Unisys ES7000 User's Guide
Important Notice: This document is under construction and may be
incomplete!! Please provide feedback to beatnic@aset.psu.edu on missing, inaccurate, or unclear
information.
User Information
This guide assumes that you already have an account on Unisys ES7000 System. If you
do not, please see the Obtaining an Account section of the Unisys ES7000 System
systems page.
- The machine name is unisys1.aset.psu.edu.
- Connections to unisys1.aset.psu.edu are only through the SSH
(Secure Shell) protocol. If you need an SSH client, please see
this page.
- There is a per-user hard disk quota of 2 GB.
- The default shell is bash, though tcsh and others are
available. See the /etc/shells file on unisys1.aset.psu.edu for
the current list.
Disk Policies
- Each user is given by default 2 GB in /home under a
directory /home/userid. Space in /home is backed up nightly.
- 3.4 TB of space is available in /scratch for shared use.
/scratch is for temporary storage only and is not backed up.
Note that files older than 30 days in /scratch will be deleted.
Logging onto Unisys ES7000 System
You must use a SSH (Secure Shell) client to log onto Unisys ES7000 System. The
following deals with the standard unix client. If you are using another
client, please refer to its own documentation.
Basic usage of ssh:
ssh -l account unisys1.aset.psu.edu
- account
- the name of your account on Unisys ES7000 System
Example:
% ssh -l
% ssh -l johndoe unisys1.aset.psu.edu
johndoe's password: John's Password
Last login: Wed Jan 12 2000 11:30:00 -0400
No mail.
John Doe will now be logged onto Unisys ES7000 System.
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For more information on ssh, please consult either its man page or URL
http://css.its.psu.edu/internet/ssh
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Copying files to and from Unisys ES7000 System
Unisys ES7000 System is not part of the AFS or DFS cells. All user code and data
must be explicitly moved to and from the Unisys ES7000 System Cluster. You can use
secure copy (scp) to copy files from your computer to Unisys ES7000 System and from
Unisys ES7000 System to your computer.
To use scp to copy files from your computer to Unisys ES7000 System:
while logged onto your computer
scp filename(s) account@unisys1.aset.psu.edu:.
- filename(s)
- file or files to copy to Unisys ES7000 System (can include wildcards)
- account
- the name of your account on Unisys ES7000 System
Example:
% scp test?.c johndoe@unisys1.aset.psu.edu:.
johndoe@unisys1.aset.psu.edu's password: John's Password
Transfering test1.c -> unisys1.aset.psu.edu:./test1.c (1k)
7 bytes transferred in 0.00 seconds [1.20 kB/sec].
Transfering test2.c -> unisys1.aset.psu.edu:./test2.c (1k)
7 bytes transferred in 0.00 seconds [1.36 kB/sec].
The files test1.c and test2.c now exist in john's home directory
(/home/johndoe) on unisys1.aset.psu.edu.
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To use scp to copy files from Unisys ES7000 System to your computer:
while logged onto your computer
scp account@unisys1.aset.psu.edu:filename(s) .
- account
- the name of your account on Unisys ES7000 System
- filename(s)
- file or files to copy from Unisys ES7000 System (can include wildcards)
Example:
% scp johndoe@unisys1.aset.psu.edu:test.dat .
johndoe@unisys1.aset.psu.edu's password: John's Password
Transfering unisys1.aset.psu.edu:test.dat -> ./test.dat (1k)
9 bytes transferred in 0.00 seconds [1.18 kB/sec].
The file test.dat now exists in the current directory of John's computer.
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For more information on scp, please consult its man page.
You can also use a program called sftp to copy files to and from
Unisys ES7000 System if you are have ssh2.
Basic usage of sftp:
while logged onto your computer
sftp unisys1.aset.psu.edu account
- account
- the name of your account on Unisys ES7000 System
Example:
% sftp unisys1.aset.psu.edu johndoe
local path : /home/john
johndoe's password: John's Password
remote path : /home/johndoe
sftp>put test.c
Transferring /home/john/test.c -> /home/johndoe/test.c (1k)
sftp>get test.dat
Transferring /home/johndoe/test.dat -> /home/john/test.dat (1k)
sftp>quit
The file test.c has been copied from John's home directory on his
machine to his home directory on Unisys ES7000 System and the file test.dat has
been copied from Unisys ES7000 System to his machine.
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For more information on sftp, please consult its man page.
How to Compile your Code on Unisys ES7000 System
There is only one available compiler on the Unisys ES7000 System, the Intel
Compilers (C/C++/F77/F90/F95)
Information on this compiler can be found in the
Compilers and Programming Tools
web pages.
