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GDB - GNU Debugger#

GDB is a command line debugger installed on all our systems.

Resolving "could not open an executable file" or "can't open read symbols" after attaching to a process#

If you use GDB inside a Slurm job to attach to a process with gdb -p/--pid=<pid> or the GDB command attach <pid> you might encounter errors or warnings related to executable and library files than cannot be opened or symbols that cannot be read, like in the following:

warning: "target:<executable>": could not open as an executable file: Operation not permitted.
warning: `target:<executable>': can't open to read symbols: Operation not permitted.
warning: Could not load vsyscall page because no executable was specified

As a workaround execute the command set sysroot / inside GDB:

  • With gdb -p <pid>: 

    gdb -p <pid>`
# errors/warnings ...
(gdb) set sysroot /
# Reading symbols ...

  • With gdb <executable>: 

    $ gdb <executable>
(gdb) set sysroot /
(gdb) attach <pid>

Thanks to SURFsara for figuring this out.