Fix non-atomic atomic_configure_file

[zig-for]

While building very parallel project trees (for example, catkin run_tests on a large project tree that is already built without tests) on a machine with many cores (ie, an xlarge aws compute unit with 48 cores), environment configuration can fail with errors similar to:

SyntaxError: invalid syntax
CMake Error at /opt/ros/kinetic/share/catkin/cmake/safe_execute_process.cmake:11 (message):
  execute_process(/usr/bin/python2
  "/home/embark/catkin_ws/build/remote_operation/catkin_generated/generate_cached_setup.py")
  returned error code 1
Call Stack (most recent call first):
  /opt/ros/kinetic/share/catkin/cmake/all.cmake:208 (safe_execute_process)
  /opt/ros/kinetic/share/catkin/cmake/catkinConfig.cmake:20 (include)
  CMakeLists.txt:4 (find_package)
[3:22 PM] Traceback (most recent call last):
  File "/home/embark/catkin_ws/build/node_framework/catkin_generated/generate_cached_setup.py", line 22, in <module>
    code = generate_environment_script('/home/embark/catkin_ws/devel/env.sh')
  File "/opt/ros/kinetic/lib/python2.7/dist-packages/catkin/environment_cache.py", line 62, in generate_environment_script
    output = subprocess.check_output([env_script, sys.executable, '-c', python_code])
  File "/usr/lib/python2.7/subprocess.py", line 567, in check_output
    process = Popen(stdout=PIPE, *popenargs, **kwargs)
  File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
CMake Error at /opt/ros/kinetic/share/catkin/cmake/safe_execute_process.cmake:11 (message):
  execute_process(/usr/bin/python2
  "/home/embark/catkin_ws/build/node_framework/catkin_generated/generate_cached_setup.py")
  returned error code 1
Call Stack (most recent call first):
  /opt/ros/kinetic/share/catkin/cmake/all.cmake:208 (safe_execute_process)
  /opt/ros/kinetic/share/catkin/cmake/catkinConfig.cmake:20 (include)
  CMakeLists.txt:14 (find_package)

Reading the directory before and after the error will show that the file exists, with proper permissions.

As far as I can tell, there are two defects:

1. file(LOCK ...) doesn't lock between independent cmake instances, as catkin build uses.
2. There is no locking when executing scripts, so when the copy happens, there is a short time when another instance is trying to read that the script is missing. See https://gitlab.kitware.com/cmake/cmake/-/blob/master/Source/kwsys/SystemTools.cxx#L2384

I've changed atomic_configure_file to first copy alongside the destination, then do a rename. This should allow atomic configuration while not causing a regression with #422 .

[jaredjxyz]

I can confirm we have seen this issue as well

[Axel13fr]

We've had the issue as well on random occurences on a project that runs tests on ~120 packages over 8 cores. Can this get merged ?

[gbiggs]

@zig-for There is one style issue that needs to be fixed (the first line isn't indented correctly). If you can fix that, I think we'll be able to merge this.

[zig-for]

@gbiggs fixed

[zig-for]

@gbiggs what's the plan for this repo, anyhow? It's great that this is merged in, but users have to be running catkin from source to get the benefit.

[gbiggs]

I don't know if any further releases of catkin are planned in the near future, but I expect there will be at least one between now and the EOL date for Noetic.