Changes between Version 14 and Version 15 of Docs/Polaris


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Timestamp:
16/04/13 14:49:53 (6 years ago)
Author:
grenville
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  • Docs/Polaris

    v14 v15  
    9494 
    9595[[Image(hg2.png)]] 
     96 
     97= Setting up UM 7.3 to run on Polaris = 
     98 
     99== 1 Central Installation Directory Structure == 
     100The vn 7.3 installation is under /home/polaris_lds1/earhum/vn7.3/. The subdirectory HGPKG2 holds all the data files necessary to run the standard HadGEM3 job xidef (the same job on HECToR is xeozb). 
     101The various other subdirectorties hold control data for the model, and data to run xideh (a copy of xfvgc). 
     102 
     103== 2 Your Setup on Polaris == 
     104Copy 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) 
     105 
     106== 3 Model Build Information and UMUI Settings == 
     107The 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 
     108 
     109{{{-i8 -r8 -fp-model precise -O1}}} 
     110 
     111UM vn 7.3 requires the inclusion of override files to correctly set compiler and linker options. Navigate to ''model selection-> compile and modifications-> UM user override files'' and include /home/grenville/umui_jobs/overrides/polaris_7.3_machine and /home/grenville/umui_jobs/overrides/polaris_7.3_file in the tables User machine overrides and User file overrides respectively. 
     112 
     113 
     114=== FCM Branches === 
     115 
     116Navigate to ''model selection -> sub-model independent -> FCM configuration -> FCM configuration optional modifications'' and include the following branch 
     117 
     118 
     119{{{fcm:um_br/dev/grenville/vn7.3_polaris_ukca/src}}} 
     120 
     121in the '''User Modifications''' table. The naming of this necessary branch may change in future - this branch contains minor code changes to point to appropriate UKCA data files on Polaris and a script modification to ensure CRUNS behave correctly but was based on Luke's UKCA-CheM branch, hence make sure that the following branch '''does not''' appear in the list otherwise a build error will result: 
     122 
     123{{{fcm:um_br/dev/lukeVN7.3_UKCA_CheM/src}}}. 
     124 
     125 
     126 
     127=== General UMUI Settings === 
     128 
     129Navigate to ''model selection -> sub-model independent -> FCM configuration ->  FCM configuration variables''. 
     130Experience will help determine the most convenient places where the extracted model should reside. Explicitly set '''UM_ROUTDIR''' to be your user directory on /nobackup, however, note that files left in this directory may be marked for deletion in accordance with Polaris data policy. 
     131 
     132Navigate to ''model selection -> user information and target machine -> general details'' 
     133Set '''User-id''' to be your Polaris id. The '''Tic Code''' is not relevant to Polaris. We have not tested end of run email notification. 
     134 
     135Navigate to ''model selection -> user information and target machine -> target machine'' 
     136Chose 'other' for the '''Compile, Link and Run the job''' option, and set the '''Other machine name''' to polaris.leeds.ac.uk 
     137 
     138Navigate to ''model selection -> input/output control and resources -> job submission, resources and resubmission pattern'' 
     139Choose 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). 
     140 
     141Navigate to ''model selection-> compile and modifications-> UM user override files'' and include /home/grenville/umui_jobs/overrides/polaris_7.3_machine and /home/grenville/umui_jobs/overrides/polaris_7.3_file in the tables User machine overrides and User file overrides respectively. 
     142 
     143'''Gotchas for UKCA @ vn 7.3''' There are several places in the code where hard wired absolute paths are used, namely, in the routines ukca_read_aerosol.F90 and ukca_phot2d.F90. We have merely patched the code to point to files on Polaris. 
     144 
     145== 4 Example UMUI Jobs == 
     146The following jobs are currently under user grenville in the UMUI 
     147||Job Id||  Model  || 
     148||xidef||HadGEM3-A r2.0 N96 L85|| 
     149||xideh||UKCA-!StratChem N48 L60 QESM-A||