Index

fileset: Structured versus Flat Files

ALICE

Andrew File System

ANL

Arctic Region Supercomputer Center

ARSC

Cray X1: To Program Or Not

AVIDD

Introduction | IU HPC Facilities

GPFS

Working with Data on | The AVIDD GPFS

mounting point: The AVIDD GPFS
performance: The AVIDD GPFS
permissions: The AVIDD GPFS

NFS

Working with Data on

server nodes: Working with Data on

WWW page

Birman, Ken

Boehlert, Sherwood

C

arrays versus pointers

case

chmod

clock

CLOCKS_PER_SEC

command line

reading: Program mkrandfile

exit

exit status

fclose

feof

ferror

fopen

for

Data Parallel Paradigm | Program mkrandfile

fread

Program xrandfile

fscanf

fwrite

getenv

Restoring and Saving the | Exercises

gethostname

Hello World

getopt

Program mkrandfile | Handling UNIX Errors

if

INT_MAX

long long

macros

malloc

Exercises | Program xrandfile

mkdir

optarg

perror

rand

rename

sizeof

srand

sscanf

Program mkrandfile | Exercises | Program xrandfile

stat

Exercises

S_ISDIR: Exercises

strcat

strcpy

switch

time

wrap around: Timing a Job

while

Program mkrandfile | Program xrandfile

CAE XSH convention

XSI conformance: Timing a Job

capacity computing

The Focus of the | To Program Or Not

car crash analysis: To Program Or Not
distributing jobs: The Focus of the
SETI: To Program Or Not

CEA

CERN

Chameleon

Checkpointing and Resubmission

checkpointing

ChemIO

Clemson University

clusters

competition

lack of in IT: The Almighty PC

Congress

supercomputer hearing: HPC Facilities at Public

Connection Machine

Cornell University

Cray

Cascade

Red Storm

T3E

Tera

Unicos

checkpointing: Checkpointing and Resubmission

X1

Supercomputers and Clusters | Diffusion | The Discussion

at ARSC: HPC Facilities at Public

Cygwin

bash

cygrunsrv

Dfs

download

Emacs

installation

NTFS

Connecting to the AVIDD | Connecting to the AVIDD

ACLs: Connecting to the AVIDD

OpenSSH

authorized_keys

DSA keys

public: Connecting to the AVIDD

passphrase

slogin

-X: Connecting to the AVIDD | Connecting to the AVIDD

ssh-add

Connecting to the AVIDD | Connecting to the AVIDD

ssh-agent

ssh-keygen

-t dsa: Connecting to the AVIDD

SSH2

X11R6

startxwin.sh

starxwin.sh

xclock

XWin

-clipboard: Connecting to the AVIDD
-multiwindow: Connecting to the AVIDD

DARPA

High Productivity Computing Systems Program: Supercomputers and Clusters

data bases

and business

and science

as client-server systems

DB2

architecture

coordinator node

explain tools

functions as data

on AVIDD

optimizer

plans: Huge Data Bases

Parallel Edition

Finding Help and Documentation | Databases: From Small to | Huge Data Bases

parallelism

function shipping: Huge Data Bases
inter-transaction: Huge Data Bases
intra-query: Huge Data Bases
IO shipping: Huge Data Bases
pipelined: Huge Data Bases
query decomposition: Huge Data Bases

