Difference between revisions of "Applications/SAS"

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* Module names: SAS/9.4
 
* Module names: SAS/9.4
 
* License: Departmental research only multi-platform license, restricted to Accounting and Finance department
 
* License: Departmental research only multi-platform license, restricted to Accounting and Finance department
* Forum support: https://www.hpc.hull.ac.uk/forum/viewforum.php?f=22
 
* Further information: http://www.sas.com/en_gb/home.html
 
 
  
 
== Usage Examples ==
 
== Usage Examples ==
 +
=== Executables ===
 +
{| class="wikitable" style="background-color:#f5f5dc;"
 +
! Executable
 +
! Description
 +
|-
 +
| sas_en
 +
| The main SAS executable is sas_en. Depending on the options provided, this will either start SAS with the full graphical user interface, start SAS in interactive line mode, or allow you to run SAS in batch mode.
 +
|}
  
 
=== Interactive ===
 
=== Interactive ===
 
+
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
<pre style="background-color: #C8C8C8; color: black; border: 2px solid black; font-family: monospace, sans-serif;">
 
 
[username@login01 ~]$ interactive
 
[username@login01 ~]$ interactive
 
salloc: Granted job allocation 289669
 
salloc: Granted job allocation 289669
Line 22: Line 26:
  
 
To use the full SAS GUI, make sure you have your environment setup as detailed in LINK and run '''sas_en''':  
 
To use the full SAS GUI, make sure you have your environment setup as detailed in LINK and run '''sas_en''':  
<pre style="background-color: #C8C8C8; color: black; border: 2px solid black; font-family: monospace, sans-serif;">
+
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 
[username@c170 ~]$ sas_en
 
[username@c170 ~]$ sas_en
 
</pre>
 
</pre>
 +
This will open up a number of SAS windows, including Program Editor, Results, Explorer, Session Manager, Toolbox, Output and Log:
 +
[[File:SASGUI.png]]
  
 
To use the command line interactive line mode and not the GUI, run '''sas_en –nodms''':  
 
To use the command line interactive line mode and not the GUI, run '''sas_en –nodms''':  
<pre style="background-color: #C8C8C8; color: black; border: 2px solid black; font-family: monospace, sans-serif;">
+
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 
[username@c170 ~]$ sas_en –nodms
 
[username@c170 ~]$ sas_en –nodms
 
</pre>
 
</pre>
  
 
Some functions invoke a SAS window even in interactive line mode, for full line mode use '''–noterminal''' flag, i.e.:
 
Some functions invoke a SAS window even in interactive line mode, for full line mode use '''–noterminal''' flag, i.e.:
<pre style="background-color: #C8C8C8; color: black; border: 2px solid black; font-family: monospace, sans-serif;">
+
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 
[username@c170 ~]$ sas_en -nodms –noterminal
 
[username@c170 ~]$ sas_en -nodms –noterminal
 
</pre>
 
</pre>
  
 
You can then run your task using a SAS script with the following command:
 
You can then run your task using a SAS script with the following command:
<pre style="background-color: #C8C8C8; color: black; border: 2px solid black; font-family: monospace, sans-serif;">
+
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 
[username@c170 ~]$ sas_en -noteminal sas_file.sas
 
[username@c170 ~]$ sas_en -noteminal sas_file.sas
 
</pre>
 
</pre>
 
  
 
=== Batch Submission ===
 
=== Batch Submission ===
 
A better approach is to submit tasks to run automatically without any interaction. To do this, you need a job submission script, an example of which is:
 
A better approach is to submit tasks to run automatically without any interaction. To do this, you need a job submission script, an example of which is:
  
<pre style="background-color: #C8C8C8; color: black; border: 2px solid blue; font-family: monospace, sans-serif;">
+
<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
 
