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Research Computing The Apollo HPC Cluster

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1 Research Computing The Apollo HPC Cluster
Jeremy Maris Research Computing IT Services University of Sussex

2 High Performance Computing ?
Generically, computing systems comprised of multiple processors linked together in a single system. Used to solve problems beyond the scope of the desktop. High performance computing Maximising number of cycles per second, usually parallel High throughput computing Maximising number of cycles per year, usually serial Facilitating the storage, access and processing of data Coping with the massive growth in data High Performance – weather forecasting, simulations, molecular dynamics High Throughput – CERN, sequence assembly etc Lots of data – CERN, genomics, life Sciences generally

3 High Performance Computing
tasks must run quickly single problem split across many processors Weather forecasting Markov models Imaging processing 3D image reconstruction 4D visualisation Sequence assembly Whole genome analysis Assembly - aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. 1TB of output per day from shotgun sequencers Task parallel Markov – finding patterns over time in complex systems (in space as well as time)

4 High throughput computing
A lot of work done over a long time frame One program run many times, eg searching a large data set Loosely coupled. ATLAS analysis Genomics (sequence alignment, BLAST etc) Virtual Screening (eg in drug discovery) Parameter exploration (simulations) Statistical analysis (eg bootstrap analysis,) 3.4 thousand million base pairs in Human Genome, 20 – 25k genes. Data Parallel

5 Apollo Cluster - Aims Computing provision beyond capability of desktop
Priority access determined by Advisory Group Shared infrastructure and support from IT Services Extension of facility by departments Storage (adding to Lustre, access to SAN) CPU Software Licenses More compute nodes will be purchased by IT Services as budgets allow )

6 Apollo Cluster - Hardware
Total 264 cores 14 x 12 core 2.67GHz Intel nodes cores 2 x 48 core nodes 2.2GHz AMD nodes – 96 cores (17 x 8 core blades , GigE (informatics) cores) 48 GB RAM for Intel nodes 256 GB RAM for AMD nodes 20 TB Home NFS file system (backed up) 80 TB Lustre file system (scratch, not backed up) QDR (40Gbs) Infiniband interconnect )

7 Apollo Cluster - Hardware

8 Apollo Cluster - Filesystems 1
Home - 20 TB, RAID6 set of 12 x 2TB disks Exported via NFS Backed up, keep your valuable data here Easily overloaded if many cores read/write at same time Lustre parallel file system - /mnt/lustre/scratch Redundant metadata server Three object servers, each with 3 x 10 TB RAID6 OST Data striping configured by file or directory Can stripe across all 108 disks. Aggregate data rate ~ 3.8GB/s NOT backed up, for temporary storage Local 400GB scratch disk per node )

9 Apollo Cluster - Filesystems 2
The graph above demonstrates the performance of NFS, Gluster and Lustre solutions when compared on equivalent hardware. These results were obtained with the IOZONE benchmark using two SunFire X TB storage servers and five SunFire X2270 servers each running 16 simultaneous threads, all connected via trunked gigabit Ethernet. Gluster a parallel NAS, not as good as Lustre and less coverage/support. Not open source © Alces Software Limited

10 Apollo Cluster - Lustre Performance
) IOIOZONE Benchmark Summary (c ) 2010 Alces Software Ltd

11 Apollo Cluster - Lustre 1
) Figure (c)2009 Cray Inc

12 Apollo Cluster - Lustre 2
Storing a single file across multiple OSTs (striping) offers two benefits: an increase in the bandwidth available when accessing the file an increase in the available disk space for storing the file. Striping has disadvantages: increased overhead due to network operations and server contention increased risk of file damage due to hardware malfunction. Given the tradeoffs involved, the Lustre file system allows users to specify the striping policy for each file or directory of files using the lfs utility. )

13 Apollo Cluster - Lustre 3
Further reading … Lustre FAQ Lustre 1.8 operations manual I/O Tips - Lustre Striping and Parallel I/O )

14 Apollo Cluster - Software
Module system used for defining paths and libraries Need to load software required Module avail, module add XX, module unload XX Access optimised math libraries, MPI stacks, compilers etc Latest version of packages, eg python, gcc easily installed Intel parallel studio suite C C++ Fortran, MKL, performance analysis etc gcc and Open64 compilers Will compile/install software for users if asked )

15 Apollo Cluster - Software
Compilers/tools Libraries Programs ant acml adf gcc suite atlas aimpro Intel (c, c++, fortran) blas, gotoblas alberta git cloog gadget jdk 1.6_024 fftw2, fftw3 gap mercurial gmp Gaussian 09 open64 gsl hdf5 python 2.6.6 hpl idl sbcl lapack, scalapack matlab MVAPICH, MVAPICH2 mricron mpfr netcdf nag paraview openMPI stata ppl  WRF )

16 Apollo Cluster - Queues 1
Sun Grid Engine used for batch system parallel.q for MPI and OpenMP jobs Intel nodes Slot limit of 48 cores per user at present serial.q for serial and OpenMP jobs AMD nodes Slot limit of 36 cores per user inf.q for serial or openMP jobs - Informatics use only No other limits – need user input re configuration )

17 Apollo Cluster - serial job script
Queue is by default the serial.q #!/bin/sh #$ -N sleep #$ -S /bin/sh #$ -cwd #$ -M #$ -m bea echo Starting at: `date` sleep 60 echo Now it is: `date` )

18 Apollo Cluster - parallel job script
For parallel jobs you must specify the pe environment assigned to the script. parallel environments: openmpi or openmp. mvapich2 often less efficient. #!/bin/sh #$ -N JobName #$ -M #$ -m bea #$ -cwd #$ -pe openmpi NUMBER_OF_CPUS # eg 12-36 #$ -q parallel.q #$ -S /bin/bash # source modules environment: . /etc/profile.d/ module add gcc/4.3.4 qlogic/openmpi/gcc mpirun -np $NSLOTS -machinefile $TMPDIR/machines /path/to/exec )

19 Apollo Cluster - Monitoring
Ganglia statistics for apollo and feynman (the EPP cluster) are )

20 Apollo Cluster - Accounting
Simply, qacct –o Accounting monitored to show fair usage, etc Statistics may be posted on the web. )

21 Apollo Cluster - Documentation
To get an account on the cluster, Userguides and example scripts are available on the cluster in /cm/shared/docs/USERGUIDE Other documentation in /cm/shared/docs path )

22 Apollo Cluster - Adding nodes
C6100 chassis + four servers each 2.67 GHz, 12 core, 48GB RAM, IB card, licences R core 2.2GHz AMD Departments guaranteed 90% exclusive of their nodes. 10% sharing with others, plus back fill of idle time. Contact for latest pricing )

23 Apollo Cluster - Adding storage
Configuration of an additional Object Server  Server R510, 8 core  24GB RAM + 12 x 2 TB disks    JBOD MD x 2TB disks + H800 RAID card The minimum increment is the server which provides about 19TB after formatting and RAID6 Two JBODS give another 38TB. Total storage ~57 TB in 6 OST Contact for pricing )

24 Questions?

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