Hi Isabelle,
The script is not installed by default on Monsoon, so you will have to extract from the repository.
$ mkdir ~/test (or suitable folder)
$ cd ~/test/
$ fcm export fcm:moci.xm_tr/Utilities/lib/perturb_theta.py
$ chmod +x perturb_theta.py
$ cd cylc-run/u-df691/share/data/History_Data/
(assuming the atmos_main task starting 01Dec2000 is failing)
$ mv df691a.da20001201_00 df691a.da20001201_00.orig
$ module load um_tools
$ ~/test/perturb_theta.py df691a.da20001201_00.orig --output ./df691a.da20001201_00
Resubmit the failed task.