#!/bin/bash
 
#!/bin/bash
#SBATCH -J SASjob
+
#SBATCH -J SASjob           # Job name, you can change it to whatever you want
#SBATCH -N 1
+
#SBATCH -N 1               # Number of nodes (for SAS should be always one)
#SBATCH -n 1
+
#SBATCH -n 1               # Number of cores (for SAS should generally be one, see tuning)
#SBATCH -o %N-%j.log
+
#SBATCH -o %N-%j.log       # Standard output will be written here
#SBATCH -e %N-%j.err
+
#SBATCH -e %N-%j.err       # Standard error will be written here
#SBATCH -p compute
+
#SBATCH -p compute         # Slurm partition, where you want the job to be queued
#SBATCH --mem=10G
 
 
   
 
   
 
module add test-modules SAS/9.4
 
module add test-modules SAS/9.4
 
   
 
   
sas_en -memsize 10G -cpucount 1 -nothreads -noterminal my_sas_script.sas
+
sas_en -cpucount 1 -nothreads -noterminal my_sas_script.sas
 
</pre>  
 
</pre>  
 
   
 
   
Details:<br/>
+
'''Note:''' that the –cpucount in the sas_en command should match the #SBATCH -n number. Change the last .sas filename as appropriate<br />
Line 1 - just a standard line that needs to be at the top of the file<br />
 
Line 2 - the -J sets the name of the job, in this case to SASjob. This doesn’t impact on the job and doesn’t have to be unique. It helps distinguish tasks when looking in squeue (LINK) <br/>
 
Line 3 - this requests you are allocated 1 compute node. SAS should only be run on 1 node<br />
 
Line 4 - this requests one slot on the node. As you have some tasks that make use of functions which I believe may benefit from parallel computation, we may change this (and other settings) at a later date. For now leave as 1<br />
 
Line 5 and 6 - these set the output and error files. The log file will contain SAS console output, the error file will contain information that may be useful if things don’t work as expected (at a cluster level)<br />
 
Line 7 - this requests the job runs on one of the compute nodes on the compute queue. <br />
 
Line 8 - this requests 10GB of RAM be made available for the task. This can be changed as necessary for the task<br />
 
Line 9 - this provides access to the SAS software module<br />
 
Line 10 - this is the run command. Note that the –memsize size should match that requested in line 8, while –cpucount should match line 4. Change the last .sas filename as appropriate<br />
 
  
 
This submission script can be found at /path/to/sample/script
 
This submission script can be found at /path/to/sample/script
  
<pre style="background-color: #C8C8C8; color: black; border: 2px solid black; font-family: monospace, sans-serif;">
+
<pre style="background-color:#000000; color: white; font-family: monospace, sans-serif;">
 
[username@login01 ~]$ sbatch SAStest.job
 
[username@login01 ~]$ sbatch SAStest.job
 
Submitted batch job 289552
 
Submitted batch job 289552
Line 85: Line 80:
 
By default SAS uses 1 CPU core, however certain functions can use additional resources if they are available, which may result in performance improvements. These functions include SORT, SUMMARY, MEANS, REPORT, TABULATE, and SQL. In order to make use of additional CPU cores, you should request the appropriate resource ('''#SBATCH -n XX''') in your job submission script and amend your SAS command with the '''threads''' and '''cpucount''' flags, see below:  
 
By default SAS uses 1 CPU core, however certain functions can use additional resources if they are available, which may result in performance improvements. These functions include SORT, SUMMARY, MEANS, REPORT, TABULATE, and SQL. In order to make use of additional CPU cores, you should request the appropriate resource ('''#SBATCH -n XX''') in your job submission script and amend your SAS command with the '''threads''' and '''cpucount''' flags, see below:  
  
<pre style="background-color: #C8C8C8; color: black; border: 2px solid blue; font-family: monospace, sans-serif;">
+
<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
 
