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en:hpc:usage:localdisks [2019/07/01 15:55] (current)
vrintala created
Line 1: Line 1:
 +====== Use local disks ======
  
 +In some cases it might be beneficial to use local disks of calculation servers.
 +
 +Things to remember:
 +  * Writing speed is lower than with NFS server
 +  * Latency is lower than with NFS server
 +  * Limited disk space available
 +
 +As conclusion it might be beneficial to use local disks if:
 +  * Small writes are done continuously. For example calculate something from data, write it, calculate next value, write it, ...
 +  * Reading/writing large number of small files
 +
 +Example job script template:
 +
 +<file sh localdiskexample.sh>
 +#!/bin/bash
 +#SBATCH --nodes 1
 +#SBATCH --ntasks 1
 +#SBATCH --cpus-per-task 12
 +#SBATCH --mem-per-cpu=2000
 +#SBATCH --time 14-0:00:00
 +#SBATCH --job-name example
 +#SBATCH --error example.stderr.%j
 +#SBATCH --output example.stdout.%j
 +#SBATCH --partition phase1
 +#SBATCH --mail-type=end
 +#SBATCH --mail-user=<youremail@lut.fi>
 +
 +# Set your directories
 +# Your case directory in home (NFS server)
 +export CASEDIR="/home/<username>/casedir"
 +# Local directory (on calculation node)
 +export LOCALDIR="/tmp/$SLURM_JOB_ID"
 +# Results are copied to this directory (by default same as case directory)
 +export RESDIR=$CASEDIR
 +
 +module load examplesoft/exampleversion
 +
 +# Create a temporary directory on scratch
 +mkdir -p $LOCALDIR
 +
 +# Move to directory (could be different depending how your calculation software works)
 +cd $LOCALDIR
 +
 +# Copy files to local directory
 +cp -R $CASEDIR/* $LOCALDIR
 +
 +srun --mpi=pmi2 examplesoft -exampleparameters exampleinput
 +
 +# After calculation copy files from local disk
 +cp -R $LOCALDIR/* $CASEDIR
 +
 +# Cleanup local work directory
 +rm -rf /tmp/$SLURM_JOB_ID
 +</file>
 
/opt/webdata/webroot/wiki/data/pages/en/hpc/usage/localdisks.txt · Last modified: 2019/07/01 15:55 by vrintala
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