Parallel computing

GNU parallel

It has home https://www.gnu.org/software/parallel/ -- note especially with its --env to pass environment variables.

Under Ubuntu, GNU parallel is easily installed as follows,

sudo apt install parallel

Earlier version had issues with temporary direvtory, e.g., https://stackoverflow.com/questions/24398941/gnu-parallel-unlink-error if

module load parallel/20131222

The latest, http://ftp.gnu.org/gnu/parallel/parallel-latest.tar.bz2, can be used instead.

SGE

Sun Grid Engine has a wiki entry.

https://peteris.rocks/blog/sun-grid-engine-installation-on-ubuntu-server/.

To delete SGE jobs shown in qstat, use

qstat | grep $USER | cut -d" " -f1 | xargs qdel

Otherwise for a consecutive sequence we use qdel {id1..id2}.

SLURM

Under Ubuntu, it can be installed with

sudo apt install slurm-client

General information is available from https://slurm.schedmd.com/.

Job scheduling examples on CentOS 6 and RHEL 7, https://www.arc.ox.ac.uk/arc-systems-0.

command	description
sacct	report job accounting information about active or completed jobs
salloc	allocate resources for a job in real time (typically used to allocate resources and spawn a shell, in which the srun command is used to launch parallel tasks)
sbatch	submit a job script for later execution (the script typically contains one or more srun commands to launch parallel tasks)
scancel	cancel a pending or running job
scontrol	hold, holdu, release, requeue, requeuehold, suspend and resume commands
sinfo	reports the state of partitions and nodes managed by Slurm (it has a variety of filtering, sorting, and formatting options)
squeue	reports the state of jobs (it has a variety of filtering, sorting, and formatting options), by default, reports the running jobs in priority order followed by the pending jobs in priority order
srun	used to submit a job for execution in real time

e.g., squeue -u $USER -r; qstat -u $USER; also scontrol show config; scontrol show partition; scontrol show job [jobid] and sview

To see environmental variables, e.g., MaxArraySize, we use

scontrol show config | sed -n '/^MaxArraySize/s/.*= *//p'

• job array, https://slurm.schedmd.com/job_array.html
• dependency, https://hpc.nih.gov/docs/job_dependencies.html
• examples, https://github.com/statgen/SLURM-examples
• temporary directories, https://help.rc.ufl.edu/doc/Temporary_Directories

When a SLURM job starts, the scheduler creates a temporary directory for the job on the compute node's local hard drive. This $SLURM_TMPDIR directory is very useful for jobs that need to use or generate a large number of small files, as the /ufrc parallel filesystem is optimized for large file streaming and is less suitable for small files.

The directory is owned by the user running the job. The path to the temporary directory is made available as the $SLURM_TMPDIR variable. At the end of the job, the temporary directory is automatically removed.

You can use the ${SLURM_TMPDIR} variable in job scripts to copy temporary data to the temporary job directory. If necessary, it can also be used as argument for applications that accept a temporary directory argument.

Many applications and programming languages use the $TMPDIR environment variable, if available, as the default temporary directory path. If this variable is not set, the applications will default to using the /tmp directory, which is not desirable. SLURM will set $TMPDIR to the same value as $SLURM_TMPDIR unless $TMPDIR has already been set, in which case it will be ignored. Check your job script(s) and shell initialization files like .bashrc and .bash_profile to make sure you do not have $TMPDIR set.

If a personal Singularity container is used, make sure that the $SINGULARITYENV_TMPDIR variable is set within the job to export the local scratch location into the Singularity container.

Examples of an interactive session can be simply sintr, or

srun -N1 -n1 -c6 -p short,medium,long -t 12:0:0 --pty bash -i

so that the earliest available partition will be used.

SGE to SLURM

Conversion is documented at https://srcc.stanford.edu/sge-slurm-conversion.

EXAMPLES

We intended to convert a large number of PDF files (INTERVAL.*.manhattn.pdf) to PNG with smaller file sizes. To start, we build a file list,

ls *pdf | \
sed 's/INTERVAL.//g;s/.manhattan.pdf//g' > INTERVAL.list

We do this with GNU parallel as follows,

cat INTERVAL.list | \
parallel -C' ' '
  echo {}
  pdftopng -r 300 INTERVAL.{}.manhattan.pdf
  mv {}-000001.png INTERVAL.{}.png
'

or with SLURM,

#!/bin/bash

#SBATCH --ntasks=1
#SBATCH --job-name=pdftopng
#SBATCH --time=6:00:00
#SBATCH --cpus-per-task=8
#SBATCH --partition=short
#SBATCH --array=1-50
#SBATCH --output=work/pdftopng_%A_%a.out
#SBATCH --error=work/pdftopng_%A_%a.err
#SBATCH --export ALL

. /etc/profile.d/modules.sh
module load default-cardio
module load slurm
module load use.own

export p=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]' INTERVAL.list)
export TMPDIR=/scratch/jhz22/tmp

echo ${p}
pdftopng -r 300 INTERVAL.${p}.manhattan.pdf ${p}
mv ${p}-000001.png INTERVAL.${p}.png

This is a single parameter case and it is possible to allow for more parameters in both cases.

Note also that the option --array=1-50 instructs the system to schedule jobs and in jobs with large memory usage it is more preferable to change to --array 1-50%4 so that a maximum of four jobs will be run simultaneously.

Job scheduling

echo "ls -l" | at 01:00

crontab.guru, https://crontab.guru/examples.html