Software Overview

1
Software Overview Environment, libraries,
debuggers, programming tools and
applications Jonathan Carter NUG Training 3 Oct
2005
2
Overview

• Environment
• Libraries
• Debuggers
• Programming Tools
• Applications

3
Environment

• Suse Linux
• Linux Networx HPC software stack
• Pathscale compilers
• PBS Pro Batch System
• GPFS HOME and SCRATCH file systems

4
Environment (cont)

• Passwords
• NIM password, use NIM to change
• Shells
• Default shell is tcsh, to change use NIM
  interface
• Startup files
• Read-only, use ltnamegt.ext if you want to add
  customizations
• fixdots command will repair files

5
Environment (cont)

• Access to libraries, tools and applications is
  controlled via modules
• Number of modules reduced compared with seaborg,
  since we only have 64-bit ABI and fewer software
  versions

6
Libraries

• Math
• ACML, fftw, NAG, parpack, scalapack, superlu,
  (imsl, petsc)
• I/O
• hdf, hdf5, netcdf
• MPI I/O available via MVAPICH
• Visualization
• ncar

7
Libraries (cont)

• ACML
• Optimized for AMD processors
• BLAS 1-3, FFT and LAPACK
• fast math functions (log is 90 cycles instead
  of 120)
• vector math functions, e.g. vrda_log(n, x, y)
  is roughly twice as fast as log at ngt20.

8
Libraries (cont)

• Fortran I/O
• Intel/AMD hardware is little-endian, Power is
  big-endian, so binary data is incompatible
• pathf90 offers several features to write binary
  data in big-endian format

9
Libraries (cont)

• pathf90 options
• -byteswapio writes all data in format opposite to
  that of native processor
• -conversion native, little_endian, big_endian
• assign command
• FILENV.assign
• export FILENV
• assign N mips u10

10
Libraries (cont)

• Many libraries are linked at runtime, so
  LD_LIBRARY_PATH must include a path to each
  library linked against
• Modules environment takes care of this provided
  you load at compile time and at run time

11
Debuggers

• Totalview and gdb available for serial
  applications

module load totalview totalview progname
corefile gdb progname corefile
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Debuggers (cont)

• Totalview and gdb are coming for parallel
  applications
• gdb opens xterm per processor

module load totalview mpirun tv np procs
progname mpirun debug np procs progname
13
Debuggers (cont)

• Generating core files
• Serial applications
• ulimit -S -c unlimited
• Parallel applications, make shell script
  progname.sh and run this via mpirun (this problem
  will be resolved by PBS bugfix)
• !/bin/bash
• ulimit -S -c unlimited
• exec progname

14
Debuggers (cont)

• Useful Pathscale compiler options
• Use g flag to help debugging
• Use trapuv to set uninitialized (local,
  automatic, alloca() not Fortran allocatable)
  variables to NAN

15
Debuggers (cont)

• Further information on Totalview
• Etnus tutorial http//www.etnus.com/TotalView/star
  ted/getting_started.html
• LLNL tutorial
• http//www.llnl.gov/computing/tutorials/totalview/

16
Programming Tools

• AMD CodeAnalyst suite of tools to optimize code
  for Opteron coming soon
• ipm mpi overhead and performance report
• papi interface to hardware performance counters
• tau suite of tools enabling performance
  analysis of application codes
• valgrind multiple tools to check memory use,
  profile cache use, detect data race conditions in
  threaded applications

17
Applications

• Chemistry Materials Science
• GAMESS, Gaussian, Gromacs, MOLPRO, NWChem, NAMD,
  VASP
• Math
• maple, matlab, mathematica
• Visualization
• idl, vmd
• Other
• Subversion (client)