| title | teaching | exercises | questions | objectives | keypoints | |||||
|---|---|---|---|---|---|---|---|---|---|---|
Using resources effectively |
10 |
30 |
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We've touched on all the skills you need to interact with an HPC cluster: logging in over SSH, loading software modules, submitting parallel jobs, and finding the output. Let's learn about estimating resource usage and why it might matter.
Although we covered requesting resources from the scheduler earlier with the π code, how do we know what type of resources the software will need in the first place, and its demand for each? In general, unless the software documentation or user testimonials provide some idea, we won't know how much memory or compute time a program will need.
Most HPC facilities maintain documentation as a wiki, a website, or a document sent along when you register for an account. Take a look at these resources, and search for the software you plan to use: somebody might have written up guidance for getting the most out of it. {: .callout}
A convenient way of figuring out the resources required for a job to run
successfully is to submit a test job, and then ask the scheduler about its
impact using {{ site.sched.hist }}. You can use this knowledge to set up the
next job with a closer estimate of its load on the system. A good general rule
is to ask the scheduler for 20% to 30% more time and memory than you expect the
job to need. This ensures that minor fluctuations in run time or memory use
will not result in your job being cancelled by the scheduler. Keep in mind that
if you ask for too much, your job may not run even though enough resources are
available, because the scheduler will be waiting for other people's jobs to
finish and free up the resources needed to match what you asked for.
Since we already submitted pi.py to run on the cluster, we can query the
scheduler to see how long our job took and what resources were used. We will
use {{ site.sched.hist }} to get statistics about parallel-pi.sh.
{{ site.remote.prompt }} {{ site.sched.hist }}
{: .language-bash}
{% include {{ site.snippets }}/resources/account-history.snip %}
This shows all the jobs we ran recently (note that there are multiple entries per job). To get info about a specific job, we change command slightly.
{{ site.remote.prompt }} {{ site.sched.hist }} {{ site.sched.flag.histdetail }} 6008388
{: .language-bash}
It will show a lot of info, in fact, every single piece of info collected on
your job by the scheduler. It may be useful to redirect this information to
less to make it easier to view (use the left and right arrow keys to scroll
through fields).
{{ site.remote.prompt }} {{ site.sched.hist }} {{ site.sched.flag.histdetail }} 6008388 | less
{: .language-bash}
Some interesting fields include the following:
- Hostname: Where did your job run?
- MaxRSS: What was the maximum amount of memory used?
- Elapsed: How long did the job take?
- State: What is the job currently doing/what happened to it?
- MaxDiskRead: Amount of data read from disk.
- MaxDiskWrite: Amount of data written to disk.
Typically, clusters allow users to connect directly to compute nodes from the head node. This is useful to check on a running job and see how it's doing, but is not a recommended practice in general, because it bypasses the resource manager. To reduce the risk of interfering with other users, some clusters will only allow you to connect to nodes on which you have running jobs. Let's practice by taking a look at what's running on the login node right now.
The most reliable way to check current system stats is with top. Some sample
output might look like the following (type q to exit top):
{{ site.remote.prompt }} top
{: .language-bash}
{% include {{ site.snippets }}/resources/monitor-processes-top.snip %}
Overview of the most important fields:
PID: What is the numerical id of each process?USER: Who started the process?RES: What is the amount of memory currently being used by a process (in bytes)?%CPU: How much of a CPU is each process using? Values higher than 100 percent indicate that a process is running in parallel.%MEM: What percent of system memory is a process using?TIME+: How much CPU time has a process used so far? Processes using 2 CPUs accumulate time at twice the normal rate.COMMAND: What command was used to launch a process?
htop provides an overlay for top using curses, producing a
better-organized and "prettier" dashboard in your terminal. Unfortunately, it
is not always available. If this is the case, ask your system administrators to
install it for you. Don't be shy, they're here to help!
{{ site.remote.prompt }} htop
{: .language-bash}
To show all processes from your current session, type ps.
{{ site.remote.prompt }} ps
{: .language-bash}
PID TTY TIME CMD
15113 pts/5 00:00:00 bash
15218 pts/5 00:00:00 ps
{: .output}
Note that this will only show processes from our current session. To show all
processes you own (regardless of whether they are part of your current session
or not), you can use ps ux.
{{ site.remote.prompt }} ps ux
{: .language-bash}
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
{{ site.remote.user }} 67780 0.0 0.0 149140 1724 pts/81 R+ 13:51 0:00 ps ux
{{ site.remote.user }} 73083 0.0 0.0 142392 2136 ? S 12:50 0:00 sshd: {{ site.remote.user }}@pts/81
{{ site.remote.user }} 73087 0.0 0.0 114636 3312 pts/81 Ss 12:50 0:00 -bash
{: .output}
This is useful for identifying which processes are doing what.
{% include links.md %}