Changes between Initial Version and Version 1 of Docs/Polaris/UM8.4


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Timestamp:
08/02/16 16:21:01 (6 years ago)
Author:
ros
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  • Docs/Polaris/UM8.4

    v1 v1  
     1= Setting up UM 8.4 to run on Polaris = #vn8.4 
     2 
     3== 1. Central Installation Directory Structure == 
     4The vn 8.4 installation is under `/home/polaris_lds1/earhum/vn8.4`.  
     5 
     6 
     7== 2. Your Setup on Polaris == 
     8Copy the UM Setup section from `/home/polaris_lds1/ldsgl/.bashrc` to your `.bashrc`. In order to use vn 8.4 utilities make sure you source `.umsetvars_8.4`. 
     9 
     10== 3. Model Build Information and UMUI Settings == 
     11The 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 
     12 
     13{{{-i8 -r8 -fp-model precise -O1 -openmp}}} 
     14 
     15 
     16 
     17 
     18=== FCM Branches === 
     19 
     20Navigate to ''model selection -> FCM configuration -> FCM options for atmosphere and reconfiguration''. 
     21 
     22Until we introduce keywords, specify revision number 11979 for the UM code base and include the following branch 
     23 
     24 
     25{{{fcm:um_br/dev/grenville/vn8.4_polaris/src}}} 
     26 
     27in the '''User Modifications''' table. The naming of this necessary branch may change in future - this branch contains a script change needed to ensure CRUNS behave correctly. 
     28 
     29 
     30 
     31=== General UMUI Settings === 
     32 
     33Navigate to ''model selection -> FCM configuration ->  FCM extract directories and output levels ''. 
     34Experience 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. 
     35 
     36Navigate to ''model selection -> user information and submit method -> general details'' 
     37Set '''User-id''' to be your Polaris id. The '''Tic Code''' is not relevant to Polaris. We have not tested end of run email notification. 
     38 
     39Navigate to ''model selection -> user information and target machine -> job submission method'' 
     40Choose the option ''''qsub' for SGE(SGI)''' for the submission method, enter polaris.leeds.ac.uk for the '''Host name''', select '''Change machine config file''' and enter '''sgi-intel-polaris'''.  
     41 
     42Navigate to ''model selection -> input/output control and resources -> user hand edit files'' and include '''/home/grenville/umui_jobs/hand_edits/polaris_8.4.1''' in the Hand edits list. This is currently necessary to mange the way Polaris handles the module command in the k shell and selects the mvapich2 module to ensure that IO servers function correctly. Future work should see the need for this to disappear. 
     43 
     44 
     45 
     46== 4 Example UMUI Job == 
     47The following job is currently under user grenville in the UMUI 
     48||Job Id||  Model  || 
     49||xidem||HadGEM3-GA4.0 Polaris|| 
     50 
     51This job uses the UM I/O servers which require that the model run with at least two OpenMP threads. We have successfully run the model using mvapich2 as the mpi implementation which supports multi-threaded mpi. The model runs with single threading with both openmpi and intemlpi mpi implemantations - in these cases OpenMP code directives are obeyed but the model can not support I/O servers.