workshop February 5, 2010 Geert Jan Bex

What’s it all good for? Work to do on the cluster: –many things that can be done in parallel –one thing that takes a long time, but can be done in parallel However, the cluster is not a replacement for you desktop/laptop! –HPC: high performance computing –CPU intensive work

How to get started? 1.Send to: 2.Receive a temporary account 3.Follow the procedure at: center/k.u.leuven-vic-vic3-how- tos/howto-access-the-cluster-vic3 center/k.u.leuven-vic-vic3-how- tos/howto-access-the-cluster-vic3 4.When approved, get going

What can you run? All open source linux software All linux software you have a license for that covers the cluster No Windows software... for now… –pilot project on the way –however, technical & licensing issues

VIC3 at work

Running MrBayes Run MrBayes on your own computer: On VIC3, create PBS script ‘mrBayes.pbs’: Run the job: #!/bin/bash -l #PBS -N mrBayes-mpi-interleave #PBS -l walltime=71:59:00,nodes=1:ppn=8 module load openmpi/1.2.8_gcc cd $PBS_O_WORKDIR PATH="$HOME/apps/mrbayes mpi/:$PATH" mpirun mb-mpi interleave_final_Bayes PATH="$HOME/apps/mrbayes-3.1.2/:$PATH" mb interleave_final_Bayes qsub mrBayes.pbs now uses 8 processors!

Running R R is not parallelized However, some usage scenario’s can be done in parallel, e.g., –parameter exploration args <- commandArgs(TRUE) a <- as.double(args[1]) b <- as.double(args[2]) result <- c(a, b, soph_func(a + b)) print(result) my-pe.r for (a, b) in {(1.3, 5.7), (2.7, 1.4), (3.4, 2.1), (4.1, 3.8), … }

Running R, reloaded Run R on your own computer: For VIC3, create PBS script ‘my-pe.pbs’ and ‘my-data.csv’: Run the job: #!/bin/bash -l #PBS -N my-pe #PBS -l walltime=1:00:00,nodes=1:ppn=8 module load R cd $PBS_O_WORKDIR Rscript my-pe $a $b Rscript my-pe module load worker/1.0 wsub –batch my-pe.pbs –data my-data.csv a, b 1.3, , , , 3.8 …

VIC3 is shared by many compute nodes queue system: torque scheduler: moab priority queue, goals: 1.fairness 2.QoS guarantees ?

Priorities

Numbers, numbers, numbers… UHasselt total for 2009: days = year

Where to find help? –FAQs –How-To –Reference manuals –2 nd line support –3 rd line support for UHasselt

Conclusions It’s not that hard, now, is it? (oh well…) –don’t get intimidated If you need help, ask for it UHasselt has room for growth –currently 2.7 % of resources –maximum 5-6 %