Changes between Version 9 and Version 10 of Projects/OpenIFS-IO


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Timestamp:
27/09/13 11:02:31 (6 years ago)
Author:
grenville
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  • Projects/OpenIFS-IO

    v9 v10  
    4343=== Setting the HECToR environment === 
    4444 
    45 You will need to set up the correct environment to build and run OIFS jobs. Since HECToR has different hardware on its compute and service nodes, there is an extra consideration when using some OIFS-related utilities on the service nodes (more later). We have written a script which sets up the environment, however, it is worth taking a look at its main component. At the HECToR command line, type 
     45You will need to set up the correct environment to build and run OIFS jobs. Since HECToR has different hardware on its compute and service nodes, there is an extra consideration when using some OIFS-related utilities on the service nodes (more later). Setting the environment simple involves loading the appropriate environment module; at the HECToR command line, type 
    4646 
    4747{{{ 
     
    100100=== Getting data to run the model === 
    101101 
    102 Now you have an executable, you will need some data. The source for data is Glenn Carver at ECMWF; Glenn can provide start data for configurations at several resolutions and for various times. We have several jobs available for model testing at t159, t511 and t1279 resolution. Each job comes with data required to start the model, a namelist defining a set of model parameters, a PBS script set up for a "standard" run and an example trace output file. We will give a description of the important parts of the PBS script used to submit jobs to the compute nodes. 
     102Now you have an executable, you will need some data. The source for data is Glenn Carver at ECMWF; Glenn can provide start data for configurations at several resolutions and for various times. We have several jobs available for model testing at t159, t511 and t1279 resolution. Each job comes with data required to start the model, a namelist defining a set of model parameters, a PBS script (called oifs_job) set up for a "standard" run and an example trace output file. We will give a description of the important parts of the PBS script used to submit jobs to the compute nodes. 
    103103 
    104104The file has the usual PBS directives for reserving HPC resource, in this case we have requested 1024 processors with fully populated nodes, for a time limit of 25 minutes. You should edit this to specify your account and email details and change the HPC resource request as appropriate. 
     
    123123}}} 
    124124 
    125 The remainder of the PBS script refers more specifically to your job. oifs.setup is the script which loads the appropriate oifs modules. Please copy one from ...[we should put a template in the repository]. 
     125The remainder of the PBS script refers more specifically to your job.  
    126126 
    127127 
    128128{{{ 
    129 # Set environment 
    130 source $HOME/oifs.setup 
    131129 
    132130set -x 
     
    144142#  Root directory of OpenIFS 
    145143export OIFS_HOME=$HOME/oifs_extract/extract/oifs 
    146  
    147 #  Set the GRIB_SAMPLES_PATH to your installation 
    148 export GRIB_SAMPLES_PATH=$GRIB_API_PATH/share/grib_api/ifs_samples/grib1_mlgrib2 
    149144 
    150145#  use assign statement to read f77 unformatted files as big-endian 
     
    175170}}} 
    176171 
     172Once you have made the edits appropriate for your job type 
    177173 
     174{{{ 
     175qsub oifs_job 
     176}}} 
    178177 
     178=== Model ouput === 
    179179 
     180You can run the model in one of two IO modes. A namelist setting (more later) is all that is required to switch between the model generating its output synchronously through a single processor or asynchronously through multiple processors. Jobs which output large volumes of data benefit significantly in terms of reduced wall clock time by using asynchronous IO (the FDB IO model). The model produces output which is in two sub-directories of the directory from which the model was submitted. For the above example the following files appear 
    180181 
     182{{{ 
     183-rwxr-xr-x 1 grenvill n02 159249451 Sep 27 10:18 master.exe 
     184-rw-r--r-- 1 grenvill n02      4587 Sep 27 10:18 fort.4 
     185drwxr-sr-x 3 grenvill n02      4096 Sep 27 10:24 fdb9 
     186-rw------- 1 grenvill n02    784401 Sep 27 10:26 openifs.o1706747 
     187drwxr-sr-x 2 grenvill n02      4096 Sep 27 10:28 output9 
     188}}} 
     189 
     190If run in single-writer mode, the grib output is in output9 (note we set RUN=9 in the job submission script which is where the 9 comes from in the output directory names) and in FDB mode the output is in fdb9. In either case the output is in grib format - the organization of data in the output files differs in FDB and non-FDB runs, but the field data is identical (bit compares) in each case. 
     191