Posted by John Cottrell (April 17, 2017)

Mascot Security: priority settings

An earlier article looked at privacy settings in Mascot security. This article looks at priority settings; the settings that allow one user group to run bigger or longer or more complex searches than another.

Many aspects of searches can be limited by user group. The important ones are:

  • SEARCH: Allow msms no enzyme searches
  • SEARCH: Maximum number of concurrent searches per IP address
  • SEARCH: Maximum Mascot search job priority
  • SEARCH: Maximum number of queries per search
  • SEARCH: Maximum execution time
  • SEARCH: Maximum variable modifications for standard searches
  • SEARCH: Maximum variable modifications for error tolerant searches
  • SEARCH: Maximum number of queries for a no enzyme search
  • SEARCH: Maximum number of fasta files in a single search

You can set these to values that encourage short searches. On our free public web site, we have these settings for the guests group:

  • SEARCH: Allow msms no enzyme searches = False
  • SEARCH: Maximum number of concurrent searches per IP address = 2
  • SEARCH: Maximum number of queries per search = 1200

SEARCH: Maximum execution time has to be used with care because it does no-one any good if a 65 minute search is cancelled after running for 60 minutes. The user probably just submits it again in the hope of it getting through

SEARCH: Maximum Mascot search job priority can be used to ensure your searches get a greater share of processor time. This controls a user’s maximum priority, which is also their default priority, (higher values = higher priority). Users can decrease the priority for their non-urgent jobs, but they cannot increase it above this maximum.

The other useful setting is to limit access to very large databases, such as NCBIprot. Novices and optimists tend to submit searches with multiple variable modifications and no taxonomy filter that take forever. You might have SEARCH: Allow all fasta databases to be searched set true for all groups but exclude selected databases for (say) a group used for teaching students by listing them against SEARCH: Special fasta databases that override the default setting. The previous article, on privacy settings, describes how database access can be restricted in slightly greater detail.

The number of threads used for searches of a particular database cannot be limited at group level by a security setting. The architecture of Mascot doesn’t permit having different numbers of threads for different searches. The number of threads for a database is set in Database Manager: Database name; Show configuration details; Edit performance settings. The default is -1, which translates to the maximum number of threads permitted by the licence. If you want to reduce the processor time allocated to searches of a database, change this to 1 or some other small number. (Note that this doesn’t apply in cluster mode, where this setting is ignored.)

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