SQL

utilities

epidemiology

high energy physics

SLAC: Databases: From Small to

Ingress

medical information systems

Regenstrief Institute: Databases: From Small to

National Library

Oracle

personal

list of citations: Databases: From Small to

PostgreSQL

C interface

examples: Talking to a PostgreSQL

createdb

documentation

ecpg

Embedded SQL preprocessor

initdb

IPC daemon

Java interface

libpq

pg_hba.conf

pg_ident.conf

postgresql.conf

postmaster

Talking to a PostgreSQL psql

psql

PostgreSQL under Cygwin | Talking to a PostgreSQL psql

-c: Talking to a PostgreSQL
-f: Talking to a PostgreSQL psql
-l: Talking to a PostgreSQL psql
$\backslash$ ?: Talking to a PostgreSQL psql
$\backslash$ c: Talking to a PostgreSQL psql
$\backslash$ d: Talking to a PostgreSQL psql
$\backslash$ e: Talking to a PostgreSQL psql
$\backslash$ h: Talking to a PostgreSQL psql
$\backslash$ i: Talking to a PostgreSQL psql
$\backslash$ l: Talking to a PostgreSQL psql
$\backslash$ q: Talking to a PostgreSQL psql
$\backslash$ r: Talking to a PostgreSQL psql
$\backslash$ s: Talking to a PostgreSQL psql
$\backslash !$: Talking to a PostgreSQL psql
slash commands: Talking to a PostgreSQL psql

templates

SQL

atomicity: Talking to a PostgreSQL
begin: Talking to a PostgreSQL
commit: Talking to a PostgreSQL
create database: Talking to a PostgreSQL psql
create table: Talking to a PostgreSQL psql
delete: Talking to a PostgreSQL
insert: Talking to a PostgreSQL psql | Talking to a PostgreSQL
lock: Talking to a PostgreSQL
rollback: Talking to a PostgreSQL
select: Talking to a PostgreSQL psql
update: Talking to a PostgreSQL psql | Talking to a PostgreSQL

SQL Server

storage methods

tables

data parallel programming

scalability: Scalability of Parallel Programming

data parallelism

deadlock

Dell

disk IO

caching: The AVIDD GPFS
data compression: The AVIDD GPFS
writes versus reads: The AVIDD GPFS

Distributed Storage Systems Groups

DSSG

Dynix

Earth Simulator

Supercomputers and Clusters | Supercomputers and Clusters | To Program Or Not

ECMWF

Emacs

default.el: Finding Help and Documentation
info: Finding Help and Documentation

Express

FLIC

fork

Fortran 90

and MPI: Mixing Parallel Programming Paradigms
and shared memory: Shared Memory Paradigm

Fox, Geoffrey

FTP

fuddy daddies

Fujitsu

AP-3000: The Discussion

Gateway

girlfriend

upset: To Program Or Not

GNU

compilers: Finding Help and Documentation
info: Finding Help and Documentation

GPFS

ACLs

documentation

IO

dependence on block size: Exercises

memory caching

on AVIDD

Grid

.NET Password as grid: HPC and The Grid
AFS as grid: HPC and The Grid
and distributed computing: HPC and The Grid
Globus: HPC and The Grid
Legion: HPC and The Grid
Unicore: HPC and The Grid

Gropp, William

HDF4

HDF5

and Cactus

and Chombo

and Flash

and Intel Array Visualizer

and Java

and LabVIEW

and MPI-IO

and Swarm

and Vis5D

constants

H5F_ACC_EXCL: HDF5 File Creation
H5F_ACC_RDONLY: Writing On and Reading
H5F_ACC_RDWR: Writing On and Reading
H5F_ACC_TRUNC: HDF5 File Creation
H5FD_MPIO_COLLECTIVE: Contiguous Hyperslabs
H5FD_MPIO_INDEPENDENT: Contiguous Hyperslabs
H5P_DATASET_CREATE: Property Lists
H5P_DATASET_XFER: Property Lists | Activate Checksum for Error
H5P_DEFAULT: HDF5 File Creation | HDF5 Datasets | Property Lists
H5P_FILE_ACCESS: Property Lists
H5P_FILE_CREATE: Property Lists
H5S_SELECT_AND: Sequential Example
H5S_SELECT_NOTA: Sequential Example
H5S_SELECT_NOTB: Sequential Example
H5S_SELECT_OR: Sequential Example
H5S_SELECT_SET: Sequential Example
H5S_SELECT_XOR: Sequential Example
H5S_UNLIMITED: HDF5 Datasets
H5T_COMPOUND: Compound Datatypes
H5T_ENUM: Compound Datatypes
H5T_NATIVE_DOUBLE: Compound Datatypes
H5T_NATIVE_FLOAT: Compound Datatypes
H5T_NATIVE_INT: Writing On and Reading | Compound Datatypes
H5T_OPAQUE: Compound Datatypes
H5T_STD_I32BE: Structured versus Flat Files
H5Z_FILTER_FLETCHER32: Activate Checksum for Error

Folk, Michael J.

