Docs: Add note on how to create a code that uses Conda environment #5905
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
sphuber
requested review from
ltalirz and
chrisjsewell
and removed request for
ltalirz
ltalirz
previously approved these changes
Feb 25, 2023
docs/source/howto/run_codes.rst
Outdated
Comment on lines
362
to
363
| In the `prepend_text`, the required Conda environment is activated as one normally would. | ||
| This allows to simply specify the target executable by its name, and there is no need to specify an absolute path. |
There was a problem hiding this comment.
You may consider skipping these two lines (they seem obvious from the example above)
Suggested change
| In the `prepend_text`, the required Conda environment is activated as one normally would. | |
| This allows to simply specify the target executable by its name, and there is no need to specify an absolute path. |
|
|
||
| .. note:: | ||
|
|
||
| It is possible to run codes that are provided by a `Conda environment <https://docs.conda.io/en/latest/>`_. |
There was a problem hiding this comment.
Perhaps start with the computer configuration
Suggested change
| It is possible to run codes that are provided by a `Conda environment <https://docs.conda.io/en/latest/>`_. | |
| It is possible to run codes that are provided by a `Conda environment <https://docs.conda.io/en/latest/>`_. | |
| First, configure the AiiDA computer with ``--use-login-shell`` to enable access to the ``conda activate`` command. |
There was a problem hiding this comment.
Moved the computer configuration to the top. But --use-login-shell is not the correct option. It it the shebang that should be set to #!/bin/bash -l
docs/source/howto/run_codes.rst
Outdated
Comment on lines
365
to
368
| The final requirement is that the computer should be configured to create a submission script that uses a login shell. | ||
| To do so, make sure the computer sets ``#!/bin/bash -l`` for the `shebang` property. | ||
| The ``-l`` flag in bash enforces the script to be executed using a login shell. | ||
| Without this, a normal non-interactive shell is used instead, which will cause the ``conda activate`` command to fail. |
There was a problem hiding this comment.
Could also be dropped if you accept the suggestion above
Suggested change
| The final requirement is that the computer should be configured to create a submission script that uses a login shell. | |
| To do so, make sure the computer sets ``#!/bin/bash -l`` for the `shebang` property. | |
| The ``-l`` flag in bash enforces the script to be executed using a login shell. | |
| Without this, a normal non-interactive shell is used instead, which will cause the ``conda activate`` command to fail. |
If you like, you could mention the alternative of providing the absolute path and skipping conda activate (I guess conda packages are typically reasonable with using RPATH etc. to pick up the right dependencies, but I don't have much experience with it)
This is already supported but it is important that the generated submission script uses a login script or `conda activate` will not work properly.
sphuber
force-pushed
the
fix/5895/submission-script-login-shell
branch
from
598289e
to
a83959f
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixes #5895
This is already supported but it is important that the generated submission script uses a login script or
conda activatewill not work properly.