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Mitigate Interrupted system call on trace_file writes
Writes to files from bash built-ins like echo can 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 call
Here is a potential mitigation. To address this, echo commands were consolidated into a single block to write to $trace_file with 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]
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