Frequently Asked Questions

gif2h5

h4toh5

h52gif

H5Aclose

H5Acreate

attribute creation property list: HDF5 Attributes

H5Awrite

H5c++

H5Dclose

H5Dcreate

dataset creation property list: HDF5 Datasets

H5Dget_create_plist

H5Dget_space

h5diff

H5Dopen

H5Dread

h5dump

H5Dwrite

h5fc

H5Fclose

HDF5 File Creation

H5Fcreate

HDF5 File Creation

file access property list: HDF5 File Creation
file creation property list: HDF5 File Creation

H5Fopen

file access flag: Writing On and Reading
file access property list: Writing On and Reading

H5Gclose

HDF5 Groups

H5gen

H5Gget_objinfo

H5Giterate

h5import

h5ls

H5Pcreate

Modifying Property Lists

h5perf

H5Pget_chunk

Activate Checksum for Error

H5Pget_edc_check

H5Pget_layout

H5Pset_chunk

Create a Compressed Dataset

H5Pset_deflate

H5Pset_dxpl_mpio

Contiguous Hyperslabs

H5Pset_fapl_family

Create a File Family

H5Pset_fapl_mpio

Create an MPI-IO File

H5Pset_filter

Activate Checksum for Error

H5Pset_sizes

Modifying Property Lists

H5Rcreate

h5repart

H5Sclose

H5Scopy

H5Screate_simple

H5Sget_simple_extent_dims

H5Sget_simple_extent_ndims

Create an Extendible Dataset | Sequential Example

H5Sselect_elements

Point Selection

H5Sselect_hyperslab

H5Tcommit

H5Tcreate

H5Tinsert

h5toh4

H5View

HOFFSET

JHI5

MPI-IO

hyperslab selection: Hyperslab Selection

object reference

on AVIDD

Reference Manual

Tutorial

types

H5T_STD_I32BE: HDF5 Datasets
herr_t: HDF5 File Creation
hid_t: HDF5 File Creation
hsize_t: HDF5 Datasets

User's Guide

versus data bases

versus flat files

VisAD

High Performance Fortran

High Performance Storage System

Hitachi

hogs

HPC

HPF

and MPI: Message Passing Paradigm
on AVIDD: The Discussion
versus MPI: The Discussion

HPSS

Working with Data on | IU HPSS

and DB2

pftp

client: Using PFTP on AVIDD
kerberized client: Using PFTP on AVIDD

users

I-Light

Introduction | HPC and The Grid

IA32

IA64

IBM

Introduction | The Focus of the | Supercomputers and Clusters

Blue Gene/L

and DB2: Huge Data Bases

BlueGene/L

MPI IO

HPSS

PERCS

SP

at Indiana University: IU HPC Facilities

Watson Laboratory

and MPI-IO: MPI IO

ICRR

Checkpointing and Resubmission

IEEE-1003

IN2P3

India

Indiana University

IU HPC Facilities | IU HPSS

AVIDD

IU HPC Facilities

IBM SP

IU HPC Facilities

GPFS: IU HPC Facilities

LAM MPI

Message Passing Paradigm

IRAF

ISIS

and Microsoft Wolfpack: The History of MPI
virtual synchrony: The History of MPI

Jacobi, Karl Gustav Jacob

Diffusion

KEK

Kerberos

kdestroy: Using PFTP on AVIDD
kinit: Using PFTP on AVIDD
klist: Using PFTP on AVIDD

KISTI

LAM

MPI: The History of MPI

LANL

Laplace

equation

Diffusion

boundary conditions: Diffusion
discretized: Diffusion
Jacobi iterations: Diffusion

operator

Diffusion

Linux

Required Level of Skills

LLNL

Lusk, Ewing

man

configuration file: Finding Help and Documentation

Mathematica

Matlab

message passing

Message Passing Paradigm

Message Passing Interface

Message Passing Paradigm

Microsoft

Mixing Parallel Programming Paradigms

.NET Password: HPC and The Grid
Wolfpack: The History of MPI
Word: Databases: From Small to

