Long Story (This is X)

I need to start CLion with sudo so that I can attach gdb to the running process from CLion (for a debugging purpose). The reason is because when I run CLion without sudo, and trying to attach to a process (CLion GUI), I receive:

com.jetbrains.cidr.execution.debugger.backend.gdb.GDBDriver$GDBCommandException: ptrace: Operation not permitted.

As a second check, I tried running gdb in the terminal manually without sudo:

gdb -p 16741


Could not attach to process. If your uid matches the uid of the target process, check the setting of "/proc/sys/kernel/yama/ptrace_scope", or try again as the root user. For more details, see "/etc/sysctl.d/10-ptrace.conf"

ptrace: Operation not permitted.

However, if I run gdb with sudo:

sudo gdb -p 16714


Attaching to process 16714

So I think I should run CLion as root.

TLDR / The Problem (This is Y)

Now, if running sh /opt/clion/bin/clion.sh from the Ubuntu terminal, CLion does pick up the environment variables sourced in the ~/.bashrc file, and my program compiles with no error.

But because without sudo, I can't attach gdb to the process from within CLion for my debugging purpose, so I need to run the clion.sh startup script as root.

The problem is that when running sudo sh /opt/clion/bin/clion.sh, CLion doesn't seem to pick up the environment variables, leading to "CMake cannot find package ..." error, which makes my program not runnable⁠—worse.

CMake Error at CMakeLists.txt:64 (message):
  find_package(catkin) failed.  catkin was neither found in the workspace nor
  in the CMAKE_PREFIX_PATH.  One reason may be that no ROS setup.sh was
  sourced before.


How do I run the CLion startup script with sudo, and preserve the environment variables that are sourced in ~/.bashrc?

If relevant

  • I think CLion doesn't pick up the following variables. To be very specific, I have this line in my ~/.bashrc file:

    source /opt/ros/kinetic/setup.bash

    whose content is

    #!/usr/bin/env bash
    # generated from catkin/cmake/templates/setup.bash.in
    # source setup.sh from same directory as this file
    _CATKIN_SETUP_DIR=$(builtin cd "`dirname "${BASH_SOURCE[0]}"`" > 
    /dev/null && pwd)
    . "$_CATKIN_SETUP_DIR/setup.sh"

    Perhaps, there might be a way to add this directly to the startup script of CLion?

  • XY Problem
  • I am running Ubuntu 16.04
  • I'll need more coffee before I really understand what you're asking but a couple of observations: (1) sudo performs an env_reset by default - only preserving a minimal environment (2) sh is not bash (at least, not by default) and in any case, .bashrc is only sourced for interactive shells. Fundamentally, I think this likely is an XY problem - see for example How to solve “ptrace operation not permitted” when trying to attach GDB to a process? – steeldriver Dec 3 '19 at 12:57
  • @steeldriver Thanks for pointing those out to me. I agree that this is likely an XY problem; because I could go with fixing the X, which is ptrace operation not permitted when attaching gdb to the process problem. And if that solved the problem, I wouldn't need to ask the Y, which is about dealing with sudo, environment variables, sh, ~/.bashrc, etc. – IgNite Dec 3 '19 at 14:50
  • There are similar questions: here, here, and here, but none of them directly answer the question (the Y) that I asked here. – IgNite Dec 3 '19 at 14:53
  • The only workaround that works for me is to look into the ~/.bashrc file and set CMAKE_PREFIX_PATH in CLion accordingly, by pointing this variable to the folder that contains the missing packages. Also set the variables as outlined by this post. However, ~/.bashrc is something that I change frequently, so I'm not sure if this is the best way to go. – IgNite Dec 3 '19 at 15:05
  • I guess what I'm saying is that you should fix your kernel parameters so that you don't need to run the IDE with sudo - in which case, it will inherit its parent environment (including things like CMAKE_PREFIX_PATH, so long as they have been exported) in the usual way – steeldriver Dec 3 '19 at 17:34

I came back to accept @steeldriver 's comment as an answer.

Modifying /etc/sysctl.d/10-ptrace.conf as in the link in his comment does solve the problem indirectly.

That is, by modifying this file (changing from 1 to 0), I can now run GDB attach to a process within CLion without having to run CLion as root. And as usual, running CLion from terminal does pick up the environment variables.

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