reportseff 2.7.4

Tablular seff output

reportseff

A python script for tabular display of slurm efficiency information

About

Motivation

Whether a sys admin or cluster user, knowing how well you are estimating job resources can help streamline job scheduling and maximize your priority. If you have ever tried to use sacct you probably had some trouble interpreting the output. While seff or jobstats can provide detailed summaries, they don't scale easily to array jobs or offer a way to see all the jobs from a single user. reportseff aims to fill this role. Read more about the motivation for reportseff.

Audience

If you are running more than one slurm job at a time, you should try reportseff. Users of HPC systems can get an idea how well they estimate resource usage. By tuning these values, you can get scheduled earlier and not be penalized for unused allocations. Since reportseff can parse job ids from slurm output files, it simplifies the task of identifying which jobs have failed and why. Sys admins can pipe reportseff output to identify users with poor utilization or produce summaries at the end of a billing cycle.

Implementation

reportseff is a wrapper around sacct that provides more complex option parsing, simpler options, and cleaner, colored outputs. All querying is performed in a single call to sacct and should have similar performance. Multi-node and GPU utilization is acquired from information contained in the AdminComment field, as generated by jobstats.

Usage

Installation

reportseff runs on python >= 3.6. The only external dependency is click (>= 6.7). Calling

pip install --user reportseff
# OR
pipx install reportseff

will create command line bindings and install click.

Sample Usage

Try reportseff -u $USER or just reportseff in a directory with some slurm outputs. You may be surprised by your results!

Single job

Calling reportseff with a single jobid will provide equivalent information to seff for that job. reportseff 24371789 and reportseff map_fastq_24371789 produce the following output:

   JobID      State          Elapsed   CPUEff   MemEff
24371789    COMPLETED       03:08:03   71.2%    45.7%

Single array job

Providing either the raw job id or the array job id will get efficiency information for a single element of the array job. reportseff 24220929_421 and reportseff 24221219 generate:

       JobID      State          Elapsed    CPUEff   MemEff
24220929_421    COMPLETED       00:09:34    99.0%    34.6%

Array job group

If the base job id of an array is provided, all elements of the array will be added to the output. reportseff 24220929

          JobID      State          Elapsed    CPUEff   MemEff
     24220929_1    COMPLETED       00:10:43    99.2%    33.4%
    24220929_11    COMPLETED       00:10:10    99.2%    37.5%
    24220929_21    COMPLETED       00:09:25    98.8%    36.1%
    24220929_31    COMPLETED       00:09:19    98.9%    33.3%
    24220929_41    COMPLETED       00:09:23    98.9%    33.3%
    24220929_51    COMPLETED       00:08:02    98.5%    36.3%
    ...
   24220929_951    COMPLETED       00:25:12    99.5%    33.5%
   24220929_961    COMPLETED       00:39:26    99.7%    34.1%
   24220929_971    COMPLETED       00:24:11    99.5%    34.2%
   24220929_981    COMPLETED       00:24:50    99.5%    44.3%
   24220929_991    COMPLETED       00:13:05    98.7%    33.7%

Glob expansion of slurm outputs

Because slurm output files can act as job id inputs, the following can get all seff information for a given job name:

slurm_out  ❯❯❯ reportseff split_ubam_24*
              JobID      State          Elapsed   CPUEff   MemEff
split_ubam_24342816    COMPLETED       23:30:32   99.9%    4.5%
split_ubam_24342914    COMPLETED       22:40:51   99.9%    4.6%
split_ubam_24393599    COMPLETED       23:43:36   99.4%    4.4%
split_ubam_24393655    COMPLETED       21:36:58   99.3%    4.5%
split_ubam_24418960     RUNNING        02:53:11    ---      ---
split_ubam_24419972     RUNNING        01:26:26    ---      ---

No arguments

Without arguments, reportseff will try to find slurm output files in the current directory. Combine with watch to monitor job progress: watch -cn 300 reportseff --color --modified-sort

                JobID           State          Elapsed   CPUEff   MemEff
   split_ubam_24418960          RUNNING        02:56:14    ---      ---
fastq_to_ubam_24419971          RUNNING        01:29:29    ---      ---
   split_ubam_24419972          RUNNING        01:29:29    ---      ---
fastq_to_ubam_24393600         COMPLETED     1-02:00:47   58.3%    41.1%
    map_fastq_24419330          RUNNING        02:14:53    ---      ---
    map_fastq_24419323          RUNNING        02:15:24    ---      ---
    map_fastq_24419324          RUNNING        02:15:24    ---      ---
    map_fastq_24419322          RUNNING        02:15:24    ---      ---
mark_adapters_24418437         COMPLETED       01:29:23   99.8%    48.2%
mark_adapters_24418436         COMPLETED       01:29:03   99.9%    47.4%

Filtering slurm output files

One useful application of reportseff is filtering a directory of slurm output files based on the state or time since running. Additionally, if only the jobid is specified as a format output, the filenames will be returned in a pipe-friendly manner:

old_runs   ❯❯❯ reportseff --since d=4 --state Timeout

                 JobID   State      Elapsed  CPUEff   MemEff
call_variants_31550458  TIMEOUT    20:05:17  99.5%     0.0%
call_variants_31550474  TIMEOUT    20:05:17  99.6%     0.0%
call_variants_31550500  TIMEOUT    20:05:08  99.7%     0.0%
old_runs   ❯❯❯ reportseff --since d=4 --state Timeout --format jobid
call_variants_31550458
call_variants_31550474
call_variants_31550500

