NEWS.md

In UCSF-HPC/wyntonquery: Query the UCSF Wynton Environment

Version (development version)

New Features

• Now make_file_index() takes optional argument index, which should specify the index of a previous version of the input file. If specified, it will only index the end of the file that is not already indexed. This provides a quick way to update the index of a file that is continously growing.

• Add sge_make_date_index().

• Add sql_import_sge_accounting().

Version 0.3.0 [2022-06-02]

New Features

• Add beegfs_quota().

• Now read_raw_sge_accounting() and ead_sge_accounting() can read the subset of data that is given by an sge_accounting_index_by_week week index table. This is one by passing to to argument offset.

• Now read_raw_sge_accounting() and read_sge_accounting() accepts also file connections as input.

• Add sge_failed_codes().

Documentation

• Updated SGE accounting vignette.

• Updated example data for number of users over time.

Bug Fixes

• disk_free() failed because some columns were not recognized.

• Field nbr_of_jobs returned by sge_make_week_index() was a cumulative sum, not number of jobs per week.

• open_file_at(..., auto_close = TRUE) was not safe; it could end up closing the incorrect connection if the intended one had been closed and another one had been opened. Dropped options for auto_close to be on safe side.

Version 0.2.0 [2021-06-18]

New Features

• Add sge_make_week_index().

• Add add_weeks().

Version 0.1.0 [2021-06-18]

New Features

• Add users_over_time().

• Add generic function anonymize() with implementations for data.frame, raw_sge_accounting, and qstat objects.

• Add read_qstat() for getting information on the jobs currently on the SGE queue.

• Add make_file_index(), save_file_index(), and qread_file_index().

• Add open_file_at().

• read_raw_sge_accounting(), and therefore also read_sge_accounting(), gained argument offset.

Documentation

• Add vignettes 'SGE Accounting File' and 'Jobs on the SGE queue'.

Bug Fixes

• The ru_wallclock values returned by read_sge_account() were corrupted by "random" NAs.

Version 0.0.0-9005 [2021-05-05]

New Features

• Add write_raw_sge_accounting().

• Add anonymize_raw_sge_accounting().

• Now read_raw_sge_accounting() records file header in attribute header.

• Added an example SGE accounting file and examples how to process it.

Version 0.0.0-9004 [2021-01-25]

New Features

• Add job_summary_by_status().

Version 0.0.0-9003 [2020-04-04]

New Features

• Add parse_category() for sge_accounting objects.

Documentation

• Expand example of read_sge_accounting() to display how to inspect how much CPU time was spent on successful and failed jobs.

Bug Fixes

• Package did not pass R CMD check --as-cran on systems without qhost.

Version 0.0.0-9002 [2019-08-06]

New Features

• Add sge_accounting_file() and read_sge_accounting().

• Renamed host_table() column # Physical Cores to Physical Cores so that it does not conflict with #-comment lines in tab-delimited files.

Version 0.0.0-9001 [2019-06-06]

Significant Changes

• The system("scripts", "system_info.R", package="wyntonquery") script is now robust against errors; if there's an error querying a particular host, then that host is dropped from the final out.

• The system("scripts", "system_info.R", package="wyntonquery") script now caches results from individual compute nodes.

• host_info() now reports on cpu_model, which corresponds to the cpu_info() field model_name, e.g. "Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz". Previously, it tried to report on the CPU speed but that fluctuated from run to run because it was incorrectly inferred from the cpu_mhz field.

New Features

• on_hostname() gained argument cache for controlling whether cached results should be considered or not.

• It's now possible to specify which hosts to query via environment variable R_WYNTONQUERY_INCLUDE.

• on_hostname() gained argument on_error for controlling how errors should be handled.

Bug Fixes

• cpu_info() did not handle upper-case letters in field names.

Version 0.0.0-9000 [2018-06-10]

New Features

• Add host_table().

• Add round_ram().

• Add lscpu().

• Add system_info().

• Add disk_free().

• Add queues().

• Add on_hostname().

• Add qhost() and cpu_info().

UCSF-HPC/wyntonquery documentation built on March 6, 2025, 1:12 a.m.