Various improvements to the i/o code

Bugs:

• Fixes incorrect meta-data in snapshots when not writing any of the fields of a particle type (Fixes #732 (closed))
• Fixes #728 (closed)
• Add a barrier at the end of the distributed io output to make sure all ranks are done before progressing (Sibelius-dark bug with slow cosma6 disks)
• Fix an overflow in the global counter of particles in groups reported by FOF (bug had no consequence on output, just on stdout message).

Improvements:

• Refactoring of the selection of fields to unify the calls into a single simpler function
• Allow for different default values when reading optional fields (Implement #705 (closed))
• Re-read the output list when restarting a run (Implement #678 (closed))
• Allow for different snapshot basenames for the different output types (Implement #677 (closed))
• Allow users to specify a different snapshot ID for each entry in the output list (Implement #694 (closed))
• Add the list of particle type names to the snapshot headers.
• Upon restarting, check that all ranks are on the same ti_current. This prevents accidental restarts with mixed sets of restart files.

added bug code health feature request i/o labels

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• 60285eba - When using a list of outputs, set the first output time to the first entry...
• 837e509e - Move the reading of the output lists from engine_init() to engine_config()

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• cc88fcef - Add a check to verify the output list is not being overweitten by mistake
• a6c956d5 - Do not write the output list in the restart files. Re-read them from the file
• 66566e96 - Fix a bug when restarting the EAGLE feedback model in a run without feedback

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• 476c80db - Optionally read the snapshot basename from the output options yaml file

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• 6a79c24d - Also let the user select a different sub-directory name for the various output selections

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• 358389c6 - Move the subdir creation to the snapshot writing code as the names are possibly unknown on start up
• 30231347 - Missing includes
• f94a83a7 - Apply the same changes to the distributed_io code

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mentioned in issue #732 (closed)

assigned to @jborrow

@jborrow and @jkeger any thoughts on the features you requested? I still need to do the replacement of the automatic time labels (#694 (closed)).

Looks good to me, I like the changes to common_io.

@chaikin might also be interested in the feature to re-read the list of outputs.

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• 1aa30cfb - Document the new feature allowing users to change the basename and sub-dir of...

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Exactly! I was looking for it just a few days ago. Glad that we will have this feature from now on.

One drawback is that output list can't get lost any more. It must be kept alongside the run and with the same name.

added 2 commits

• dc475e6e - Optionally read integer labels from the output list
• 1dc8751f - Use the newly read list to generate the labels instead of the simply increasing snapshot numbers

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