MPI

Message Passing Paradigm | The History of MPI

and multi-threading

Argonne implementation

C++

collective operations

Greetings, Master

communicator

error handler

error class: Handling MPI Errors
error code: Handling MPI Errors
MPI_ERRORS_ARE_FATAL: Handling MPI Errors
MPI_ERRORS_RETURN: Handling MPI Errors
MPI_SUCCESS: Handling MPI Errors

group

constants

MPI_2INT: Derived Datatypes in MPI
MPI_ANY_SOURCE: Greetings, Master
MPI_ANY_TAG: Greetings, Master
MPI_BYTE: Derived Datatypes in MPI
MPI_CHAR: Greetings, Master | Derived Datatypes in MPI
MPI_COMM_NULL: The Discussion
MPI_COMM_SELF: The Discussion
MPI_COMM_WORLD: Hello World
MPI_DISTRIBUTE_BLOCK: Defining File Views in | The Discussion
MPI_DISTRIBUTE_CYCLIC: Defining File Views in | Exercises
MPI_DISTRIBUTE_DFLT_DARG: Defining File Views in | The Discussion
MPI_DISTRIBUTE_NONE: Defining File Views in
MPI_DOUBLE: Dividing the Pie | Derived Datatypes in MPI
MPI_DOUBLE_INT: Derived Datatypes in MPI
MPI_ERRORS_ARE_FATAL: Handling MPI Errors
MPI_ERRORS_RETURN: Handling MPI Errors
MPI_FLOAT: Derived Datatypes in MPI
MPI_FLOAT_INT: Derived Datatypes in MPI
MPI_INFO_NULL: The Discussion
MPI_INT: Derived Datatypes in MPI
MPI_LB: Derived Datatypes in MPI | Derived Datatypes in MPI
MPI_LONG: Derived Datatypes in MPI
MPI_LONG_DOUBLE: Derived Datatypes in MPI
MPI_LONG_DOUBLE_INT: Derived Datatypes in MPI
MPI_LONG_INT: Derived Datatypes in MPI
MPI_LONG_LONG: Derived Datatypes in MPI
MPI_LONG_LONG_INT: Derived Datatypes in MPI
MPI_MAX_INFO_KEY: File Hints
MPI_MAX_INFO_VAL: File Hints
MPI_ORDER_C: Defining File Views in | The Discussion
MPI_ORDER_FORTRAN: Defining File Views in
MPI_SHORT: Derived Datatypes in MPI
MPI_SHORT_INT: Derived Datatypes in MPI
MPI_SUCCESS: Handling MPI Errors
MPI_SUM: Dividing the Pie
MPI_UB: Derived Datatypes in MPI | Derived Datatypes in MPI
MPI_UNSIGNED: Derived Datatypes in MPI
MPI_UNSIGNED_CHAR: Derived Datatypes in MPI
MPI_UNSIGNED_LONG: Derived Datatypes in MPI
MPI_UNSIGNED_SHORT: Derived Datatypes in MPI
MPI_WCHAR_T: Derived Datatypes in MPI

data types

debugging programs with fprintf

Bank Queue

file handle

Fortran 90

instrumenting a program

LAM MPI

Message Passing Paradigm | Finding Help and Documentation | The History of MPI

MPE

MPI Graphics and Process

alog file

automatic logging

clog file

clog2alog

clogTOslog2

constants

MPE_AQUAMARINE: Program cxgraphics.c
MPE_BLACK: Program cxgraphics.c
MPE_BLUE: Program cxgraphics.c
MPE_BROWN: Program cxgraphics.c
MPE_CORAL: Program cxgraphics.c
MPE_CYAN: Program cxgraphics.c
MPE_FORESTGREEN: Program cxgraphics.c
MPE_GRAY: Program cxgraphics.c
MPE_GREEN: Program cxgraphics.c
MPE_MAGENTA: Program cxgraphics.c
MPE_MAROON: Program cxgraphics.c
MPE_ORANGE: Program cxgraphics.c
MPE_PINK: Program cxgraphics.c
MPE_RED: Program cxgraphics.c
MPE_SUCCESS: Program cxgraphics.c
MPE_WHITE: Program cxgraphics.c
MPE_YELLOW: Program cxgraphics.c

