NAME HPC::Runner::Slurm - Job Submission to Slurm VERSION Version 0.01 SYNOPSIS Indepth documentation is at https://wcmc-q.atlassian.net/wiki/display/HPCSLURM/HPC-Runner-Slurm . package Main; extends 'HPC::Runner::Slurm'; Main->new_with_options(infile => '/path/to/commands'); This module is a wrapper around sbatch and can be used to submit arbirtary bash commands to slurm. It has two levels of management. The first is the main sbatch command, and the second is the actual job, which runs commands in parallel, controlled by HPC::Runner::Threads or HPC::Runner::MCE. It supports job dependencies. Put in the command 'wait' to tell slurm that some job or jobs depend on some other jobs completion. Put in the command 'newnode' to tell HPC::Runner::Slurm to submit the job to a new node. The only necessary option is the --infile. Submit Script cmd1 cmd2 && cmd3 cmd4 \ --option cmd4 \ #Tell HPC::Runner::Slurm to put in some job dependencies. wait cmd5 #Tell HPC::Runner::Slurm to pass things off to a new node, but this job doesn't depend on the previous newnode cmd6 User Options User options can be passed to the script with script --opt1 or in a configfile. It uses MooseX::SimpleConfig for the commands configfile Config file to pass to command line as --configfile /path/to/file. It should be a yaml or xml (untested) This is optional. Paramaters can be passed straight to the command line example.yml --- infile: "/path/to/commands/testcommand.in" outdir: "path/to/testdir" module: - "R2" - "shared" infile infile of commands separated by newline example.in cmd1 cmd2 --input --input \ --someotherinput wait #Wait tells slurm to make sure previous commands have exited with exit status 0. cmd3 ##very heavy job newnode #cmd3 is a very heavy job so lets start the next job on a new node module modules to load with slurm Should use the same names used in 'module load' Example. R2 becomes 'module load R2' jobname Specify a job name, and jobs will be jobname_1, jobname_2, jobname_x afterok The afterok switch in slurm. --afterok 123 will tell slurm to start this job after job 123 has completed successfully. cpus_per_task slurm item --cpus_per_task defaults to 4, which is probably fine commands_per_node --commands_per_node defaults to 8, which is probably fine partition #Should probably have something at some point that you can specify multiple partitions.... Specify the partition. Defaults to the partition that has the most nodes. nodelist Defaults to the nodes on the defq queue submit_slurm Bool value whether or not to submit to slurm. If you are looking to debug your files, or this script you will want to set this to zero. Don't submit to slurm with --nosubmit_to_slurm from the command line or $self->submit_to_slurm(0); within your code template_file actual template file One is generated here for you, but you can always supply your own with --template_file /path/to/template serial Option to run all jobs serially, one after the other, no parallelism The default is to use 4 procs user user running the script. Passed to slurm for mail information use_threads Bool value to indicate whether or not to use threads. Default is uses processes If using threads your perl must be compiled to use threads! use_processes Bool value to indicate whether or not to use processes. Default is uses processes use_gnuparallel Bool value to indicate whether or not to use processes. Default is uses processes use_custom Use a custom command Internal Variables You should not need to mess with any of these. template template object for writing slurm batch submission script cmd_counter keep track of the number of commands - when we get to more than commands_per_node restart so we get submit to a new node. node_counter Keep track of which node we are on batch_counter Keep track of how many batches we have submited to slurm node Node we are running on cmd Current command specified by infile batch List of commands to submit to slurm cmdfile File of commands for mcerunner/parallelrunner Is cleared at the end of each slurm submission slurmfile File generated from slurm template SUBROUTINES/METHODS run() First sub called Calling system module load * does not work within a screen session! check_files() Check to make sure the outdir exists. If it doesn't exist the entire path will be created get_nodes Get the nodes from sinfo if not supplied If the nodelist is supplied partition must be supplied parse_file_slurm Parse the file looking for the following conditions lines ending in `\` wait nextnode Batch commands in groups of $self->cpus_per_task, or smaller as wait and nextnode indicate check_meta allow for changing parameters mid through the script #Job1 echo "this is job one" && \ bin/dostuff bblahblahblah #HPC cpu_per_task=12 echo "This is my new job with new HPC params!" work Get the node #may be removed but we'll try it out Process the batch Submit to slurm Take care of the counters process_batch() Create the slurm submission script from the slurm template Write out template, submission job, and infile for parallel runner process_batch_command splitting this off from the main command submit_slurm() Submit jobs to slurm queue using sbatch. This subroutine was just about 100% from the following perlmonks discussions. All that I did was add in some logging. http://www.perlmonks.org/?node_id=151886 You can use the script at the top to test the runner. Just download it, make it executable, and put it in the infile as perl command.pl 1 perl command.pl 2 #so on and so forth AUTHOR Jillian Rowe, BUGS Please report any bugs or feature requests to bug-runner-init at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=HPC-Runner-Slurmm. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. SUPPORT You can find documentation for this module with the perldoc command. perldoc HPC::Runner::Slurm You can also look for information at: * RT: CPAN's request tracker (report bugs here) http://rt.cpan.org/NoAuth/Bugs.html?Dist=HPC-Runner-Slurm * AnnoCPAN: Annotated CPAN documentation http://annocpan.org/dist/HPC-Runner-Slurm * CPAN Ratings http://cpanratings.perl.org/d/HPC-Runner-Slurm * Search CPAN http://search.cpan.org/dist/HPC-Runner-Slurm/ Acknowledgements This module was originally developed at and for Weill Cornell Medical College in Qatar within ITS Advanced Computing Team. With approval from WCMC-Q, this information was generalized and put on github, for which the authors would like to express their gratitude. LICENSE AND COPYRIGHT Copyright 2014 Weill Cornell Medical College in Qatar. This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). 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