Running NIMROD with OMFIT

V.A. Izzo, O. Meneghini

NIMROD Summer Meeting

15 August 2015

OMFIT incorporates modules for a large number of codes

and has fairly broad adoption

•List of public physics modules

• 2POINTSOL

• BOUT++

• BOUT++interface

• CALTRANS

• CURRAY

• EFIT

• ELITE

• ELMprofiles

• ELMremoval

• EPED

• ESC

• FASTRAN

• FIDASIM

• GAprofiles

• GATO

• GCNMP

• GENRAY

• GKS

• IPScore

• IPSmonitor

• IPSworkflow

• ITMactor

• kineticEFIT

• kineticEFITmulti

• M3DC1

• MagneticFlutter

• NIMROD

• NUBEAM

• ONETWO

• Osborne_profiles

• PEST3

• profiles

• PROFILES_GEN_GACODE

• raffi_test

• SCOPE

• SOLPS

• SURFMN

• TGLF_GACODE

• TGLF_scan

• TGYRO_GACODE

• TIMINGS

• TORAY

• TORBEAM

• TRANSP

• TRIP3DGPU

• UEDGE

• VARYPED

• ZIPFITprofiles

OMFIT modules allow you to execute code, parse and

plot inputs and outputs, and interact with other modules

http://gafusion.github.io/OMFIT-source/modules.htmlhttp://gafusion.github.io/OMFIT-source/modules.html#pointsolhttp://gafusion.github.io/OMFIT-source/modules.html#bouthttp://gafusion.github.io/OMFIT-source/modules.html#bout-interfacehttp://gafusion.github.io/OMFIT-source/modules.html#caltranshttp://gafusion.github.io/OMFIT-source/modules.html#currayhttp://gafusion.github.io/OMFIT-source/modules.html#efithttp://gafusion.github.io/OMFIT-source/modules.html#elitehttp://gafusion.github.io/OMFIT-source/modules.html#elmprofileshttp://gafusion.github.io/OMFIT-source/modules.html#elmremovalhttp://gafusion.github.io/OMFIT-source/modules.html#epedhttp://gafusion.github.io/OMFIT-source/modules.html#eschttp://gafusion.github.io/OMFIT-source/modules.html#fastranhttp://gafusion.github.io/OMFIT-source/modules.html#fidasimhttp://gafusion.github.io/OMFIT-source/modules.html#gaprofileshttp://gafusion.github.io/OMFIT-source/modules.html#gatohttp://gafusion.github.io/OMFIT-source/modules.html#gcnmphttp://gafusion.github.io/OMFIT-source/modules.html#genrayhttp://gafusion.github.io/OMFIT-source/modules.html#gkshttp://gafusion.github.io/OMFIT-source/modules.html#ipscorehttp://gafusion.github.io/OMFIT-source/modules.html#ipsmonitorhttp://gafusion.github.io/OMFIT-source/modules.html#ipsworkflowhttp://gafusion.github.io/OMFIT-source/modules.html#itmactorhttp://gafusion.github.io/OMFIT-source/modules.html#kineticefithttp://gafusion.github.io/OMFIT-source/modules.html#kineticefitmultihttp://gafusion.github.io/OMFIT-source/modules.html#m3dc1http://gafusion.github.io/OMFIT-source/modules.html#magneticflutterhttp://gafusion.github.io/OMFIT-source/modules.html#nimrodhttp://gafusion.github.io/OMFIT-source/modules.html#nubeamhttp://gafusion.github.io/OMFIT-source/modules.html#onetwohttp://gafusion.github.io/OMFIT-source/modules.html#osborne-profileshttp://gafusion.github.io/OMFIT-source/modules.html#pest3http://gafusion.github.io/OMFIT-source/modules.html#profileshttp://gafusion.github.io/OMFIT-source/modules.html#profiles-gen-gacodehttp://gafusion.github.io/OMFIT-source/modules.html#raffi-testhttp://gafusion.github.io/OMFIT-source/modules.html#scopehttp://gafusion.github.io/OMFIT-source/modules.html#solpshttp://gafusion.github.io/OMFIT-source/modules.html#surfmnhttp://gafusion.github.io/OMFIT-source/modules.html#tglf-gacodehttp://gafusion.github.io/OMFIT-source/modules.html#tglf-scanhttp://gafusion.github.io/OMFIT-source/modules.html#tgyro-gacodehttp://gafusion.github.io/OMFIT-source/modules.html#timingshttp://gafusion.github.io/OMFIT-source/modules.html#torayhttp://gafusion.github.io/OMFIT-source/modules.html#torbeamhttp://gafusion.github.io/OMFIT-source/modules.html#transphttp://gafusion.github.io/OMFIT-source/modules.html#trip3dgpuhttp://gafusion.github.io/OMFIT-source/modules.html#uedgehttp://gafusion.github.io/OMFIT-source/modules.html#varypedhttp://gafusion.github.io/OMFIT-source/modules.html#zipfitprofiles