To find all lines with output: in jobs which have timed out or failed in the last 4 days:

reportseff --since 'd=4' --state TO,F --format jobid | xargs grep output:

Arguments

Jobs can be passed as arguments in the following ways:

• Job ID such as 1234567. If the id is part of an array job, only the element for that ID will be displayed. If the id is the base part of an array job, all elements in the array will be displayed.
• Array Job ID such as 1234567_89. Will display only the element specified.
• Slurm output file. Format must be BASE_%A_%a. BASE is optional as is a '.out' suffix. Unix glob expansions can also be used to filter which jobs are displayed.
• From current directory. If no argument is supplied, reportseff will attempt to find slurm output files in the current directory as described above. If a user is provided, instead reportseff will show recent jobs for that user. If only since is set, all recent jobs for all users will be shown (if allowed).
• Supplying a directory as a single argument will override the current directory to check for slurm outputs.

Options

• --color/--no-color: Force color output or not. By default, will force color output. With the no-color flag, click will strip color codes for everything besides stdout.
• --modified-sort: Instead of sorting by filename/jobid, sort by last modification time of the slurm output file.
• --debug: Write sacct result to stderr.
• --user/-u: Ignore job arguments and instead query sacct with provided user. Returns all jobs from the last week.
• --state/-s: Output only jobs with states matching one of the provided options. Accepts comma separated values of job codes (e.g. 'R') or full names (e.g. RUNNING). Case insensitive.
• --not-state/-S: Output only jobs with states not matching any of the provided options. Accepts comma separated values of job codes (e.g. 'R') or full names (e.g. RUNNING). Case insensitive.
• --format: Provide a comma separated list of columns to produce. Prefixing the argument with + adds the specified values to the defaults. Values can be any valid column name to sacct and the custom efficiency values: TimeEff, cpuEff, MemEff. Can also optionally set alignment (<, ^, >) and maximum width. Default is center-aligned with a width of the maximum column entry. For example, --format 'jobid%>,state%10,memeff%<5' produces 3 columns with:
  • JobId aligned right, width set automatically
  • State with width 10 (center aligned by default)
  • MemEff aligned left, width 5
• --slurm-format: The filename pattern passed to sbatch during job submission. Overrides the default regex for job id parsing from filenames. E.g. to match filenames like 123456.out set --slurm-format %j.out.
• --since: Limit results to those occurring after the specified time. Accepts sacct formats and a comma separated list of key/value pairs. To get jobs in the last hour and a half, can pass h=1,m=30. ---until: Limit results to those occurring before the specified time. Accepts sacct formats and a comma separated list of key/value pairs. Useful in combination with the 'since' option to query a specific range.
• --partition: Limit results to a specific partition.
• --node/-n: Display information for multi-node jobs; requires additional sacct fields from jobstats.
• --node-and-gpu/-g: Display information for multi-node jobs and GPU information; requires additional sacct fields from jobstats.
• --parsable/-p: Ignore formatting and output as a | delimited table. Useful for piping into more complex analyses.

Status, Contributions, and Support

reportseff is actively maintained but currently feature complete. If there is a function missing, please open an issue to discuss its merit!

Bug reports, pull requests, and any feedback are welcome! Prior to submitting a pull request, be sure any new features have been tested and all unit tests are passing. In the cloned repo with poetry installed:

poetry install
poetry run pytest
poetry run pre-commit install
nox

Troubleshooting

I can't install, what is pip?

pip is the package installer for python. If you get an error that pip isn't found, look for a python/anaconda/conda module. pipx ensures that each application is installed in an isolated environment. This resolves issues of dependency versions and allows applications to be run from any environment.

The output has no color with many jobs!

Click should determine if the output supports color display and react automatically in a way you expect. Check that your terminal is setup to display colors and that your pager (probably less) will display color by default. Some commands, e.g. watch aren't handled properly even when invoked to support color. Here are some useful settings for your .bashrc:

# have less display colors by default.  Will fix `reportseff` not showing colors
export LESS="-R"
# for watch aliases, include the `--color` option
watch -cn 300 reportseff --color --modified-sort
#      ^                 ^^^^^^^

You can always for display of color (or suppress it) with the --color/--no-color options

I get an error about broken pipes when chaining to other commands

Python will report that the consumer of process output has closed the stream (i.e. the pipe) while still attempting to write. Newer versions of click should suppress the warning output, but it seems to not always work. Besides some extra printing on stderr, the output is not affected.

My jobs don't have any information about multiple nodes or GPU efficiency

Because sacct doesn't currently record this information, reportseff retrieves it from a custom field from jobstats, developed at Princeton University. If you are outside a Research Computing cluster, that information will likely be absent. Node-level reporting is only shown for jobs which use multiple nodes or GPUs. If you need a list of where jobs were run, you can add --format +NodeList.

Acknowledgments

The code for calling sacct and parsing the returning information was taken from Slurmee.

Style and tooling from hypermodern python

Code review provided from a repo-review which vastly improved this readme.