Mitigate Interrupted system call on trace_file writes #5397
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…ove robustness Echo commands were combined into a single block to write to $trace_file more efficiently, reducing the number of system calls. Added error handling to prevent tracing from causing workflow failures. Signed-off-by: Nico Holguin <nholguin@illumina.com>
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modules/nextflow/src/main/resources/nextflow/executor/command-trace.txt
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Signed-off-by: Nico Holguin <nholguin@illumina.com>
Signed-off-by: Nico Holguin <nholguin@illumina.com>
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Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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Writes to files from bash built-ins like
echocan be fallible, particularly in older versions of bash, such as versions 4.2.x and 4.4.x. This often lead to errors when running numerous processes with tracing enabled on network-based file systems, such as:.command.run: line 172: echo: write error: Interrupted system callHere is a potential mitigation. To address this,
echocommands were consolidated into a single block to write to$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 nholguin@illumina.com