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Running WRF model on a HPC cluster

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I have successfully installed WPS, WRF model and the necessary libraries on the HPC computers that have a cluster (cores).

The problem I am facing is that there is limited storage space on the working directory where I installed everything.

Is it possible to run simulations from within the WRF sub-directory run but store the wrfout files on another project directory/no backup directory outside of the WRF directory?

If yes, appreciate guidance.

Appreciate your assistance and advice.

Yes, this is possible. In the &time_control section of your namelist, you can set:
history_outname = '/directory/wrfout_d<domain>_<date>'

This will send the history files to a different location. Obviously 'directory' would be the path to where you want this output to go, but then keep the syntax just as is written above for "wrfout_d<domain>_<date>." No need to actually enter the domain or date, as this syntax will tell the model to use the appropriate one.