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-<!--#include virtual="header.txt"-->
-<!-- Copyright (C) 2013 Bull S. A. S.
- Bull, Rue Jean Jaures, B.P.68, 78340, Les Clayes-sous-Bois. -->
-
-<h1>Profiling Using HDF5 User Guide</h1>
-
-<h2>Contents</h2>
-<a href="#Overview">Overview</a><br>
-<a href="#Administration">Administration</a><br>
-<a href="#Profiling">Profiling Jobs</a><br>
-<a href="#HDF5">HDF5</a><br>
-<a href="#DataSeries">Data Series</a><br>
-
-
-
-<a id="Overview"></a>
-<h2>Overview</h2>
-The AcctGatherProfileType/hdf5 plugin allows SLURM to coordinate collecting
-data on jobs it runs on a cluster that is more detailed than is practical to
-include in its database. The data comes from periodically sampling various
-performance data either collected by SLURM, the operating system, or
-component software. The plugin will record the data from each source
-as a <b>Time Series</b> and also accumulate totals for each statistic for
-the job.
-
-<p>Time Series are energy data collected by an AcctGatherEnergy plugin,
-I/O data from a network interface collected by an AcctGatherInfiniband plugin,
-I/O data from parallel file systems such as Lustre,
-and task performance data such as local disk I/O, cpu consumption,
-and memory us, as well as potential data from other sources.
-
-<p>The data is collected into a file on a shared file system for each step on
-each allocated node of a job and then merged into a HDF5 file.
-Individual files on a shared file system was chosen because it is possible
-that the data is voluminous so solutions that pass data to the SLURM control
-daemon via RPC may not scale to very large clusters or jobs with
-many allocated nodes.
-
-<p>A seperate <a href="acct_gather_profile_plugins.html">
-SLURM Profile Accounting Plugin API (AcctGatherProfileType)</a> documents how
-write other Profile Accounting plugins.
-
-<a id="Administration"></a>
-<h2>Administration</h2>
-
-<h3>Shared File System</h3>
-<div style="margin-left: 20px;">
-The HDF5 Profile Plugin requires a common shared file system on all the compute
-nodes. While a job is running, the plugin writes a file into this file
-system for each step of the job on each node. When the job ends,
-the merge process is launched and the node-step files are combined into one
-hdf5 file for the job.
-<p>
-The root of the directory structure is declared in the <b>ProfileHDF5Dir</b>
-option in the acct_gather.conf file. The directory will be created by slurm
-if it doesn't exist.
-<p>
-Each user that creates a profile will have a subdirector to the profile
-directory that has read/write permission only for the user.
-</span>
-</div>
-<h3>Configuration parameters</h3>
-
-<div style="margin-left: 20px;">
-The profile plugin is enabled in the
-<a href="slurm.conf.html">slurm.conf</a> file, but is internally
-configured in the
-<a href="acct_gather.conf.html">acct_gather.conf</a> file.
-</div>
-<div style="margin-left: 20px;">
-<h4>slurm.conf parameters</h4>
-<div style="margin-left: 20px;">
-This line the slum.conf enables the HDF5 Profile Plugin.
-<br><b>AcctGatherProfileType=acct_gather_profile/hdf5</b>
-</div>
-</div>
-<div style="margin-left: 20px;">
-<h4>act_gather.conf parameters</h4>
-<div style="margin-left: 20px;">
-There are parameters directly used by the HDF5 Profile Plugin.
-<dl>
-<dt><B>ProfileHDF5Dir</B>=<path></dt>
-<dd>This parameter is the path to the shared folder into which the
-acct_gather_profile plugin will write detailed data as an HDF5 file.
-The directory is assumed to be on a file system shared by the controller and
-all compute nodes. This is a required parameter.
-<dt><B>ProfileHDF5CollectDefault</B>=opt{,opt{,opt}}</dt>
-<dd>Default <b>--Profile</b value> for data types collected for each job
-submission. It ia a comma separated list of data streams.
-Use this option with caution. A node-step file will be created for on every
-node of every step for every job. They will not automatically be merged
-into job files. (Even job files for small jobs would fill the fill the
-file system.) This option is intended for test environments where you
-might want to profile a series of jobs but do not want to have to
-add the --profile option to the launch scripts.</dd>
-</dl>
-</div>
-</div>
-
-
-<div style="margin-left: 20px;">
-<h4>Time Series Control Paramters</h4>
-<div style="margin-left: 20px;">
-Other plugins add time series data to the HDF5 collection. They typically
-have a polling frequency specified in one of the above configuration files.
-<p>
-The following table summarized parameters that control sample frequency.