See OMFIT documentation site for basic info on getting

started with OMFIT:

http://gafusion.github.io/OMFIT-source/

As NIMROD module is still being developed, best to run the unstable version of OMFIT

Load the NIMROD module into your OMFIT project

File…

Import module…

NIMROD…

Load

(1) (2)

Start by opening the nimrod GUI

At the top of the ‘Run’ tab, set what server

you want to run NIMROD on, the path of

the installation, and executable name

(assumes path/bin/executable-name, and

is not used for batch jobs)

Then set a top level

directory on the sever for

your NIMROD runs, and a

Run ID for this particular

case

Since NIMROD dump files

are generally large, you

probably don’t want to pull

them into the tree. By

default they will be kept in

a permanent storage

directory on the server.

As you load your files, the GUI

will automatically update to

prompt you for additional files

you need, such as fluxgrid.in

or EFIT file

Load your NIMROD input files into the tree

If you want to begin from a

template, you can also load all

files from one of the NIMROD

regression test cases, using

the Regression cases tab

Note: loading of regression

case will only work if you are

pointed to the AToM NIMROD

installation on NERSC (the

default)

Add any additional input files you need for your case

This is a ‘catch-all’ in case your simulation needs special input files that you are not

specifically prompted for by the GUI.

Specify the number of additional files next to “Additional input files? # =’

Load in each additional input file, then explicitly specify the full file name you want this

file to have when it is deployed into the run directory (obviously, can be the same as the

name of the file you loaded in).

Specify for each additional file whether it is needed to run nimset, nimrod or both.

All of your inputs are now in the tree, you can view and

modify the contents of your namelists, then run nimset

Modify your

input namelists

parameters in

the tree

Click the ‘Run

NIMSET’

button. The

standard

output will be

displayed in

the upper right

window

Preprocessor output files are found under outputs_nimset.

Create automatic or custom plots:

Automatic plot

created by

highlighting

‘grid’ file and

hitting

Custom plot using python

command window (hint: full

paths to variable tree

locations are copied and

pasted from the tree)

Run nimrod in serial, parallel, or as a batch job

Select how you want to run the code

(1) (2)

When you choose ‘with batch script

using qsub’ a batch file will auto-

generate and open in your default

browser. Modify as needed.

Example 1: Run in serial- Uploads input files, executes

code, downloads outputs (usually excluding dump files)

Click ‘Run NIMROD’ to start

Output files are parsed and

can be automatically plotted

Follows the standard output

Example 2: Run batch job- Uploads input files,

submits/monitors job, downloads outputs

Tracks queue status until job begins,

then follows standard out

If you kill the local process, batch job is still

in queue. Click ‘Submit NIMROD job +

monitor + fetch’ to resume following job

To continue a run from where it left off, just hit that ‘run

nimrod’ button again.

Output files are renamed

according to initial time

step both locally and on

the server

Restart dump file is

automatically updated to

last available dump file

Very simple script to

string together multiple

batch jobs

You can store the results of multiple jobs in on OMFIT

project using the Store/Restore tab

Store: Copy all inputs and

move all outputs to

STORED_RUNS subtree.

[‘FILES’][‘outputs_*’] trees

are now empty

(1) (2)

Restore: Select from a list of

stored runs to repopulate

[‘FILES’] to continue run or

further post-process

You can automatically generate a scan over any

parameter in nimrod.in or fluxgrid.in

Set up initial case in ‘Run’ tab, then switch to

‘Run a scan’. Specify any variable name and a

list of values for the scan. Specify if nimset

needs to be rerun for each instance.

All instances of scan are automatically placed in

the STORED_RUNS tree.

Simple comparison plots from the results of your scan

Script to loop over the

cases in my scan and plot

some variable is quickly

generated by copying and

pasting tree locations

Other GUI tabs can be used for post-processing

GUIs for nimplot and nimfl. Output files

from nimplot are parsed, Log files with

inputs automatically generated.

Example of simple integrated task: Gaprofiles for density

Script to extract density profile information

from Gaprofiles module, map onto density

vs flux using my EFIT file, and include as

nimset input

You can also run post-processing tasks with other codes

(on other machines)

Another possibility: modules to create “easy” versions of

NIMROD for very specific tasks

reOrbit module uses ONLY the RE orbit

following routines in NIMROD to calculate

orbits on fixed 3D fields. Use of NIMROD

is transparent to user.

Summary

I find OMFIT very useful for running NIMROD– suggest giving it a try.

More users will help work out bugs.

Some features are lacking because I don’t use them, but I can

develop them as needed.

Send questions, suggestions, problems, bugs to me at

izzo@fusion.gat.com

mailto:izzo@fusion.gat.com