NAME
HPC::Runner::Scheduler - Base Library for HPC::Runner::Slurm and HPC::Runner::PBS
SYNOPSIS
pbsrunner.pl/slurmrunner.pl/mcerunner.pl --infile list_of_commandsDESCRIPTION
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 parametersPlease 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 nodemodule
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 <jillian.e.rowe@gmail.com>
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.