{"id":1589,"date":"2014-06-12T10:34:52","date_gmt":"2014-06-12T10:34:52","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=1589"},"modified":"2017-07-31T07:46:39","modified_gmt":"2017-07-31T07:46:39","slug":"ncl","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/ncl\/","title":{"rendered":"NCL"},"content":{"rendered":"

Overview<\/h2>\n

NCL<\/a> (NCAR Command Language) is a free interpreted language designed specifically for scientific data processing and visualization. It is often used with WRF<\/a> to present results of weather model simulations (although it is not exclusively for use with WRF!)<\/p>\n

Version 6.4.0, and 6.2.0 are installed on the CSF. These are binary installations so\u00a0NCL can be used on any node.<\/p>\n

This version contains experimental OpenMP (multicore) features in contouring routines. Please see the release notes<\/a> for details. If using multiple cores, ensure your jobscript is correct (example jobscripts are given below).<\/p>\n

NCAR Graphics<\/a> is a Fortran and C based software package for scentific visualization and is included in this installation.<\/p>\n

Restrictions on use<\/h2>\n

There are no restictions on accessing this software on the CSF.<\/p>\n

Please see the NCL citation instructions<\/a> for how to cite use of the software in your publications.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load one of the modulefiles:<\/p>\n

module load apps\/binapps\/ncl\/6.4.0\r\nmodule load apps\/binapps\/ncl\/6.2.0\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run NCL on the login node. Jobs should be submitted to the compute nodes via batch or can be run interactively via qrsh<\/code>.<\/p>\n
Serial batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -l short         # Optional: assumes max 1 hour runtime\r\n                    # There are dedicated nodes for 'short jobs'\r\n\r\nncl my_script.ncl\r\n\r\n<\/pre>\n
Submit the jobscript using:<\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -l short         # Optional: assumes max 1 hour runtime\r\n                    # There are dedicated nodes for 'short jobs'\r\n#$ -pe smp.pe  8    # EG: use 8 cores (max allowed is 16)\r\n\r\n# Ensure we use the requested number of cores\r\nexport OMP_NUM_THREADS=$NSLOTS\r\n\r\nncl my_script.ncl\r\n\r\n<\/pre>\n
Submit the jobscript using:<\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Interactive Use via qrsh<\/h3>\n
To run NCL interactively you must schedule an interactive session using qrsh<\/code> as follows:<\/p>\n
qrsh -l inter -l short\r\n  #\r\n  # Wait for a new prompt on a backend node (e.g., int00)\r\n\r\n# We are now on the backend node...\r\nmodule load apps\/binapps\/ncl\/6.2.0\r\nncl my_script.ncl\r\n<\/pre>\n
A Simple Example<\/h2>\n
Two example NCL scripts are available for you to run. These are based on the coastlines example<\/a> provided by NCAR. You do not need to download anything from NCAR to run these examples.<\/p>\n
Batch Example – PDF Output<\/h3>\n
Run the following commands on the login node:<\/p>\n
module load apps\/binapps\/ncl\/6.2.0\r\ncp $NCL_EXAMPLES\/*.ncl ~\/scratch\r\ncd ~\/scratch\r\n<\/pre>\n
You now have two .ncl<\/code> files in your scratch area: coast_2_pdf.ncl<\/code> and coast_2_x11.ncl<\/code>.<\/p>\n
Run the following command to submit a batch job without writing a jobscript (the -b y<\/code> flag means the ncl<\/code> command is a binary (executable) rather than the more usual jobscript file.<\/p>\n
qsub -b y -cwd -V -l short ncl coast_2_pdf.ncl\r\n<\/pre>\n
Run qstat<\/code> to check on the job. When there is no output from qstat<\/code> the job has finished and you should have a file named coast.pdf<\/code> in your scratch directory.<\/p>\n
View the output file:<\/p>\n
evince coast.pdf\r\n<\/pre>\n
Interactive Example – X11 Output<\/h3>\n
Ensure you have logged in to the CSF with X11 forwarding<\/a> enabled.<\/p>\n
Run the following on the CSF login node to start an interactive session on a backend node:<\/p>\n
qrsh -l inter -l short\r\n  #\r\n  # Wait for new prompt. Try again later if asked.\r\n\r\nmodule load apps\/binapps\/ncl\/6.2.0\r\ncp $NCL_EXAMPLES\/*.ncl ~\/scratch\r\ncd ~\/scratch\r\nncl coast_2_x11.ncl\r\n  #\r\n  # A window should pop-up with an image of a map\r\n\r\nCtrl-C to exit\r\n<\/pre>\n
Further info<\/h2>\n