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Getting Started with High Performance Computing at UHasselt: Workshop on February 5, 2010

Learn about running MrBayes and R, accessing the cluster, and utilizing HPC for CPU-intensive tasks. Discover available software and licensing options for VIC3. Get guidance on how to start and where to find helpful resources.

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Getting Started with High Performance Computing at UHasselt: Workshop on February 5, 2010

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  1. VSC@Uhasselt workshop February 5, 2010 Geert Jan Bex geertjan.bex@uhasselt

  2. 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

  3. How to get started? • Send email to: hpcinfo@cc.kuleuven.be • Receive a temporary account • Follow the procedure at: https://vscentrum.be/vsc-help-center/k.u.leuven-vic-vic3-how-tos/howto-access-the-cluster-vic3 • When approved, get going

  4. 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

  5. VIC3 at work

  6. Running MrBayes • Run MrBayes on your own computer: • On VIC3, create PBS script ‘mrBayes.pbs’: • Run the job: PATH="$HOME/apps/mrbayes-3.1.2/:$PATH" mb interleave_final_Bayes #!/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-3.1.2-mpi/:$PATH" mpirun mb-mpi interleave_final_Bayes now uses 8 processors! qsub mrBayes.pbs

  7. 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 Running R • R is not parallelized • However, some usage scenario’s can be done in parallel, e.g., • parameter exploration for (a, b) in {(1.3, 5.7), (2.7, 1.4), (3.4, 2.1), (4.1, 3.8), … }

  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: Rscript my-pe 1.3 5.7 #!/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 a, b 1.3, 5.7 2.7, 1.4 3.4, 2.1 4.1, 3.8 … module load worker/1.0 wsub –batch my-pe.pbs –data my-data.csv

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

  10. Priorities

  11. UHasselt Numbers, numbers, numbers… total for 2009: 280490.16 days = 768.47 year

  12. Where to find help? • https://vscentrum.be/vsc-help-center • FAQs • How-To • Reference manuals • hpcinfo@cc.kuleuven.be • 2nd line support • geertjan.bex@uhasselt.be • 3rd line support for UHasselt

  13. 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 %

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