# Running xp65 analysis on ARE **URL:** \ **Category:** Infrastructure\ **Tags:** help, conda\ **Created:** [16 April 2025 02:39 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419 "2025-04-16T02:39:45Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\ **Post date:** [16 April 2025 02:39 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419/1 "2025-04-16T02:39:45Z")
Hi all. Has anyone managed to run the `xp65 analysis3` environment on ARE yet? You could load `hh5 analysis3` by specifying ![Screenshot 2025-04-08 at 11.42.17 am (1)](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/3/35c840b4425b2216afa5faf039dd207e6fd887f4.png) as all the environments are present in `/g/data/hh5/public/apps/miniconda3/envs/`. The `xp65` directory structure is a bit different. The directory `/g/data/xp65/public/apps/med_conda/envs` exists but all the links to `analysis` environment are broken (they point to `/opt/conda`). The `xp65` python interpreter (when loaded from `modules`) is located at `/g/data/xp65/public/apps/med_conda_scripts/analysis3-25.03.d/bin/` Can you access `xp65` using `module` commands in ARE? Or do we have to build our own `pylab` `kernel` ? Thanks. ---
**Author:** ![lidefi87](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/lidefi87/32/91_2.png) [@lidefi87](https://forum.access-hive.org.au/u/lidefi87)\ **Post date:** [16 April 2025 02:55 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419/2 "2025-04-16T02:55:47Z")
Hi Paul, I followed the instructions here: [conda/analysis3 Python Environment - ACCESS-Hive Docs](https://access-hive.org.au/getting_started/environments/#use-the-environment-within-a-pbs-job) and I was able to start a session without issues. I’m including a screenshot below just in case. ![image](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/d/df0d84348fd3af983c6e8ee8ffe398630e34be21.png) The only issue is that I’m getting a bunch of warnings when loading zarr files with `xarray`. **Edit:** It seems like selecting `analysis3-25.04` as the preferred conda environment gets rid off all the warnings. As I understand, you can use `conda/analysis3-25.04` under **Modules** in ARE (last line in screenshot above) and it will load this environment straight away. Otherwise, you can simply select it from the drop down list on the top right of your Jupyter notebook. ---
**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\ **Post date:** [16 April 2025 03:38 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419/3 "2025-04-16T03:38:16Z")
Hi @lidefi87 . Thanks for pointing me to the NRI docs. The Jupyter session starts as follows. ![Screenshot 2025-04-16 at 1.27.19 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/b/bad9f2a19eec372295490e9d0b544fc5d4f81a2b.png) I select the default kernel ![Screenshot 2025-04-16 at 1.31.27 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/d/d9cf07e3d84ea88b8660530c90bee60f84d24427.png) I can import `xarray`, `iris` and `metpy`. But I can’t import `ants`. I assume I’m running the `xp65 analysis3` environment. What’s the best way to check? I don’t generate the list of `analysis3` kernels inside the notebook. ---
**Author:** ![lidefi87](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/lidefi87/32/91_2.png) [@lidefi87](https://forum.access-hive.org.au/u/lidefi87)\ **Post date:** [16 April 2025 04:57 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419/4 "2025-04-16T04:57:33Z")
You should select one of the environments made available by the ACCESS-NRI team. There is no need for you to generate a list of available environments because they’re all available in the dropdown list you show in your screenshot. Simply click on that box where it says _Python 3 (ipykernel)_ and a list of all available environments will appear. If you scroll up, you’ll find the different versions of `analysis3`. I chose the latest `analysis3-25.04`. Below, I’m highlighting the boxes I clicked to get this list. ![image](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/4/4f3168f6e0672439476f64b9f6d5fdb9eacb028d.png) The link I shared above has some information about the different environments, but you can also refer to the release notes [here](https://forum.access-hive.org.au/t/access-nri-analysis3-conda-environments-new-release-announcement/4377). The `ants` package appears to be available on `analysis3-25.04` based on this [repo](https://github.com/ACCESS-NRI/ACCESS-Analysis-Conda/blob/main/environments/analysis3/environment.yml). But the docs on the previous paragraph have instructions on how to request a package that is not available in the conda environment. ---
