Wooki is a shared resource which is essential for the research projects of all group members. To help ensure Wooki’s smooth operation please read the following set of guidelines.<\/span><\/span><\/p>\n Use your\u00a0scratch<\/tt>\u00a0directory when running jobs.<\/span><\/p>\n<\/li>\n The queuing system controls the scheduling, distribution and execution of jobs on the cluster. On Wooki, all compute jobs should be run through the queuing system. Rocks is fully integrated with the Gridengine queue system, also known previously as Sun Grid Engine and Oracle Grid Engine, for historical reasons this document will refer to it as SGE.<\/span><\/span><\/p>\n Basic Commands for Viewing the Status of the Queue<\/strong><\/span><\/span><\/p>\n All commands are documented with help by adding the\u00a0-h<\/tt>\u00a0option (i.e.\u00a0qstat\u00a0-h<\/tt>) or using the\u00a0man<\/tt>\u00a0command (i.e.\u00a0man\u00a0qstat<\/tt>).<\/span><\/span><\/p>\n qstat<\/em><\/span><\/span><\/p>\n Displays the current status of your running and waiting jobs on the queue.<\/span><\/span><\/p>\n qstat\u00a0-u\u00a0\\*<\/tt>\u00a0shows jobs for all users in priority order.<\/span><\/p>\n<\/li>\n qstat\u00a0-f<\/tt>\u00a0shows the nodes that each job is running on.<\/span><\/p>\n<\/li>\n qstat\u00a0-g\u00a0c<\/tt>\u00a0shows the number of nodes free in the system<\/span><\/span><\/span><\/p>\n<\/li>\n<\/ul>\n We are currently in the process of developing some customised scripts to display usage on the cluster in a friendlier manner. For full information or to make requests for functionlaity see the development page:\u00a0https:\/\/bitbucket.org\/tdaff\/wsge\/<\/a>\u00a0where you can also open issues for feature requests. Currently commands include:<\/span><\/span><\/p>\n wstat<\/tt><\/strong>\u00a0gives a more user friendly list of all jobs on the cluster;<\/span><\/p>\n wstat\u00a0-u\u00a0username<\/tt><\/strong>\u00a0only shows\u00a0username<\/tt>‘s jobs.<\/span><\/p>\n<\/li>\n<\/ul>\n<\/li>\n cluster_stat<\/tt><\/strong>\u00a0shows a comprehensive overview of jobs and users on the cluster.<\/span><\/span><\/p>\n<\/li>\n<\/ul>\n For most codes that come as a module there will be a\u00a0$code-submit<\/tt><\/strong>\u00a0script that takes care of building an SGE script and submitting the job, for example\u00a0vasp-submit<\/tt><\/strong>\u00a0or\u00a0gaussian-submit<\/tt><\/strong>. Please use these if they are available. These scripts ensure the proper usage of the local scratch disks and for parallel jobs, they set up the parallel execution environments and message passing systems.<\/span><\/span><\/p>\n The submit scripts are located with their modules in:\u00a0\/share\/apps<\/em>, but when you\u00a0load the module<\/em>\u00a0they will be available as commands in your shell.<\/span><\/span><\/p>\n If a commonly used program is missing a submit script, you may open a ticket to ask for one to be written.<\/span><\/span><\/p>\n To show the basic usage and behaviour of the submit scripts we will use the example of submitting a vasp job. Most submit scripts operate in a very similar way.<\/span><\/span><\/p>\nMost Important Rules and Guidelines<\/h2>\n
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The Queuing System on Wooki<\/h3>\n
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Submitting Jobs on Wooki<\/h3>\n
Basic Usage of Submit Scripts<\/h3>\n
1<\/a> <\/span><\/span><\/span>$<\/span> module help <\/span>vasp<\/span>\r\n 2<\/a> <\/span><\/span><\/span><\/span>\r\n 3<\/a> <\/span><\/span><\/span>----------- Module Specific Help for 'vasp\/5.3.5' -----------------<\/span><\/span>\r\n 4<\/a> <\/span><\/span><\/span><\/span>\r\n 5<\/a> <\/span><\/span><\/span> Provides VASP 5.3.5<\/span><\/span>\r\n 6<\/a> <\/span><\/span><\/span><\/span>\r\n 7<\/a> <\/span><\/span><\/span> Use `module load vasp` to load the package then<\/span><\/span>\r\n 8<\/a> <\/span><\/span><\/span> use the command `vasp-submit` to run jobs through<\/span><\/span>\r\n 9<\/a> <\/span><\/span><\/span> the queue.<\/span><\/span>\r\n 10<\/a> <\/span><\/span><\/span>$<\/span> module load vasp<\/span>\r\n 11<\/a> <\/span><\/span><\/span>$<\/span> vasp-submit --help<\/span>\r\n 12<\/a> <\/span><\/span><\/span>usage: vasp-submit [-h] [-i] [-r RUNTIME] [-t] [-g] [-d] job_name [num_cpu]<\/span><\/span>\r\n 13<\/a> <\/span><\/span><\/span><\/span>\r\n 14<\/a> <\/span><\/span><\/span>Submit a vasp job.<\/span><\/span>\r\n 15<\/a> <\/span><\/span><\/span><\/span>\r\n 16<\/a> <\/span><\/span><\/span>positional arguments:<\/span><\/span>\r\n 17<\/a> <\/span><\/span><\/span> job_name vasp job name<\/span><\/span>\r\n 18<\/a> <\/span><\/span><\/span> num_cpu number of processosr to run on (default: 1)<\/span><\/span>\r\n 19<\/a> <\/span><\/span><\/span><\/span>\r\n 20<\/a> <\/span><\/span><\/span>optional arguments:<\/span><\/span>\r\n 21<\/a> <\/span><\/span><\/span> -h, --help show this help message and exit<\/span><\/span>\r\n 22<\/a> <\/span><\/span><\/span> -i, --infiniband run on infiniband for large parallel jobs<\/span><\/span>\r\n 23<\/a> <\/span><\/span><\/span> -r RUNTIME, --runtime RUNTIME<\/span><\/span>\r\n 24<\/a> <\/span><\/span><\/span> maximum length of time for the job to run, specify as<\/span><\/span>\r\n 25<\/a> <\/span><\/span><\/span> number of seconds or hh:mm:ss<\/span><\/span>\r\n 26<\/a> <\/span><\/span><\/span> -t, --threaded keep the processes in a single node<\/span><\/span>\r\n