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Introduction to the NERSC J90 Cluster

This document provides an overview of the NERSC J90 Cluster, including hardware details, file systems, environment shells, compiling and linking options, execution methods, debugging tools, libraries, and available applications.

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Introduction to the NERSC J90 Cluster

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  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) 13 April, 1999 Intro to the J90 Systems 2

  3. Hardware Overview (cont.) NERSC J90 Cluster MachineCPUs/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 13 April, 1999 Intro to the J90 Systems 3

  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 13 April, 1999 Intro to the J90 Systems 4

  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 13 April, 1999 Intro to the J90 Systems 5

  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 13 April, 1999 Intro to the J90 Systems 6

  7. Environment Shells Supported sh csh ksh (same as sh) Unsupported tcsh (module load tcsh) bash (module load tools) 13 April, 1999 Intro to the J90 Systems 7

  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 modfilemodfile.rev module display modfile module help modfile 13 April, 1999 Intro to the J90 Systems 8

  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 13 April, 1999 Intro to the J90 Systems 9

  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 13 April, 1999 Intro to the J90 Systems 10

  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 13 April, 1999 Intro to the J90 Systems 11

  12. Compiler Options Comparison Featurecf77f90 Static storage -a -ev Autotasking -Zp -Otask3 Vectorization -Zv -Otask0,scalar3,vector3 Optimization -Zp -Zv -Otask3,scalar3,vector3 Overindexing(default) -Ooverindex 13 April, 1999 Intro to the J90 Systems 12

  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 13 April, 1999 Intro to the J90 Systems 13

  14. Execution Multiprocessing setenv NCPUS 4 (csh) export NCPUS=4 (ksh) "a.out: Command not found." ./a.out ... 13 April, 1999 Intro to the J90 Systems 14

  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 13 April, 1999 Intro to the J90 Systems 15

  16. Debugging totalview -h Display brief summary of commands totalview -L Line-mode interface (similar to cdbx) 13 April, 1999 Intro to the J90 Systems 16

  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 13 April, 1999 Intro to the J90 Systems 17

  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 13 April, 1999 Intro to the J90 Systems 18

  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 13 April, 1999 Intro to the J90 Systems 19

  20. Tools ja ./name ja -cst -n name hpm prof flowview atexpert 13 April, 1999 Intro to the J90 Systems 20

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