Introduction to the NERSC J90 Cluster - PowerPoint PPT Presentation

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Introduction to the NERSC J90 Cluster

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Title: Improving the Usability and Accessibility of the ACTS Toolkit Author: LBNL PC User Last modified by: Thomas M. DeBoni Created Date: 1/6/1998 5:21:08 PM – PowerPoint PPT presentation

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Title: Introduction to the NERSC J90 Cluster


1
Introduction to the NERSC J90 Cluster
  • David Turner Tom DeBoni
  • NERSC User Services Group
  • April 1999

2
Hardware Overview
  • J90se CPU
  • 100 MHz, 200 MFlop, 64-bit vector processor
  • "Scalar enhanced"
  • J90 System
  • Multiple J90se CPUs
  • 1 GWord shared memory
  • Large, fast RAID filesystem (/tmp)

3
Hardware Overview (cont.)
  • NERSC J90 Cluster
  • Machine CPUs /tmp
  • killeen 20 161 GB
  • bhaskara 28 368 GB
  • franklin 28 371 GB
  • seymour 28 334 GB
  • fcrick 28 229 GB
  • jwatson 28 229 GB

Interactive System ssh, telnet, cqsub

Batch Systems cqsub
4
File Systems
  • HOME
  • permanent (but not archival)
  • 5 GB quota, regular backups, file migration
  • 93.7 GB total
  • local to killeen, NFS-mounted on batch systems
  • poor performance for batch jobs
  • /u/repo/user
  • /Un/user
  • /u/ccc/dpturner
  • /U0/dpturner

5
File Systems (cont.)
  • TMPDIR
  • temporary (created/destroyed each session)
  • no quota (but NQS limits 4 GB - 32 GB)
  • no backups, no migration
  • local to each machine
  • high-performance RAID arrays
  • system manages this for you
  • A.K.A. BIG

6
File Systems (cont.)
  • /tmp
  • location of TMPDIR
  • 14-day lifetime
  • A.K.A. /big
  • you manage this for yourself
  • HPSS
  • archival tape storage (and file migration)
  • no quota (but tracked by SRU)
  • access with hsi, pftp, or ftp

7
Environment
  • Shells
  • Supported
  • sh
  • csh
  • ksh (same as sh)
  • Unsupported
  • tcsh (module load tcsh)
  • bash (module load tools)

8
Environment (cont.)
  • Modules
  • Found on many Unix systems
  • Sets environment variables, aliases, executable
    search paths, man search paths, header file
    include paths, and/or library load paths
  • Exercise care modifying startup files!
  • Useful options
  • module list
  • module avail
  • module load modfile
  • module switch modfile modfile.rev
  • module display modfile
  • module help modfile

9
Compiling and linking
  • Programming
  • Fortran 90 - f90
  • No Fortran 77 compiler
  • C/C - cc, CC
  • Assembler - as
  • Cray Message Passing Toolkit
  • Use compiler (f90, cc, CC) for linking also
  • f90 file naming conventions
  • Use for Fortran 77-style code
  • filename.f - fixed form
  • filename.F - fixed form, run preprocessor first
  • Use for Fortran 90-style code
  • filename.f90 - free form
  • filename.F90 - free form, run preprocessor first

10
Compiling and linking (cont.)
  • Useful compiler options
  • -dp Disable double precision
  • -rlistop Controls content of listing file
  • -Gn Debugging level
  • 0 Full debugging (same as -g)
  • 1 Block by block debugging
  • -Rrunop Run-time checking
  • a Argument number and type
  • b Array bounds

11
Compiling and linking (cont.)
  • Useful compiler options (cont.)
  • -ev Static storage
  • -On Optimization level
  • 0 None
  • 1 Conservative global scalar optimization
  • 2 Moderate loop nest restructuring
  • 3 Aggressive autotasking

12
Compiler Options Comparison
  • Feature cf77 f90
  • Static storage -a -ev
  • Autotasking -Zp -Otask3
  • Vectorization -Zv -Otask0,scalar3,vector3
  • Optimization -Zp -Zv -Otask3,scalar3,vector3
  • Overindexing (default) -Ooverindex

13
Compiling and linking (cont.)
  • Use make for large projects
  • setenv NPROC 2
  • Fortran 90 modules
  • Don't confuse with module command
  • Each Fortran 90 module must be compiled before
    any routine that uses it
  • Useful linker options
  • -Mopt Load map options

14
Execution
  • Multiprocessing
  • setenv NCPUS 4 (csh)
  • export NCPUS4 (ksh)
  • "a.out Command not found."
  • ./a.out ...

15
Execution(cont.)
  • Interactive
  • killeen, during business hours
  • Small (.le. 80MW), short (.le. 10 hours) jobs
  • Batch
  • killeen, night and weekends
  • Small (.le. 40MW), short (.le. 6 hours) jobs
  • bhaskara, franklin, seymour, fcrick, jwatson
  • Big (.le. 512MW), long (.le. 168 hours) jobs

16
Debugging
  • totalview -h
  • Display brief summary of commands
  • totalview -L
  • Line-mode interface (similar to cdbx)

17
Libraries
  • Mathematics
  • default includes nag, imsl, slatec
  • modules for lsode, harwell
  • Graphics
  • ncar
  • gnuplot
  • I/O
  • HDF - module load hdf
  • netCDF - module load netcdf

18
Applications
  • Amber
  • module load amber41
  • Ansys
  • module load ansys54
  • Basis
  • module load basis11.8
  • Gamess
  • module load gamess
  • Gaussian
  • module load g98
  • Nastran
  • module load nastran

19
Batch Computing
  • User creates shell script myscript
  • Submits to NQE with cqsub myscript
  • Returns NQE task id (e.g., t1234)
  • NQE selects machine and forwards to NQS
  • Job remains pending (NPend) until resources
    available
  • NQS runs the job
  • Assigns NQS job id (e.g., 5678.bhaskara)
  • Run job in appropriate batch queue
  • Job log returned upon completion

20
Tools
  • ja
  • ./name
  • ja -cst -n name
  • hpm
  • prof
  • flowview
  • atexpert
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