NAME HPC::Runner::Scheduler - Base Library for HPC::Runner::Slurm and HPC::Runner::PBS SYNOPSIS pbsrunner.pl/slurmrunner.pl/mcerunner.pl --infile list_of_commands DESCRIPTION HPC::Runner::Scheduler is a base library for creating templates of HPC Scheduler (Slurm, PBS, etc) submission scripts. All the scheduler variables: memory, cpus, nodes, partitions/queues, are abstracted to a template. Instead of writing an entire submission template slurmrunner.pl --infile list_of_commands #with list of optional parameters Please see the indepth usage guide at HPC::Runner::Usage 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' 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 nodes_count Number of nodes to use on a job. This is only useful for mpi jobs. PBS: #PBS -l nodes=nodes_count:ppn=16 this Slurm: #SBATCH --nodes nodes_count 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. walltime Define PBS walltime mem 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 first_pass Do a first pass of the file to get all the stats 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 Supply your own command instead of mcerunner/threadsrunner/etc 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. This is the number of commands within a batch. Each new batch resets it. node_counter Keep track of which node we are on batch_counter Keep track of how many batches we have submited to slurm 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 slurm_decides Do not specify a node or partition in your sbatch file. Let Slurm decide which nodes/partition to submit jobs. job_stats HashRef of job stats - total jobs submitted, total processes, etc job_deps #HPC jobname=assembly #HPC job_deps=gzip,fastqc job_scheduler_id Job Scheduler ID running the script. Passed to slurm for mail information jobname Specify a job name, and jobs will be jobname_1, jobname_2, jobname_x jobref Array of arrays details slurm/process/scheduler job id. Index -1 is the most recent job submissisions, and there will be an index -2 if there are any job dependencies SUBROUTINES/METHODS run() First sub called Calling system module load * does not work within a screen session! do_stats Do some stats on our job stats Foreach job name get the number of batches, and have a put that in batches->batch->job_batches check_files() Check to make sure the outdir exists. If it doesn't exist the entire path will be created 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 collect_stats Collect job stats 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 AUTHOR Jillian Rowe COPYRIGHT Copyright 2016- Jillian Rowe LICENSE This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. SEE ALSO HPC::Runner::Slurm HPC::Runner::PBS HPC::Runner::MCE