jumpshot

Timeline Window: Instrumenting MPI Programs with

MPE_Close_graphics

MPE_Describe_event

MPE_Describe_state

MPE_Draw_circle

MPE_Draw_line

MPE_Draw_point

MPE_Draw_string

MPE_Finish_log

MPE_Init_log

MPE_Log_event

MPE_Log_get_event_number

MPE_Make_color_array

MPE_Num_colors

MPE_Open_graphics

MPE_Start_log

MPE_Update

slog2 file

MPI-2

MPI-IO

and IBM Watson Laboratory: MPI IO

MPI-IO

The History of MPI | What is in MPI?

HDF5

hyperslab selection: Hyperslab Selection

MPI_Abort

Handling MPI Errors | The Discussion | Striding Data

MPI_Address

Derived Datatypes in MPI

MPI_Allgather

MPI_Allgatherv

MPI_Allreduce

The Discussion | Handling UNIX Errors | The Discussion

MPI_Barrier

Exercises | Instrumenting MPI Programs with

MPI_Bcast

MPI_Cart_coords

MPI_Cart_create

MPI_Cart_shift

MPI_Comm

MPI_Comm_create

MPI_Comm_free

MPI_Comm_group

MPI_Comm_rank

What is in MPI? | Hello World | The Discussion

MPI_Comm_size

What is in MPI? | Hello World

MPI_Dims_create

Program darray.c | The Discussion

MPI_Errhandler_set

MPI_Error_class

MPI_Error_string

MPI_File_close

MPI_File_Delete

Writing Sequential Files with | The Discussion

MPI_File_get_info

MPI_File_get_position

MPI_File_get_size

MPI_File_iread

MPI_File_iwrite

MPI_File_open

MPI_File_read

MPI_File_read_all

Program darray.c

MPI_File_seek

MPI_File_set_errhandler

MPI_File_set_info

MPI_File_set_view

Defining File Views in | Program darray.c

MPI_File_write

MPI_File_write_all

Program darray.c | The Discussion | Striding Data

MPI_Finalize

What is in MPI? | Hello World | Exercises | Striding Data

MPI_Gather

The Discussion | The Discussion

MPI_Get_address

Derived Datatypes in MPI | Compound Datatypes

MPI_Get_count

MPI_Get_processor_name

MPI_Group

MPI_Group_excl

MPI_Group_free

MPI_Info_create

MPI_Info_get

MPI_Info_get_nkeys

MPI_Info_get_nthkey

MPI_Info_set

MPI_Init

What is in MPI? | Hello World

and the command line: Program life_g.c

MPI_Irecv

MPI_Isend

Dividing the Pie | Instrumenting MPI Programs with

MPI_Recv

What is in MPI? | Greetings, Master | The Discussion

status

The Master Program

MPI_SOURCE: The Master Program
MPI_TAG: The Master Program

MPI_Reduce

MPI_Request

MPI_Send

What is in MPI? | Greetings, Master

MPI_Sendrecv

MPI_Ssend

MPI_Status

MPI_Test

MPI_Type_commit

The Discussion | The Discussion

MPI_Type_contiguous

The Discussion | Derived Datatypes in MPI

MPI_Type_create_darray

Defining File Views in | Defining File Views in | Program darray.c | The Discussion | The Discussion

