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Lab System Environment

Lab System Environment. Paul Kapinos 2014.10.07. Lab nodes: integrated to HPC Cluster. OS: Scientific Linux 6.5 ( RHEL6.5 compatible) Batch system: LSF 9.1  not for this lab  Storage: NetApp filer ($HOME / $ WORK) no backup on $WORK Lustre ($ HPCWORK ) not available.

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Lab System Environment

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  1. Lab System Environment Paul Kapinos 2014.10.07

  2. Lab nodes: integrated to HPC Cluster OS: • Scientific Linux 6.5 (RHEL6.5 compatible) Batch system: • LSF 9.1 •  not for this lab  Storage: • NetApp filer ($HOME / $WORK) no backup on $WORK • Lustre($HPCWORK) not available

  3. Software Environment Compiler: • Intel 15.0 (and older) • GCC 4.9 (and older) • Oracle Studio, PGI MPI: • Open MPI, Intel MPI • No InfiniBand! 1GE only • Warnings and 1/20 of usual performance Default: • intel/14.0 + openmpi/1.6.5

  4. Howtologin Frontends • login/ SCP File transfer: • $ ssh [-Y] user@cluster.rz.rwth-aachen.de$ scp [[user@]host1:]file1 [...] [[user@]host2:]file2 • then jump totheassigned lab node • $ sshlab5[.rz.rwth-aachen.de]

  5. Lab Node Assignment Please use your’s allocated node only • or agree in advance with the node owner

  6. Lab nodes Intel(R) Xeon(R) CPU E5-2699 v3 @ 2.30GHz • Packages(sockets) / Cores per package / Threads per core : 2/18/2 • Cores / Processors(CPUs) : 36 / 72 • AVX2: 256bit register • 2x Fused Multiply Add (FMA) >> double peak performance cf. previous chips 64GB RAM • Stream: >100Gb/s (Triad) No InfiniBand connection • MPI via 1GE network still possible • Warnings and 1/20 of usual performance

  7. Module System Many compilers, MPIs and ISV software The module system helps to manage all the packages • List loaded modules / available modules • $ module list • $ module avail • Load / unload a software • $ module load <modulename> • $ module unload <modulename> • Exchange a module (Some modules depend on each other) • $ module switch <oldmodule> <newmodule> • $ module switch intel intel/15.0 • Reload all modules (May fix your environment) • $ module reload • Find out in which category a module is: • $ module apropos <modulename>

  8. MPI No InfiniBand connection • MPI via 1GEnetwork, >> warnings and 1/20 of usual performance Default: Open MPI 1.6.5 • e.g. switch to Intel MPI: • $ module switch openmpiintelmpi Wrapper in $MPIEXEC redirects the processes to ‘back end nodes’ • by default your processes run on (random) non-Haswell node • use the ‘-H’ option to start the processes on favoured node • $ $MPIEXEC -H lab5,lab6-np 12 MPI_FastTest.exe other options of the interactive wrapper • $ $MPIEXEC -help | less

  9. Documentation RWTH Compute Cluster Environment • HPC Users‘sGuide (a bitoutdated):http://www.rz.rwth-aachen.de/hpc/primer • Online documentation (includingexamplescripts):https://doc.itc.rwth-aachen.de/ • Man-Pages for all commandsavailable • In caseoferrors / problemsletusknow:servicedesk@itc.rwth-aachen.de

  10. Lab Weprovidelaptops • Log in tothelaptopswiththelocal „hpclab“ account(yourown PC poolaccountsmight also work) • Use X-Win32 to log in to the cluster (use “hpclab0Z” or your own account) • Log in to the labZnode (use “hpclab0Z” account) • Feelfreetoaskquestions Source: D. Both, Bull GmbH

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