christian kocks april 3, 2012 high-performance computing cluster in aachen

Christian KocksApril 3, 2012

High-Performance Computing Cluster in Aachen


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Typical Simulation Workflow

Simulator development

Simulation

Evaluation and visualization of results


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Workflow for Simulations on HPC Cluster

• Develop simulator on local PC / server• Perform short tests on local PC / server• Transfer simulator to HPC cluster (Subversion!)• Perform short tests on HPC cluster using the Linux login shell• Enqueue simulations on HPC cluster• Wait for notification e-mail from HPC cluster• Transfer results to local PC / server (e.g. with WinSCP using SCP

protocol)• Evaluate and visualize results on local PC

HPC High-Performance ComputingSCP Secure Copy


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Local Simulations vs. HPC Cluster Simulations

Local simulations HPC cluster simulation

Execution of simulations can be directly controlled Simulations must be enqueued

Very low setup time necessary to start simulation Some preparation necessary for running simulations

Number of available resources very limited “Unlimited” resources

Number of parallel jobs limited “Unlimited” number of parallel jobs

Arrangements with colleagues necessary No arrangements necessary

number of simulations

tota

l sim

ulat

ion

time

local

HPC cluster


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Using Matlab on HPC Cluster

• Connect to Linux login shell using SSH client (e.g. PuTTY):• Server name: cluster-linux.rz.rwth-aachen.de

• Load Matlab modules:module load MISCmodule load matlab

• Start Matlab:matlab -nodisplay -nodesktop -nosplash -nojvm

-logfile job.log -c @lic-serv.uni-due.de

• Alternative: use graphical remote session (with NX client)


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Using Subversion on HPC Cluster

• Use Subversion module svntest for first tests• Check out Subversion module (e.g. svntest) from KT server:

svn checkout https://134.91.99.160/svn/svntest/trunk [dst]

• Update local working copy:svn update

• Add file test.m:svn add test.m

• Commit changes to KT server:svn commit


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Sample Queue Script Filehttps://versions1.kt.uni-due.de/svn/lib/trunk/simulators/sim_awgn_matlab/sample_simple.sh

#!/usr/bin/env zsh#BSUB -J sim_awgn_matlab # job name#BSUB -o sim_awgn_matlab.%J # job output (use %J for job id)#BSUB -e sim_awgn_matlab.e%J # error output#BSUB -W 0:20 # hard limits in hours:minutes#BSUB -M 512 # memory in MB#BSUB -u [email protected] # e-mail address for notification#BSUB -N # enable e-mail notification#BSUB -n 2 # request number of compute slots#BSUB -a openmp # use esub for OpenMP/shared memory jobs

### load matlab modulesmodule load MISCmodule load matlab

### change to the work directorycd $HOME/svn/lib/simulators/sim_awgn_matlab

### run matlabmatlab -nodisplay -nodesktop -nosplash -nojvm -logfile job.log

-c @lic-serv.uni-due.de <sim_awgn_matlab_run.m


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Sample Queue Script File – Advancedhttps://versions1.kt.uni-due.de/svn/lib/trunk/simulators/sim_awgn_matlab/sample_advanced.sh

#!/usr/bin/env zsh#BSUB -J sim_awgn_matlab # job name#BSUB -o sim_awgn_matlab.%J # job output (use %J for job id)#BSUB -e sim_awgn_matlab.e%J # error output#BSUB -W 0:20 # hard limits in hours:minutes#BSUB -M 512 # memory in MB#BSUB -u [email protected] # e-mail address for notification#BSUB -N # enable e-mail notification#BSUB -n 2 # request number of compute slots#BSUB -a openmp # use esub for OpenMP/shared memory jobs

### load matlab modulesmodule load MISCmodule load matlab

### change to the work directorycd $HOME/svn/lib/simulators/sim_awgn_matlab

### run matlabmatlab -nodisplay -nodesktop -nosplash -nojvm -logfile job.log -c @lic-serv.uni-due.de <<EOFsim_awgn_matlab('ebn0', 6.78952, 'ModulationOrder', 2, 'Log', 'true', 'NumSymbols', 1000,

‚Filename', 'sample_advanced');EOF


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Job Management

• Enqueue a job:bsub <myscript.sh

• Query unfinished jobs:bjobs

• Kill unfinished job:bkill [job ID]


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General Hints for using HPC Cluster

• Ask Mrs. Tiedtke from Uni DuE for HPC cluster account• Write the simulator in a way to allow the execution of multiple small

simulations instead of one long simulation• Collect simulation parameters and results in MAT file• Deactivate all graphical outputs• Read “HPC Primer” for further information on using the cluster• Visit http://www.rz.rwth-aachen.de/aw/cms/rz/Themen/~mem/hochleistungsrechnen


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High-Performance Computing Cluster in Aachen

Demonstration…

christian kocks april 3, 2012 high-performance computing cluster in aachen

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