Update container handling with charliecloud #5300
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-use writeFake as default -run by name with writeFake and CH_IMAGE_STORAGE -run by path with writeFake when CH_IMAGE_STORAGE is not set -run by path without writeFake, but writeable, check that the path is not CH_IMAGE_STORAGE Signed-off-by: Niklas Schandry <[email protected]>
Signed-off-by: Niklas Schandry <[email protected]>
…GE_STORAGE is preferred, in other cases charliecloud.cacheDir over NXF_CHARLIECLOUD_CACHE over work/charliecloud, prevent usage of CH_IMAGE_STORAGE when not using writeFake Signed-off-by: Niklas Schandry <[email protected]>
Signed-off-by: Niklas Schandry <[email protected]>
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Signed-off-by: Niklas Schandry <[email protected]>
Signed-off-by: Niklas Schandry <[email protected]>
phue
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Sep 12, 2024
How was it fixed? |
Signed-off-by: Niklas Schandry <[email protected]>
Trying to catch it and retry https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudCache.groovy#L186 |
phue
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Sep 12, 2024
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Thanks for the helpful discussion and review @phue ! @pditommaso do you have any additional comments on this? |
pditommaso
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Sep 16, 2024
modules/nextflow/src/main/groovy/nextflow/container/CharliecloudCache.groovy
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Signed-off-by: Niklas Schandry <[email protected]>
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Thanks @pditommaso, I have put in the suggested change. |
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Nice, let's wait for the tests |
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Here are changes to the charliecloud driver.
charliecloud.writeFakeis true by default (!)if
charliecloud.writeFakeis true and$CH_IMAGE_STORAGEis set, images will go into$CH_IMAGE_STORAGEand be run from there with --write-fake (will be run by name in that case).if charliecloud.writeFake is true, but
$CH_IMAGE_STORAGEis unset, images will go intocharliecloud.cacheDir,$NXF_CHARLIECLOUD_CACHEorwork/charliecloud(order of priority) and will be run by path (since run by name only works if$CH_IMAGE_STORAGEis set)if
charliecloud.writeFakeis set tofalse, images will need to be run with-wto enable mounting of the workDir. In this case$CH_IMAGE_STORAGEwill not be used to store images, since$CH_IMAGE_STORAGEis incompatible with-w. Images will instead go intocharliecloud.cacheDir,$NXF_CHARLIECLOUD_CACHEorwork/charliecloud(order of priority). If the folder used to store images is the same as$CH_IMAGE_STORAGE, throw an exception. Images will be run by path.In summary:
Give preference to
$CH_IMAGE_STORAGEin the default case ofwriteFakeMake some effort to avoid using
$CH_IMAGE_STORAGEwhenwriteFakeisfalse.No longer create temporary containers for each task.
This is the same as #5212, but without the many merge conflicts created by a failed sign-off.
@phue I have updated the documentation. I have not added a unit test for switching between
imageandimageNamein the builder, since I do not know of a way to set an env var for the tests. I have tested this locally (i.e. running tests with the var set or not) and it produced the expected results. Is it really worth adding a way to inject fake environments into the BuilderTest to test this specific behaviour?