-<p>
-<table border="1" style="margin-left: 20; padding: 5
-px;" >
-<tr><th>Conf file</th><th>Parameter</th><th>Time Series</th></tr>
-<tr><td>slurm.conf</td><td>JobAcctGatherFrequency</td><td>Task, Lustre</td></tr>
-<tr><td>acct_gather.conf</td><td>EnergyIPMIFrequency</td><td>Energy</td></tr>
-<tr><td>acct_gather.conf</td><td>InfinibandOFEDFrequency</td>
-<td>Network</td></tr>
-</table>
-</div>
-</div>
-<a id="Profiling"></a>
-<h2>Profiling Jobs</h2>
-<h3>Data Collection</h3>
-The --profile option on salloc|sbatch|srun controls whether if data is
-collected and what type of data is collected. If --profile is not specified
-the default is no data collected (unless the <B>ProfileHDF5CollectDefault</B>
-option is used in acct_gather.conf. --profile on the command line overrides
-any value specified in the configuration file.)<p>
-
-<DT><B>--profile</B>=<all|none|[energy[,|task[,|lustre[,|network]]]]>
-<DD>
-enables detailed data collection by the acct_gather_profile plugin.
-Detailed data are typically time-series that are stored in an HDF5 file for
-the job.</DD>
-</DT>
-<P>
-<div style="margin-left: 20px;">
-<DL>
-<DT><B>All</B>
-<DD>All data types are collected. (Cannot be combined with other values.)
-</DD></DT>
-<P>
-<DT><B>None</B>
-<DD>No data types are collected. This is the default.
-<BR> (Cannot be combined with other values.)
-</DD></DT>
-
-<DT><B>Energy</B>
-<DD>Energy data is collected.</DD></DT>
-
-<DT><B>Task</B>
-<DD>Task (I/O, Memory, ...) data is collected.</DD></DT>
-
-<DT><B>Lustre</B>
-<DD>Lustre data is collected.</DD></DT>
-
-<DT><B>Network</B>
-<DD>Network (InfiniBand) data is collected.</DD></DT>
-
-</DL>
-</div>
-
-<h3>Data Consolidation</h3>
-The node-step files are merged into one HDF5 file for the job using the
-<a href="sh5util.html">sh5util</a>.
-
-<p>The command line may added to the normal launch script, if the job is
-started with sbatch. For example;
-<pre>
-sbatch -n1 -d$last_job_id --wrap="sh5util --profile=none -j $last_job_id"
-</pre>
-Note that --profile=none is required if the enclosing sbatch command included
-a --profile parameter.
-
-<h3>Data Extraction</h3>
-The <a href="sh5util.html">sh5util</a> program can also be used to extract
-specific data from the hdf5 file an write it in <i>comma separated value</i>
-for importation into other analysis tools such as spreadsheets.
-
-<a id="HDF5"></a>
-<h2>HDF5</h2>
-HDF5 is a well known structured data set that allows heterogeneous data but
-related data to be stored in one file.
-(.i.e. sections for energy statistics, sections for network I/O,
-sections for Task data, …)
-Its internal structure resembles a
-file system with <b>groups</b> being similar to <i>directories</i> and
-<b>data sets</b> being similar to <i>files</i>. It also allows <b>attributes</b>
-to be attached to groups to store application defined properties.
-
-<p>There are commodity programs, notably
-<a href="http://www.hdfgroup.org/hdf-java-html/hdfview/index.html">
-HDFView</a> for viewing and manipulating these files.
-
-<p>Below is a screen shot from HDFView expanding the job tree and showing the
-attributes for a specific task.
-<p>
-<img src="hdf5_task_attr.png" width="275" height="275" >
-
-
-<a id="DataSeries"></a>
-<h2>Data Structure</h2>
-
-<table>
-<tr>
-<td><img src="hdf5_job_outline.png" width="205" height="570"></td>
-<td style="vertical-align: top;">
-<div style="margin-left: 5px;">
-In the job file, there will be a group for each <b>step</b> of the job.
-Within each step, there will be a group for nodes, and a group for tasks.
-</div>
-<ul>
-<li>
-The <b>nodes</b> group will have a group for each node in the step allocation.
-For each node group, there is a sub-group for Time Series and another
-for Totals.
-<ul>
-<li>
-The <b>Time Series</b> group
-contains a group/dataset containing the time series for each collector.
-</li>
-<li>
-The <b>Totals</b> group contains a corresponding group/dataset that has the
-Minimum, Average, Maximum, and Sum Total for each item in the time series.
-</li>
-</ul>
-<li>
-The <b>Tasks</b> group will only contain a subgroup for each task.
