sh5util - Man Page

Tool for merging HDF5 files from the acct_gather_profile plugin that gathers detailed data for jobs running under Slurm

Synopsis

sh5util

Description

sh5util merges HDF5 files produced on each node for each step of a job into one HDF5 file for the job. The resulting file can be viewed and manipulated by common HDF5 tools such as HDF5View, h5dump, h5edit, or h5ls.

sh5util also has two extract modes. The first, writes a limited set of data for specific nodes, steps, and data series in "comma separated value" form to a file which can be imported into other analysis tools such as spreadsheets.

The second, (Item-Extract) extracts one data time from one time series for all the samples on all the nodes from a jobs HDF5 profile.

- Finds sample with maximum value of the item.

- Write CSV file with min, ave, max, and item totals for each node for each sample

Options

-L,  --list

Print the items of a series contained in a job file.

List mode options
-i, --input=path

Merged file to extract from (default ./job_$jobid.h5)

-s, --series=[Energy | Filesystem | Network | Task]

-E,  --extract

Extract data series from a merged job file.

Extract mode options
-i, --input=path

merged file to extract from (default ./job_$jobid.h5)

-N, --node=nodename

Node name to extract (default is all)

-l, --level=[Node:Totals | Node:TimeSeries]

Level to which series is attached. (default Node:Totals)

-s, --series=[Energy | Filesystem | Network | Task | Task_#]

Task is all tasks, Task_# (# is a task id) (default is everything)

-I,  --item-extract

Extract one data item from all samples of one data series from all nodes in a merged job file.

Item-Extract mode options
-s, --series=[Energy | Filesystem | Network | Task]
-d, --data

Name of data item in series (See note below).

-j,  --jobs=<job(.step)>

Format is <job(.step)>. Merge this job/step (or a comma-separated list of job steps). This option is required. Not specifying a step will result in all steps found to be processed.

-h,  --help

Print this description of use.

-o,  --output=path
Path to a file into which to write.
Default for merge is ./job_$jobid.h5
Default for extract is ./extract_$jobid.csv
-p,  --profiledir=dir

Directory location where node-step files exist default is set in acct_gather.conf.

-S,  --savefiles

Instead of removing node-step files after merging them into the job file, keep them around.

--user=user

User who profiled job. (Handy for root user, defaults to user running this command.)

--usage

Display brief usage message.

Data Items per Series

Energy
Power
CPU_Frequency
Filesystem
Reads
Megabytes_Read
Writes
Megabytes_Write
Network
Packets_In
Megabytes_In
Packets_Out
Megabytes_Out
Task
CPU_Frequency
CPU_Time
CPU_Utilization
RSS
VM_Size
Pages
Read_Megabytes
Write_Megabytes

Performance

Executing sh5util sends a remote procedure call to slurmctld. If enough calls from sh5util or other Slurm client commands that send remote procedure calls to the slurmctld daemon come in at once, it can result in a degradation of performance of the slurmctld daemon, possibly resulting in a denial of service.

Do not run sh5util or other Slurm client commands that send remote procedure calls to slurmctld from loops in shell scripts or other programs. Ensure that programs limit calls to sh5util to the minimum necessary for the information you are trying to gather.

Examples

Merge node-step files (as part of a sbatch script):
$ sbatch -n1 -d$SLURM_JOB_ID --wrap="sh5util --savefiles -j $SLURM_JOB_ID"
Extract all task data from a node:
$ sh5util -j 42 -N snowflake01 --level=Node:TimeSeries --series=Tasks
Extract all energy data:
$ sh5util -j 42 --series=Energy --data=power

Copying

Copyright (C) 2013 Bull.
Copyright (C) 2013 SchedMD LLC. Slurm is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Slurm is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

See Also

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February 2021 Slurm Commands