#!/bin/bash
 
#!/bin/bash
 
#SBATCH -J SASjob
 
#SBATCH -J SASjob
Line 99: Line 94:
 
sas_en -memsize 40G -cpucount 28 -threads -noterminal my_sas_script.sas
 
sas_en -memsize 40G -cpucount 28 -threads -noterminal my_sas_script.sas
 
</pre>
 
</pre>
 +
 +
== Further Information ==
 +
* [http://www.sas.com/en_gb/home.html SAS website]
 +
* [http://support.sas.com/documentation/cdl/en/hostunx/69602/HTML/default/viewer.htm#titlepage.htm SAS 9.4 Companion for UNIX <Linux> Environments ]
 +
 +
{{Licensepagenav}}

Latest revision as of 11:21, 16 November 2022

Application Details

  • Description: SAS (Statistical Analysis System) is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics.
  • Versions: 9.4
  • Module names: SAS/9.4
  • License: Departmental research only multi-platform license, restricted to Accounting and Finance department

Usage Examples

Executables

Executable Description
sas_en The main SAS executable is sas_en. Depending on the options provided, this will either start SAS with the full graphical user interface, start SAS in interactive line mode, or allow you to run SAS in batch mode.

Interactive

[username@login01 ~]$ interactive
salloc: Granted job allocation 289669
Job ID 289669 connecting to c170, please wait...
Last login: Thu Jan 26 12:59:11 2017 from 10.254.5.246
[username@c170 ~]$ module add test-modules SAS/9.4

To use the full SAS GUI, make sure you have your environment setup as detailed in LINK and run sas_en:

[username@c170 ~]$ sas_en

This will open up a number of SAS windows, including Program Editor, Results, Explorer, Session Manager, Toolbox, Output and Log: SASGUI.png

To use the command line interactive line mode and not the GUI, run sas_en –nodms:

[username@c170 ~]$ sas_en –nodms

Some functions invoke a SAS window even in interactive line mode, for full line mode use –noterminal flag, i.e.:

[username@c170 ~]$ sas_en -nodms –noterminal

You can then run your task using a SAS script with the following command:

[username@c170 ~]$ sas_en -noteminal sas_file.sas

Batch Submission

A better approach is to submit tasks to run automatically without any interaction. To do this, you need a job submission script, an example of which is:

#!/bin/bash
#SBATCH -J SASjob           # Job name, you can change it to whatever you want
#SBATCH -N 1                # Number of nodes (for SAS should be always one)
#SBATCH -n 1                # Number of cores (for SAS should generally be one, see tuning)
#SBATCH -o %N-%j.log        # Standard output will be written here
#SBATCH -e %N-%j.err        # Standard error will be written here
#SBATCH -p compute          # Slurm partition, where you want the job to be queued
 
module add test-modules SAS/9.4
 
sas_en -cpucount 1 -nothreads -noterminal my_sas_script.sas

Note: that the –cpucount in the sas_en command should match the #SBATCH -n number. Change the last .sas filename as appropriate

This submission script can be found at /path/to/sample/script

[username@login01 ~]$ sbatch SAStest.job
Submitted batch job 289552

Tuning SAS tasks

Memory

By default the memory allocation for a SAS is 2GB. As long as the appropriate resources are requested in the job submission script (#SBATCH --mem=XXG) this can be increased as required. The value provided with the SBATCH flag should match that provided to SAS via the -memsize option (see submission script below).

cpucount and threads

By default SAS uses 1 CPU core, however certain functions can use additional resources if they are available, which may result in performance improvements. These functions include SORT, SUMMARY, MEANS, REPORT, TABULATE, and SQL. In order to make use of additional CPU cores, you should request the appropriate resource (#SBATCH -n XX) in your job submission script and amend your SAS command with the threads and cpucount flags, see below:

#!/bin/bash
#SBATCH -J SASjob
#SBATCH -N 1
#SBATCH -n 28
#SBATCH -o %N-%j.log
#SBATCH -e %N-%j.err
#SBATCH -p compute
#SBATCH --mem=40G
 
module add test-modules SAS/9.4
 
sas_en -memsize 40G -cpucount 28 -threads -noterminal my_sas_script.sas

Further Information





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