Changes between Initial Version and Version 1 of Docs/Polaris/UM663


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26/11/15 19:24:41 (2 years ago)
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ros
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  • Docs/Polaris/UM663

    v1 v1  
     1= Setting up UM 6.6.3 to run on Polaris = 
     2 
     3== 1. Central Installation Directory Structure == 
     4The 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.  
     5 
     6The central installation of UM vn 6.6.3 is in `/home/polaris_lds1/earhum/hg6.6.3` 
     7||'''Directory'''||'''Description of Contents'''|| 
     8||HG2ES_ancils||Ancillary files for the HadGEM2-ES model|| 
     9||HG2CCL60_ancils||Ancillary files for the HadGEM2-CC L60 model and example start files|| 
     10||HG2AO_ancils||Ancillary files for the HadGEM2 coupled Atmosphere-Ocean model and example start files|| 
     11||HG2AMIP_ancils||Ancillary files for the HadGem2 AMIP model and an example start file|| 
     12||dumps||example start dumps for the HadGEM2-ES model|| 
     13||ctldata||STASHmaster, ANCILmaster, spectral data, and vertical-levels files|| 
     14||sgi||small executables and UM utilities, and installation information|| 
     15 
     16== 2. Environment Variables and Your Files == 
     17Standard UM environment variables are set thus 
     18||'''Environment Variable'''||'''Value'''|| 
     19|| UMDIR ||/home/polaris_lds1/earhum|| 
     20|| WORKDIR ||/nobackup/$USER|| 
     21|| DEVTDIR ||$WORKDIR|| 
     22||DATADIR||$WORKDIR|| 
     23||TMPDIR||$WORKDIR/tmp/tmp.polaris.$$|| 
     24 
     25 
     26 
     27 
     28so 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/$USER/output`. 
     29 
     30 
     31'''Start files. ''' 
     32Example start files for the four HadGEM2 jobs are provided. We have mimicked the file structure as it exists on HECToR, so start files for HadGEM2-ES are in `$UMDIR/hg6.6.3/dumps`, all other models are provided with example start files along with their ancillary files. 
     33 
     34== 3. Your Setup on Polaris == 
     35Copy 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) 
     36 
     37== 4. Model Build Information and UMUI Settings == 
     38The 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 
     39 
     40{{{-i8 -r8 -fp-model precise -O1}}} 
     41 
     42To ensure that these and all other Polaris build settings are picked up by FCM, navigate to ''model selection -> sub-model independent -> FCM configuration ->  FCM configuration variables'' and set the variable '''UM_SVN_BIND''' to  
     43 
     44{{{fcm:um_br/dev/ros/hg6.6.3_polaris_machine_cfg/src/configs/bindings}}} 
     45 
     46 
     47=== FCM Branches === 
     48 
     49We 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 
     50 
     51 
     52{{{fcm:um_br/dev/grenville/hg6.6.3_polaris_fixes}}} 
     53 
     54in the '''User Modifications''' table 
     55 
     56 
     57 
     58=== General UMUI Settings === 
     59 
     60Navigate to ''model selection -> sub-model independent -> FCM configuration ->  FCM configuration variables''. 
     61Experience 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. 
     62 
     63Navigate to ''model selection -> user information and target machine -> general details'' 
     64Set '''User-id''' to be your Polaris id. The '''Tic Code''' is not relevant to Polaris. We have not tested end of run email notification. 
     65 
     66Navigate to ''model selection -> user information and target machine -> target machine'' 
     67Chose 'other' for the '''Compile, Link and Run the job''' option, and set the '''Other machine name''' to polaris.leeds.ac.uk 
     68 
     69Navigate to ''model selection -> sub-model independent -> job submission, resources and resubmission pattern'' 
     70Choose 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). 
     71 
     72'''Gotchas for HadGEM2-AMIP:''' \\ 
     73At two places in the UMUI, files need to be specified by full paths: navigate to ''model selection -> atmosphere -> ancillary and input data files -> climatologies and potential climatologies -> natural climate forcing'' and specify /home/polaris_lds1/earhum/hg6.6.3/HG2AMIP_ancils as the path for the '''solar forcing'''  and '''volcanic forcing''' files. 
     74 
     75We have undertaken limited testing of Climate Meaning to find that inclusion of STASH item 262 (section 0) BOUNDARY LAYER CONVECTION FLAG causes a checksum failure. Switch off this stash item when running with Climate Meaning. 
     76 
     77== 5. Example UMUI Jobs == 
     78The following jobs are currently under user grenville in the UMUI 
     79||Job Id||  Model  || 
     80||xidee||HadGEM2-ES|| 
     81||xidex||HadGEM2-AMIP|| 
     82||xidey||HadGEM2-CC L60|| 
     83||xidez||HadGEM2-AO|| 
     84 
     85 
     86== 6. Performance and Scaling == #Performance 
     87 
     88 
     89The following figure summarizes results from test running the four HadGEM2 jobs with increasing processor count. The jobs were run for 3 model days, with the exception of HadGEM2-CC was run for 1 model day. The results for total wall clock time for HadGEM2-ES running on HECToR and CURIE (a PRACE machine (Bull)) are also shown. Data points in red refer to the compute time for the Polaris jobs. All models display a lack of scaling when run on 96 processors. 
     90 
     91{{{#!imagebox 
     92[[Image(hg2.png, 800px)]] 
     93}}}