remove python3 incompatibility #2
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This is primarily a formatting change to the Manifest code support. Specific non-style changes mentioned below: - `hash` as a variable is renamed in many cases, to avoid conflict with the `hash` builtin. - Strings are updated to support 2.6 format syntax - The git support functions are moved out of fsops modules (intended for filesystem operations) and moved into the manifest module - Additional variables were introduced in some places to reduce the number of commands per line.
The three git subcommand functions have been removed from the manifest module, since they were not called anywhere.
Added scheduler/pbs.py for PBS specific commands. Dump environment and job information separately. Follow the same pattern as stdout/stderr and move to output on completion, or error_logs on failure. pep8 cleanup
Added git commit hash to job yaml dump file.
PEP8 indentation cleanup resulting from above change.
Enforced correct indentation on continuation lines Removed dump_yaml function, inlined code Standardised handling of output files (stderr, stdout and yaml dumps) Cleaned up imports in manifest.py
Dump some job information stats
adding to list self.config_files. Addresses https://github.com/marshallward/payu/issues/148.
Parse MITgcm config files to check they are correct namelists
stays deleted. Previous behaviour recreated the archive directory to store logs. Fixes https://github.com/marshallward/payu/issues/136
Fixes issue with hard sweep not removing archive correctly
Added control path to job yaml dump
…#158) * Add option to collate restart files as well as output files This will collate the previous restart, to avoid issues with half collated restarts if collate doesn't complete before next run starts. Also avoids any possible speed hit when using collated restarts for the next run.
Now use git commit hash to uniquely identify logs if PBS id not available, e.g. using payu-run.
…rt directories. (payu-org#160) * Added support for ability of cice5 to define separate input and restart directories. * Added code to check consistency of paths between namelist variables in cice. Changed some of the logic in cice set_model_pathnames as a result, so consistency checks are done, whether or not the input and restart directories are separate. * Check the restart pointer path is consistent but only warn, as this can be the case in older models * Initialised runlog manifest when create_manifest is called, otherwise subruns (which do not init runlog) were doing multiple git add steps for each config file. * Use os.path.curdir * Delete restart pointer file when using split paths in cice * Fixed logic for removing INPUT directory in case of split paths
Primarily a whitespace cleanup, two specific changes below. - The Win32 path with forward backslash was converted to a raw string - Core dump support was added to config.yaml to enable Fortran core dumps `coredump: True` should work. May organise this better someday, take this as a temporary thing.
Added support for the older Intel compilers (ca. v15), and confirmed that it is working as intended.
NRUN and force ASTART to be last restart dump. This emulates ACCESS-ESM run script
Changed to self.copy_restarts when populating manifests. Walk input paths to properly support sub-directories by adding all files explicitly.
cice: Made copy_inputs default False cice: Added logic for init_path (where restarts are read from) cice: Added checks for consistent paths. cice: commented out get_prior_restart_files as it was returning only one iced file, ignoring other restarts. Added in logic later to only pick up latest restart when it is required. cice: Moved some of the restart cleaning logic from cice5 to cice so iced restarts don't accumulate. cice: Cleaned more paths of symlinks in archive
manifest: renamed make_links to check_manifests, as it no longer creates links.
In particular, takes care of linking the o2i.nc into cice work/RESTART access: override set_local_pathnames and pass it. Model does not have work path so redundant, and errors otherwise.
remove redundant path information.
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