Mitigate Interrupted system call on trace_file writes #5397
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
✅ Deploy Preview for nextflow-docs-staging canceled.
|
…ove robustness Echo commands were combined into a single block to write to $trace_file more efficiently, reducing the number of system calls. Added error handling to prevent tracing from causing workflow failures. Signed-off-by: Nico Holguin <[email protected]>
infinite-turtles
force-pushed
the
trace-file-eintr-mitigation
branch
from
0003896
to
379299b
Compare
jorgee
requested changes
Nov 21, 2024
| echo "peak_rss=${nxf_stat_ret[5]}" | ||
| echo "vol_ctxt=${nxf_stat_ret[6]}" | ||
| echo "inv_ctxt=${nxf_stat_ret[7]}" | ||
| } >> "$trace_file" || >&2 echo "Error: Failed to append to file: $trace_file" |
There was a problem hiding this comment.
In functional term, I see the change correct, but not sure about the error message. If am not wrong, when running a command group in bash, the exit code of the group is the exit code of the last command. So, the error message will be printed only if the last echo command fails. Is this the intended behavior? I don't know if it will be a bit redundant
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Writes to files from bash built-ins like
echocan be fallible, particularly in older versions of bash, such as versions 4.2.x and 4.4.x. This often lead to errors when running numerous processes with tracing enabled on network-based file systems, such as:.command.run: line 172: echo: write error: Interrupted system callHere is a potential mitigation. To address this,
echocommands were consolidated into a single block to write to$trace_filewith an error message on failure. This is assuming that the lack of a .command.trace file will not cause any downstream failures.Reference
For more details on similar issues, see: https://unix.stackexchange.com/a/487260
Signed-off-by: Nico Holguin [email protected]