MPI_Type_create_struct

Derived Datatypes in MPI

MPI_Type_extent

Program darray.c | The Discussion

MPI_Type_indexed

Derived Datatypes in MPI

MPI_Type_size

Program darray.c | The Discussion

MPI_Type_struct

Derived Datatypes in MPI | Compound Datatypes

MPI_Type_vector

The Discussion | Derived Datatypes in MPI

MPI_Wait

MPI_Waitall

Program life_g.c

MPI_Win_set_errhandler

MPI_Wtime

Dividing the Pie | Exercises

MPICH

Message Passing Paradigm | Finding Help and Documentation | The History of MPI

MPICH2

MPI Documentation and Literature | mpdtrace-l

.mpd.conf

mpd.hosts

MPD_USE_USER_CONSOLE

Running MPI on the | Running MPI on the

mpdboot

mpdringtest

mpdrun

-l: Running MPI on the

mpds

mpicc

Hello World

mpiexec

Ohio Supercomputer Center implementation

on AVIDD

process rank

Finding Help and Documentation | The History of MPI

programming examples

Programming Examples

ROMIO

Standard 1.1

Standard 2.0

synchronization

cost of: Greetings, Master

The Complete Reference

Using MPI

Using MPI-2

windows

N-cube

NASA

IU HPSS | The History of MPI

NCDC

NCEP

NCSA

HPC Facilities at Public | HPC and The Grid | The AVIDD GPFS | The AVIDD GPFS

NEC

Cenju-3: The Discussion
Earth Simulator: Supercomputers and Clusters

NEOS

NetMeeting

Using NetMeeting

Nitzberg, Bill

NSF

Introduction | HPC Facilities at Public

Ohio Supercomputer Center

OpenMP

ORNL

IU HPSS | The History of MPI

P4

The History of MPI | The History of MPI

parallel programming

cost of communication: Scalability of Parallel Programming
scalability: Scalability of Parallel Programming

parallelism

data: Data Parallel Paradigm

PBS

PBS_NODEFILE

qdel

qhold

qrls

qsig

PBS Configuration | Submitting, Inspecting and Cancelling

qstat

-f: PBS Dependency Lists
-q: PBS Configuration

qsub

-C

-e

Submitting Jobs From Within

-I

Exercises | Interactive PBS Jobs

-j

-l

nodes=8: Running MPI on the

-m

Simple PBS Directives | Simple PBS Directives

-o

-q

-S

-V

A Multi-Job Job | A Multi-Job Job

-W

PBS Dependency Lists

submitting jobs interactively

Not Quite Interactive PBS

submitting X11 jobs

Interactive PBS Jobs

using here-input in scripts

qusb

-V: Running MPI on the

PC

The Almighty PC

cluster of: Supercomputers and Clusters
memory bottleneck: The Almighty PC

PETSc

PFLOPS

PGHPF

PICL

Supercomputers and Clusters | Data Parallel Paradigm

PIM

Pittsburgh Supercomputer Center

Portland Group

Checkpointing and Resubmission

POSIX

processor in memory

Supercomputers and Clusters | Data Parallel Paradigm

PSC

Ptools

PVFS

PVM

Python

Regenstrief Institute

RIKEN

rlogin

RSL

SAN

Sandia

SC2003 conference

Scarafino, Vincent

SDSC

HPC Facilities at Public | The AVIDD GPFS | The AVIDD GPFS | IU HPSS

secure shell

security bugs

shared memory

skills

Required Level of Skills

Skjellum, Anthony

skulker

SLAC

SMP

Snir, Marc

spawn

speed of light

Stewart, Craig

Storage Area Network

Sun

clockless computing: Supercomputers and Clusters

supercomputing

Supercomputing 92

TEX

TCGMSG

telnet

Thakur, Rajeev

this course

rationale for: To Program Or Not

threads

High Performance Data Management

time and venue

Trilab

Turner, George W. M.

Your AVIDD Account

University of Michigan

University of Stuttgart

University of Texas

UNIX

BSD

fee per campus: Databases: From Small to

chmod

install

INT_MAX

IO caching

writes versus reads: The AVIDD GPFS

make

Makefile: Program mkrandfile

RCS

co: Program mkrandfile | Exercises
rcsclean: Program mkrandfile

shell

io redirection: A Multi-Job Job

signals

catching: Submitting, Inspecting and Cancelling

sleep

tar

time

Submitting Jobs From Within | Timing a Job

troff

man

directives: Program mkrandfile
example input: Program mkrandfile

US supercomputer industry

near death experience: Supercomputers and Clusters

Windows

Required Level of Skills

2000: Using NetMeeting
Dfs: Connecting to the AVIDD
NTFS: Connecting to the AVIDD
XP: Using NetMeeting

X11

mkdirhier: Program mkrandfile

year 2000 bug

year 2038 bug