-It primarily contains an attribute stating the node on which the task was
-executed. This set of groups is essentially a cross reference table.
-</li>
-</ul>
-</td></tr>
-</table>
-
-<h3>Energy Data</h3>
-<b>AcctGatherEnergyType=acct_gather_energy/ipmi</b>
-is required in slurm.conf to collect energy data.
-Also appropriately set
-<b>EnergyIPMIFrequency</b>
-in acct_gather.conv
-<DL>
-<DT><B>Date Time</B>
-<DD>Time of day at which the data sample was taken. This can be used to
-correlate activity with other sources such as logs.</DD></DT>
-<DT><B>Time</B>
-<DD>Elapsed time since the begining of the step.</DD></DT>
-<DT><B>Power</B>
-<DD>Power consumption during the interval.</DD></DT>
-<DT><B>CPU Frequency</B>
-<DD>CPU Frequency at time of sample in kilohertz.</DD></DT>
-</DL>
-
-<h3>Infiniband Data</h3>
-<b>JobAcctInfinibandType=acct_gather_infiniband/ofed</b>
-is required in slurm.conf to collect task data.
-Also appropriately set
-<b>InfinibandOFEDFrequency</b>
-in acct_gather.conf
-Each data sample in the Lustre Time Series contains the following data items.
-<DL>
-<DT><B>Date Time</B>
-<DD>Time of day at which the data sample was taken. This can be used to
-correlate activity with other sources such as logs.</DD></DT>
-<DT><B>Time</B>
-<DD>Elapsed time since the begining of the step.</DD></DT>
-<DT><B>Packets In</B>
-<DD>Number of packets coming in.</DD></DT>
-<DT><B>Megabytes Read</B>
-<DD>Number of megabytes coming in through the interface.</DD></DT>
-<DT><B>Packets Out</B>
-<DD>Number of packets going out.</DD></DT>
-<DT><B>Megabytes Write</B>
-<DD>Number of megabytes going out through the interface.</DD></DT>
-</DL>
-
-<h3>Luster Data</h3>
-<b>JobAcctGatherType=jobacct_gather/linux</b>
-is required in slurm.conf to collect task data.
-Also appropriately set
-<b>JobAcctGatherFrequency</b>
-in slurm.conf
-<p>
-Each data sample in the Lustre Time Series contains the following data items.
-<DL>
-<DT><B>Date Time</B>
-<DD>Time of day at which the data sample was taken. This can be used to
-correlate activity with other sources such as logs.</DD></DT>
-<DT><B>Time</B>
-<DD>Elapsed time since the begining of the step.</DD></DT>
-<DT><B>Reads</B>
-<DD>Number of read operations.</DD></DT>
-<DT><B>Megabytes Read</B>
-<DD>Number of megabytes read.</DD></DT>
-<DT><B>Writes</B>
-<DD>Number of write operations.</DD></DT>
-<DT><B>Megabytes Write</B>
-<DD>Number of megabytes written.</DD></DT>
-</DL>
-
-<h3>Task Data</h3>
-<b>JobAcctGatherType=jobacct_gather/linux</b>
-is required in slurm.conf to collect task data.
-Also appropriately set
-<b>JobAcctGatherFrequency</b>
-in slurm.conf
-<DL>
-<DT><B>Date Time</B>
-<DD>Time of day at which the data sample was taken. This can be used to
-correlate activity with other sources such as logs.</DD></DT>
-<DT><B>Time</B>
-<DD>Elapsed time since the begining of the step.</DD></DT>
-<DT><B>CPU Frequency</B>
-<DD>CPU Frequency at time of sample.</DD></DT>
-<DT><B>CPU Time</B>
-<DD>Seconds of CPU time used during the sample.</DD></DT>
-<DT><B>CPU Utilization</B>
-<DD>CPU Utilization during the interval.</DD></DT>
-
-
-<DT><B>RSS</B>
-<DD>Value of RSS at time of sample.</DD></DT>
-<DT><B>VM Size</B>
-<DD>Value of VM Size at time of sample.</DD></DT>
-<DT><B>Pages</B>
-<DD>Pages used in sample.</DD></DT>
-<DT><B>Read Megabytes</B>
-<DD>Number of megabytes read from local disk.</DD></DT>
-<DT><B>Write Megabytes</B>
-<DD>Number of megabytes written to local disk.</DD></DT>
-</DL>
-
-
-<p class="footer"><a href="#top">top</a></p>
-
-<p style="text-align:center;">Last modified 17 May 2013</p>
-
-<!--#include virtual="footer.txt"-->