item Viewer'' list. 

[[File:ICE_CreateItem.png]] 

In the list that appears, select ''Nek5000 Launcher''. Note that because of all of the different Items supported, you may need to scroll down to the bottom of the list to find the ''Nek5000 Launcher''. 

[[File:ICE_NekLauncherSelection.png|400px]] 

The central editor area of the workbench will change once you click ''OK'' on the ''Item Selection'' menu. It will display a form that requires some information about the job that you would like to run. 

[[File:ICE_NekLauncher.png|625px]]

=== Setting the Input File and Hostname ===

The first thing that you need to do is select the input file for Nek5000, which is the input file that you created in the previous section. Start by clicking the box labelled ''Input File'' and select your Nek5000 neutronics <tt>*.rea</tt> file. Remember that the file you created in the previous section will be named <tt>Nek5000_Model_Builder_{num}.rea</tt> where <tt>{num}</tt> is the number of your model Item. In the case of our example, the model was number 1 and the input file is <tt>Nek5000_Model_Builder_1.rea</tt>.

[[File:ICE_NekInputSelection.png]]

Next, select a problem from the list of ''Available Executables'' upon which your input file is based. In this example, we would chose <tt>conj_ht</tt>. Currently, the list of Nek5000 examples supported in ICE for launching is limited to the following:

<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* 2d_eigtest
* 3dbox
* axi
* blasius
* conj_ht
* cyl_restart
* eddy
* eddy_psi_omega
* expansions
* ext_cyl
* fs_2
* fs_hydro
* hemi
* kov_st_state
* kovasznay
* lowMach_test
* mhd
* moab
* moab_conjht
* os7000
* peris
* pipe
* rayleigh
* robin
* shear4
* solid
* strat
* taylor
* thermal_io
* timing
* turbChannel
* turbJet
* var_vis
* vortex
* vortex2
</div>

[[File:ICE_NekAvailableExecutables.png]]

Lastly, select the machine on which ICE will launch Nek5000; this can be either local or remote. You can add or remove hosts from the table to suit your needs. 

[[File:ICE_NekHostSelection.png]]

=== Launching the Job ===

After selecting both the input file and the host machine, save the project by clicking the floppy disk icon in the upper left-hand corner (or ''Ctrl''+''S'' / ''⌘''+''S''). Next, use the drop-down menu in the upper right-hand corner to tell ICE to launch the Nek5000 job. Select the ''Launch the Job'' task from the drop-down menu and click the ''Go!'' button. ICE will then launch Nek5000 on your host machine when you click the ''OK'' button. If you are launching on a remote machine, ICE will ask for your credentials on that machine. 

== Viewing Results ==

You can view the results of the Nek5000 run by clicking on the ''Output Files and Data'' tab at the bottom of the ''Nek5000 Job Launcher''. If Nek5000 ran successfully, you should be able to view the results by double-clicking the ''Nek5000 Launcher Standard Output'' resource. To visualize the .nek5000 data files, you must [[ICE_Embedded_Visualizations|set up a connection to VisIt]] before double clicking on the file to open it.

== Known Issues ==

* ICE only supports 2 dimensional examples for input creation currently. We plan to increase the pool of available examples to choose from, and eventually allow the user to define their own custom problems. 
* When using a predefined example like <tt>conj_ht</tt>, any sections of the original <tt>*.rea</tt> file with a predefined number of lines in a particular section will remain that length for now, i.e. <tt>conj_ht</tt> has 6 lines of ''Output Field Specification'' data, and thus the user is not able to add or remove any more than that. This also extends to sections with 0 lines initially defined, meaning they will remain empty. 
* Similar to the previous bullet point, if the number of passive scalars (<tt>NPSCAL</tt>, <tt>p23</tt>) is initially set to 0 in a particular example, even if the user changes this value in the ''Parameters'' section, the problem will launch with no ''Passive Scalar Data'' defined. 
* The <tt>conj_ht</tt> example initializes with 96 elements (64 thermal, 32 fluid), and allows a maximum of 4100 total elements. It's very unlikely a user will create more than 4100 elements by hand for this example, however if they do, they will likely encounter errors when running Nek5000 because ICE does not yet rewrite the Nek's <tt>SIZE</tt> file.