Compiling MPI Applications
Unisys ES7000 System has a high-speed network called Myrinet to run MPI applications
over. Information on how to do this can be found in the MPIGM
software page.
Running Jobs on Unisys ES7000 System
All jobs on Unisys ES7000 System are run through a batch queueing system called PBS.
There are two steps in submitting a job to run through PBS:
- Create a job script specifying what resources you need and what
commands you would like to be executed. This file is similar to a
shell script.
- Submit the job script to PBS. PBS will run your job when the
requested resources become available.
Creating a job script
A job script is divided into two sections: the PBS directives and the
body. Lines starting with #PBS are PBS directives. All other lines
starting with # are comments. Lines not starting with # are part of the
body and will function the same way they would if they were in a shell
script. #PBS directives specify the resources the program(s) you intend
to run will need. These resources should not exceed the queue limits.
The body of the script actually specifies how to run the program(s). It
is recommended that you use the below script as a starting point for
your script.
Queues and queue limits
The default, public queue has a 48 hour walltime limit. Special purpose queues
are available upon request.
PBS script directives
There are three script directives that you should be concerned with.
- #PBS -l nodes=x:ppn=y. The '-l nodes' directive is how you
request your nodes and processors. 'x' is the number of nodes that
you would like to use and 'y' is the number of processors that you
wish to use on each node. There are currently available 2 nodes and
the number of processors on all nodes is 16.
- #PBS -l walltime=hh:mm:ss. The '-l walltime' directive is how
you request the walltime for your job. See the queue descriptions
for the limits. The better that you estimate your runtime, the
better your job will run. Short jobs are favored over long jobs.
- #PBS -j oe. The '-j oe' option tells PBS to put STDOUT and
STDERR into the same file.
A sample PBS script
Example:
# This is a sample PBS script. It will request 1 processor on 1 node
# for 4 hours.
#
# Request 1 processors on 1 node
#
#PBS -l nodes=1:ppn=1
#
# Request 4 hours of walltime
#
#PBS -l walltime=4:00:00
#
# Request that regular output and terminal output go to the same file
#
#PBS -j oe
#
# The following is the body of the script. By default,
# PBS scripts execute in your home directory, not the
# directory from which they were submitted. The following
# line places you in the directory from which the job
# was submitted.
#
cd $PBS_O_WORKDIR
#
# Now we want to run the program "hello". "hello" is in
# the directory that this script is being submitted from,
# $PBS_O_WORKDIR.
#
echo " "
echo " "
echo "Job started on `hostname` at `date`"
./hello
echo " "
echo "Job Ended at `date`"
echo " "
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Note that the above example script is for a non-MPI job. Information on
how to write PBS scripts for MPI jobs can be found in the software pages
for each MPI (see the links in the "Compliling MPI Applications" section
above).
Submitting a job script to PBS:
Use qsub to submit a PBS job.
Basic syntax of qsub:
qsub script
- script
- the job script
Example:
% qsub myjob
95.unisys1.aset.psu.edu
The job script *myjob* has just been submitted to PBS and has been
assigned the Job ID *95.unisys1.aset.psu.edu*. This Job ID can later be
used to control your job.
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Checking Job Status
qstat [flags]
i.e., qstat -s (displays status and elapsed time of job)
Example: qstat -s
unisys1.aset.psu.edu:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
28.unisys1.aset. nucci unisys1 submit.cmd 16743 16 -- -- 01:10 R 00:00
Job started on Fri Aug 20 at 09:37
29.unisys1.aset. nucci unisys1 submit.cmd 16784 16 -- -- 01:10 R 00:00
Job started on Fri Aug 20 at 09:38
30.unisys1.aset. nucci unisys1 submit.cmd -- 32 -- -- 01:10 Q --
Not Running: Not enough of the right type of nodes are available
Where:
- Job ID: ID of users' job in queue
- Username: job owner
- Queue: Job queue on cluster job submitted to
- Jobname: name of script submitted to PBS or STDIN if user is in
an interactive session
- NDS: number of nodes allocated
- Req'd Memory User requested memory
- Req'd Time: maximum wall clock run time
- S (State): R - Running; Q - Waiting in queue; E - Job is in
error state
- Elap Time: job's current elapsed time
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Deleting a Job from the Queue
qdel (job_id)
where job_id can be obtained from the queue listing using qstat.
Output and Error files
Unless over-ridden by options to PBS to control file output, the
standard error and output are written to two files with the names that
are of the form:
Jobname.eJob_ID
Jobname.oJob_ID
where the Jobname and Job_ID are from your job as they are listed in the
queue.
For more PBS Information
For more information on creating and submitting job scripts, consult
qsub's man page.
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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