From 204a1b3ce25a0c20c9d542d5007c2fde00068e0c Mon Sep 17 00:00:00 2001 From: arsalanakhter Date: Tue, 16 Jul 2024 14:56:57 -0400 Subject: [PATCH 1/4] Add a note to not initialize conda during install --- docs/source/software/packagemanagers/conda.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/source/software/packagemanagers/conda.md b/docs/source/software/packagemanagers/conda.md index bd8401e3..3637371e 100644 --- a/docs/source/software/packagemanagers/conda.md +++ b/docs/source/software/packagemanagers/conda.md @@ -42,6 +42,9 @@ To create a new Conda environment where `` is the path and nam conda create --prefix=// python=3.11 anaconda ::: +::::{attention} +Do NOT select the setting to automatically initialize conda on startup, as it sometimes interferes with the other environments on the HPC. If you have previously set conda to initialize on startup, remove the conda initialization script from the `.bashrc` file. See {ref}`conda-and-bashrc` for more details. + Follow the prompts to complete the Conda install, then activate the environment. :::{code} bash @@ -168,6 +171,7 @@ conda activate my-py38env To deactivate the environment, type `conda deactivate`. You can type this command again to deactivate the base Miniconda environment. +(conda-and-bashrc)= ## Conda and `.bashrc` In addition to editing your `.bashrc` file as outlined in the example above, programs you install can also modify your `.bashrc` file. For example, if you follow the procedure outlined in {ref}`mini-conda`, there may be a section added to your `.bashrc` file (if you didn't use the `-b` batch option) that automatically loads your conda environment every time you sign in to Discovery. See the figure below for an example of this: From 4d88d9d1dbb1c0ad4032c016423498d93925d705 Mon Sep 17 00:00:00 2001 From: arsalanakhter Date: Tue, 16 Jul 2024 15:00:38 -0400 Subject: [PATCH 2/4] Some formatting --- docs/source/software/packagemanagers/conda.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/software/packagemanagers/conda.md b/docs/source/software/packagemanagers/conda.md index 3637371e..bb475e4e 100644 --- a/docs/source/software/packagemanagers/conda.md +++ b/docs/source/software/packagemanagers/conda.md @@ -42,8 +42,8 @@ To create a new Conda environment where `` is the path and nam conda create --prefix=// python=3.11 anaconda ::: -::::{attention} -Do NOT select the setting to automatically initialize conda on startup, as it sometimes interferes with the other environments on the HPC. If you have previously set conda to initialize on startup, remove the conda initialization script from the `.bashrc` file. See {ref}`conda-and-bashrc` for more details. +:::{attention} +Do NOT automatically initialize conda on startup, as it sometimes interferes with other environments on the HPC. If you have previously set conda to initialize on startup, remove the conda initialization script from the `.bashrc` file. See {ref}`conda-and-bashrc` for more details. Follow the prompts to complete the Conda install, then activate the environment. From a96bda4efc32ab5b604b94b59b16c3222dbad0db Mon Sep 17 00:00:00 2001 From: arsalanakhter Date: Tue, 16 Jul 2024 15:05:50 -0400 Subject: [PATCH 3/4] More formatting for attention block --- docs/source/software/packagemanagers/conda.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/software/packagemanagers/conda.md b/docs/source/software/packagemanagers/conda.md index bb475e4e..4b9e8ef7 100644 --- a/docs/source/software/packagemanagers/conda.md +++ b/docs/source/software/packagemanagers/conda.md @@ -42,7 +42,7 @@ To create a new Conda environment where `` is the path and nam conda create --prefix=// python=3.11 anaconda ::: -:::{attention} +::{attention} Do NOT automatically initialize conda on startup, as it sometimes interferes with other environments on the HPC. If you have previously set conda to initialize on startup, remove the conda initialization script from the `.bashrc` file. See {ref}`conda-and-bashrc` for more details. Follow the prompts to complete the Conda install, then activate the environment. From 9b3c4e4b749ad279ce3318cb419f063b60fb4bfd Mon Sep 17 00:00:00 2001 From: arsalanakhter Date: Tue, 16 Jul 2024 15:08:58 -0400 Subject: [PATCH 4/4] More formatting for the attention block --- docs/source/software/packagemanagers/conda.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/source/software/packagemanagers/conda.md b/docs/source/software/packagemanagers/conda.md index 4b9e8ef7..0e168bbf 100644 --- a/docs/source/software/packagemanagers/conda.md +++ b/docs/source/software/packagemanagers/conda.md @@ -42,8 +42,9 @@ To create a new Conda environment where `` is the path and nam conda create --prefix=// python=3.11 anaconda ::: -::{attention} +::::{attention} Do NOT automatically initialize conda on startup, as it sometimes interferes with other environments on the HPC. If you have previously set conda to initialize on startup, remove the conda initialization script from the `.bashrc` file. See {ref}`conda-and-bashrc` for more details. +:::: Follow the prompts to complete the Conda install, then activate the environment.