Changes between Version 9 and Version 10 of Projects/OpenIFS-IO
- Timestamp:
- 27/09/13 11:02:31 (7 years ago)
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Projects/OpenIFS-IO
v9 v10 43 43 === Setting the HECToR environment === 44 44 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, type45 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). Setting the environment simple involves loading the appropriate environment module; at the HECToR command line, type 46 46 47 47 {{{ … … 100 100 === Getting data to run the model === 101 101 102 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.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 (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. 103 103 104 104 The 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. … … 123 123 }}} 124 124 125 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].125 The remainder of the PBS script refers more specifically to your job. 126 126 127 127 128 128 {{{ 129 # Set environment130 source $HOME/oifs.setup131 129 132 130 set -x … … 144 142 # Root directory of OpenIFS 145 143 export OIFS_HOME=$HOME/oifs_extract/extract/oifs 146 147 # Set the GRIB_SAMPLES_PATH to your installation148 export GRIB_SAMPLES_PATH=$GRIB_API_PATH/share/grib_api/ifs_samples/grib1_mlgrib2149 144 150 145 # use assign statement to read f77 unformatted files as big-endian … … 175 170 }}} 176 171 172 Once you have made the edits appropriate for your job type 177 173 174 {{{ 175 qsub oifs_job 176 }}} 178 177 178 === Model ouput === 179 179 180 You 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 180 181 182 {{{ 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.4 185 drwxr-sr-x 3 grenvill n02 4096 Sep 27 10:24 fdb9 186 -rw------- 1 grenvill n02 784401 Sep 27 10:26 openifs.o1706747 187 drwxr-sr-x 2 grenvill n02 4096 Sep 27 10:28 output9 188 }}} 189 190 If 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