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U Mon HPCX

How to run a UM experiment on the National Academic HPC Services (HPCX)

If you want to run an Ensemble Experiments on HPCX you might want to read Run Simple UMCET Job

To run a UM experiment on the HPCX machines you need to have

• access to the UMUI (UM User Interface) locally. (See UMUI web pages for more information)
• an account on the appropriate HPCX machines. (Contact NERC or hpc_support@met.rdg.ac.uk)
• be in the UM access groups on the appropriate machines. (Managed by hpc_support@met.rdg.ac.uk)
• signed the UM access agreement for UK academic researchers. (Managed by BADC)

Then implement the following stages where appropriate

1. Set up an experiment using the UMUI

• either download a standard job from this web site (see example jobs web pages)
• or copy a similar job from another user of your UMUI
• or upload a job basis file from a user of a different UMUI

2. Use the UMUI to tailor your starting job to the experiment’s requirements considering

• the information layer (user and machine details)
• the set up layer (technical information like compilation, directories, run length)
• the science layer for each submodel (atmopshere, ocean, slab, wave)

3. Save and process the job. This creates a set of scripts on your local system which then need to be transferred to the National academic HPC services

4. You should be using the Korn shell (ksh) and the following line must be added to your .profile in your home directory

• On HPCX for UM version 4.5 use

 
. ~umx/setvars_4.5 

5. The UMUI submit button may not work for your jobs to run on the remote machines. There are local arrangements which may differ at each UMUI site. At the Department of Meteorology, University of Reading, use

 
~jeff/bin/umsubmit -h [host] [jobid]

and follow the instructions given by the command. For this command to work you need to have a file (.umrc) in your home directory. Use

 
cp ~jeff/.umrc.example $HOME/.umrc 

and change PASSWORD to be your password on the appropriate machine. IMPORTANT please make sure that noone can read this file and gain access to your password ie run the command

 
chmod 600 $HOME/.umrc

6. The system for creating the UM exectuable is run as a separate job and involves several steps

• using the source code maintenance tool (nupdate or pumscm) to extract the UM code which produces a separate .f file for each subroutine
• compiling using a makefile, which first produces the .o files and then the exectuable
• saving the above files, where the files are tarred and tar file gzipped to compress it, to reduce any re-compilation necessary

which temporarily uses a large amount of disk space so for compilation please use

7. Reconfiguration is a stand alone program, which allows the user to modify start/dump files. The reconfiguration can be run separately or as part of the UM run. Reconfiguration in version 4.5 runs on a single processor which can cause problems, but in version 5.5 reconfirguration has been re-written and is now a parallel job.

8. The UM job is then run

• On the HPCX IBM the queue is determined by the number of processors and the time requested.