**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\ **Post date:** [16 April 2025 06:02 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419/5 "2025-04-16T06:02:38Z")
Hi @lidefi87 I can’t select the NRI environments. To recap. I launch the notebook with the following advanced options. ![Screenshot 2025-04-16 at 3.51.43 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/a/a15e13091823cddc5505b03e5078a0686cdbaa48.png) But when Jupyter is launched, it can only see the following. ![Screenshot 2025-04-16 at 4.00.17 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/7/77c125530857a5c789abf2b7c2ac1cb02d99c921.png) ![Screenshot 2025-04-16 at 4.00.42 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/e/e227da23c213662e44af5166ae451a1687d7ed72.png) Which is the contents of my `~/.local/share/jupyter/kernels/` directory ```auto $ ls -lt ~/.local/share/jupyter/kernels/ total 16 drwxrwxr-x 2 pag548 gb02 4096 Apr 16 14:54 xp65_extras lrwxrwxrwx 1 pag548 gb02 70 Apr 10 16:52 hackathon_env -> /g/data/gb02/public/hackathon_env/share/jupyter/kernels/hackathon_env/ drwxr-sr-x 2 pag548 gb02 4096 Dec 20 18:23 rmom6_env drwxr-sr-x 2 pag548 gb02 4096 Oct 7 2024 ipylab_env ``` So I can see all my local kernels, but none of the standard NRI environments. What am I doing wrong? NOTE : gdata/xp65 is added as a storage option ![Screenshot 2025-04-16 at 4.04.29 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/7/7639bd7558909745de8b51dab0ad0e6231737255.png) ---
**Author:** ![lidefi87](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/lidefi87/32/91_2.png) [@lidefi87](https://forum.access-hive.org.au/u/lidefi87)\ **Post date:** [16 April 2025 06:19 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419/6 "2025-04-16T06:19:19Z")
If you have `gdata/xp65` in the **Storage** option, then I suspect this may be one of the potential issues described in the docs when the `.bashrc` or `.bash_profile` files call `hh5` automatically. I was having some issues too when running PBS jobs, but I realised my `.condarc` file was calling `hh5` and when I changed this to `xp65`, the issues went away. I highly recommend you go through the documentation I shared in this thread. It helped me sort out the issues I encountered. ---
**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\ **Post date:** [16 April 2025 06:43 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419/7 "2025-04-16T06:43:33Z")
I don’t have any `conda` or `hh5` logic in my `.bashrc` or `.bash_profile.` I had some old files `~/.condarc` and directories in `~/.conda/` so I purged them. I’m now able to see all the NRI pylabl kernels! Looks like my old `~/.conda*` files and directories were causing the issue? Thanks for the tip. ---
**Author:** ![rbeucher](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/rbeucher/32/11_2.png) [@rbeucher](https://forum.access-hive.org.au/u/rbeucher)\ **Post date:** [16 April 2025 23:51 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419/8 "2025-04-16T23:51:37Z")
Thanks @lidefi87 for helping with this. Let us know if there are any more issues. ---
**Author:** ![Scott](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/scott/32/37_2.png) [@Scott](https://forum.access-hive.org.au/u/Scott)\ **Post date:** [17 April 2025 03:43 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419/9 "2025-04-17T03:43:11Z")
A possibly related issue is that with a `~/.condarc` file defining `envs_dirs` e.g. ```yaml envs_dirs: - /scratch/$PROJECT/$USER/conda/envs ``` kernels don’t get listed - you need to add `/g/data/xp65/public/apps/med_conda/envs` to this search path if `envs_dirs` is defined for kernels to be detected. It should be possible to set this centrally. The command `python -m nb_conda_kernels list` can be used to show what kernels are available. ---
**Author:** ![rbeucher](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/rbeucher/32/11_2.png) [@rbeucher](https://forum.access-hive.org.au/u/rbeucher)\ **Post date:** [17 April 2025 04:28 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419/10 "2025-04-17T04:28:19Z")
Thanks @Scott, I was not aware of this. ---
**Author:** ![atteggiani](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/atteggiani/32/212_2.png) [@atteggiani](https://forum.access-hive.org.au/u/atteggiani)\ **Post date:** [22 April 2025 04:10 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419/11 "2025-04-22T04:10:52Z")
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**Author:** ![navidcy](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/navidcy/32/101_2.png) [@navidcy](https://forum.access-hive.org.au/u/navidcy)\ **Post date:** [15 June 2025 06:48 UTC](https://forum.access-hive.org.au/t/running-xp65-analysis-on-are/4419/12 "2025-06-15T06:48:22Z")
Thanks all! This was useful. Both the `hh5` references at the `.bashrc`, `.bash_profile` and the inclusion of the path mentioned by @Scott were crucial to make this work for me!