Introduction to HPC Systems

Presented by Galen Arnold
The page shows your list of possible hosts under My Teragrid -> Accounts.

Security starts with you. We recommend using a password management package such as Keepass

Example ssh sessions from a local site system to various TeraGrid login hosts:
[arnoldg@co-login ~]$ myproxy-logon -s
Enter MyProxy pass phrase:
A credential has been received for user arnoldg in /tmp/x509up_u25114.
[arnoldg@co-login ~]$ ssh hostname
[arnoldg@co-login ~]$ ssh hostname
[arnoldg@co-login ~]$ ssh hostname
[arnoldg@co-login ~]$ ssh hostname

[arnoldg@co-login ~]$ ssh hostname
[arnoldg@co-login ~]$
Consult local site documentation for details about:
  • compiling code
  • batch system
  • filesystem policies
  • technical specifications for the system
Ranger User Guide
Lonestar User Guide
Kraken User Guide
The Big Red Cluster
Queen Bee User Guide
Purdue Steele User Guide
PSC resources
NCAR Bluefire User Guide

Batch system specifics

Loni, Queenbee
#LONI queues
#1.Use the queue named: workq
#PBS ?q workq
#2.Use no more than 4 nodes, always use 8 processes per node. Yields 32 cores per job:
#PBS -l nodes=4:ppn=8
#3.Use no more than 1hr of wall clock time per job request.
#PBS ?l wallclock=1:0:0
IU, Bigred
#@ class = NORMAL
#@ account_no = TG-TRA900337N
Purdue, Steele
#PBS -q standby
#PBS -A TG-TRA100001S
#PBS -l wallclock=00:15:00
Tacc, Lonestar or Ranger
qsub -q development
#PBS -q debug


[arnoldg@co-login ~]$ ssh "tg-policy -data"

Site Data Policy:

The TACC HPC platforms have several different file systems with distinct storage
characteristics. There are predefined, user-owned directories in these file
systems for users to store their data. Of course, these file systems are shared
with other users, so they are managed by either a quota limit, a purge policy
(time-residency) limit, or a migration policy.

Home directory
The system automatically changes to a user's home directory at login and this
is the recommend location to store your source codes and build your executables.
$HOME are quota limited. Use to quota command to determine your quota.
Use $HOME to reference your home directory in scripts.
Use cd to change to $HOME.

Work directory
Store large files and perform most of your job runs from this file system.
This file system is accessible from all the nodes.
Work files are subject to a 7 day purge policy.
Use $WORK to reference your work directory in scripts.
Use cdw to change to $WORK.

Scratch or Temporary directory
Directory on each node where you can store files and perform local I/O for

the duration of a batch job. Often, in batch jobs it is more efficient to use
and store files directly on $WORK (to avoid moving files from scratch at the end
of a job). Available for the duration of a job.
Use $SCRATCH to reference a temporary directory in scripts.

San directory
The SAN directory is available on login nodes (front-ends) of Lonestar
(and Longhorn). Space on the SAN is an allocatable resource; that is,
space is not automatically allocated to a project, the Principal Investigator
must request space on this file system.

Archive directory
Store permanent files here. This file system has "archive" characteristics
(See TACC Lonestar User Guide.) The access speed is low relative to the work
Use $ARCHIVE to reference your archive directory in scripts.
Use cda to change to $ARCHIVE.

Home directories are backed up daily for protection agains catastrophic events.
Daily management of data files therefore is the user's responsibility.
Scratch areas and parallel filesystems are not backed up and data storage for
any length of time beyond the purge period is not guaranteed.

[arnoldg@co-login ~]$

Moving Data

File Transfer Performance Example ?( from )

Transferring files can take a significant time, even when done with optimal tuning. We provide the following examples to compare and demonstrate transfer performance using the methods we have discussed.

Comparing Transfer Methods between TeraGrid Resources

This example compares the performance of using various methods to transfer a 4GB file between Cobalt at NCSA and Ranger at TACC.

First, let's take a look at performance with no tuning using SCP:
$ time scp test.tar 100% 4124MB 8.3MB/s 08:19
452.052u 20.476s 8:20.72 94.3% 0+0k 0+0io 39pf+0w
From the output we see that it took approximately eight minutes to transfer 4GBs. That is not impressive performance so let's see if Grid-FTP capable tools can improve on that. In our examples, we use `pwd`, a Unix idiom that expands the current directory in place, with the source URLs. It's a convenient shorthand to use with commands that require full pathnames.

First, we obtain a certificate proxy because uberftp and globus-url-copy require proxy authentication.
$ myproxy-logon -s myproxy
Enter MyProxy pass phrase: XXXXXXXXXXXXXXXX
A credential has been received for user arnoldg in /tmp/x509up_u25114.
$ grid-proxy-info
subject : /C=US/O=National Center for Supercomputing Applications/CN=Galen Arnold
issuer : /C=US/O=National Center for Supercomputing Applications/OU=Certificate Authorities/CN=MyProxy
identity : /C=US/O=National Center for Supercomputing Applications/CN=Galen Arnold
type : end entity credential
strength : 1024 bits
path : /tmp/x509up_u25114
timeleft : 11:59:26
Now that we have our certificate proxy we'll try uberftp without any tuning options for a baseline:
$ time uberftp \
gsi`pwd`/test.tar \
21.020u 45.372s 1:07.85 97.8% 0+0k 0+0io 0pf+0w
The transfer time dropped from eight minutes to a little over one minute, so there's good reason to use something other than scp for large files or tar bundles.

Next we add some tuning options to uberftp for parallel striping and tcp buffer size which yields:
$ time uberftp -parallel 8 -tcpbuf 8000000
gsi`pwd`/test.tar \
15.080u 26.940s 0:43.60 96.3% 0+0k 0+0io 7pf+0w
The transfer time of about 44 seconds is more than an order of magnitude improvement over the time required to scp the file. If the data to be moved were hundreds of gigabytes or a few terabytes, selecting the proper transfer method could make the difference between minutes and hours or days.

Debugging Table (NCSA clusters)