Kettlebrook Cluster

Error message

  • Deprecated function: Constant PDO::MYSQL_ATTR_USE_BUFFERED_QUERY is deprecated since 8.5, use Pdo\Mysql::ATTR_USE_BUFFERED_QUERY instead in DatabaseConnection_mysql->__construct() (line 332 of /var/www/drupal-sites/adgenetics.org/drupal-7.82/includes/database/mysql/database.inc).
  • Deprecated function: Constant PDO::MYSQL_ATTR_MULTI_STATEMENTS is deprecated since 8.5, use Pdo\Mysql::ATTR_MULTI_STATEMENTS instead in DatabaseConnection_mysql->__construct() (line 344 of /var/www/drupal-sites/adgenetics.org/drupal-7.82/includes/database/mysql/database.inc).

Kettlebrook has cluster software Grid Engine (formerly known as Sun Grid Engine) installed. Below are some tips on using it.

qstat - show the status of Grid Engine jobs and queues

qsub - submit jobs to Grid Engine

qhost - show the status of Grid Engine hosts, queues, jobs

qacct - report and account for Grid Engine usage

 

see man pages for full details, or type -help parameter for a quick list of options.

Usage Rules

- Submit as a cluster job for any task with long-running CPU and/or high RAM usage.

- Tasks with multiple CPU use must match slot request ( see parallel processing)

 

Example Basic Usage

qsub -N my-script-01 -cwd -b y bash script01.sh