Version 6 (modified by grenville, 8 years ago) (diff)

This page is under construction and details presented here are likely to change

Setting up UM 6.6.3 to run on Polaris

1 Central Installation Directory Structure

The central UM directory is /home/polaris_lds1/earhum. FCM (code management system), gcom (UM communications software), and UM vn 6.6.3 are held in this directory. Other versions of the UM and related software will also be installed here.

The central installation of UM vn 6.6.3 is in /home/polaris_lds1/earhum/hg6.6.3.

DirectoryDescription of Contents
HG2ES_ancilsAncillary files for the HadGEM2-ES model
HG2CCL60_ancilsAncillary files for the HadGEM2-CC L60 model and example start files
HG2AO_ancilsAncillary files for the HadGEM2 coupled Atmosphere-Ocean model and example start files
HG2AMIP_ancilsAncillary files for the HadGem2 AMIP model and an example start file
dumpsexample start dumps for the HadGEM2-ES model
ctldataSTASHmaster, ANCILmaster, spectral data, and vertical-levels files
sgismall executables and UM utilities, and installation information

2 Environment Variables and Your Files

Standard UM environment variables are set thus

Environment VariableValue
UMDIR /home/polaris_lds1/earhum
WORKDIR /nobackup/$USER

so dumps, diagnostics, lbcs, history files, and intermediate output will by default be sent to /nobackup/$USER/$RUNID. The final leave file for a run will be saved in /home/polaris_lds1/$USER/output.

Start files. Example start files for the four HadGEM2 jobs are provided. We have mimicked the file structure as it exists on HECToR, so start files for HadGEM2-ES are in $UMDIR/hg6.6.3/dumps, all other models are provided with example start files along with the ancillary files.

3 Your Setup on Polaris

Copy the UM Setup section from /home/polaris_lds1/ldsgl/.bashrc to your .bashrc (note if you wish to use utilities for a version of the UM other than 6.6.3, you will need to source the appropriate .umsetvars file)

4 Model Build Information and UMUI Settings

The model build information is kept in configuration files which are read by the FCM build system. The appropriate compiler flags are used to build the model along with information about which libraries to link. We have used the following flags for the Polaris intel compiler for both model and communications builds

-i8 -r8 -fp-model precise -O1

These and all other Polaris build settings are picked up by FCM by navigating to model selection → sub-model independent → FCM configuration → FCM configuration variables and setting the variable UM_SVN_BIND to


FCM Branches

We have created a branch with code changes to account for slight differences in the way the intel compiler handles some aspects of the UM code (mostly because of its intolerance to multiple declarations of the same variable). Navigate to model selection → sub-model independent → FCM configuration → FCM configuration optional modifications and include the following branch


in the User Modifications table

General UMUI Settings

Navigate to model selection → sub-model independent → FCM configuration → FCM configuration variables Experience will help determine the most convenient places to extract the model to. Set UM_ROUTDIR to be your user directory on /nobackup, however, note that these files may be marked for deletion in accordance with Polaris data policy.

Navigate to model selection → user information and target machine → general details Set User-id to be your Polaris id. The Tic Code is not relevant to Polaris. We have not tested end of run email notification.

Navigate to selection → user information and target machine → target machine Chose 'other' for the Compile, Link and Run the job option, and set the Other machine name to

Navigate to selection → sub-model independent → job submission, resources and resubmission pattern Choose the option 'qsub' for SGE(SGI) for the submission method. The Job memory limit is not relevant (all jobs currently request the default memory/core of 4GB).

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