• Symbol
• .netrc fileauto-initialize ftp sessions and define ftp macros 273
  
• /dev/stdinaccessing stdin as a file 338
  
• [shell syntax for conditional tests, "/usr/bin/[" versus "/usr/bin/test" versus "[[" 348
  
• A
• AMD Opterondetermine the core a process is using 396
  
• AutotoolsMakefile style advice 418
  
• aliasesreader favorites 146 290 363
  using within scripts 342
  
• apportioning K tasks among M PEs 132
  
• arrunning ar command on 32 and 64 bit libraries on IBM systems 333
  using ar or ld to combine .o files and reduce over-sized argument string 300
  
• argument list too longwhen the shell can't handle wildcard expansion 216 300
  
• assign commandtranslating unformatted files 219
  
• automobile engine heaterunplugging 156
  
• awkchecking number of inputs per line 409
  examples 272 316 337 356 370 375 391 409
  extracting fields from ls output 356
  
• B
• BLACSglobal reductions with BLACS, coding from communication primitives 351
  
• babelconnecting C/C++ to python 344
  
• base conversionconverting numbers between bases in Unix 282
  
• basename/dirname commandsreturn file name or directory path from a path/filename string 268
  
• bashcommand completion in bash 353
  command line editing 397
  extracting the extension from a filename using pattern matching operators 347
  
• batchsubmitting batch jobs in IRIX 249
  
• batch removeusing Unix commands 179
  
• bcevaluating math expressions found in a text file 285 406
  
• bearsdefense against 197
  
• blankets on your carwarming your car when it's cold out 334
  
• blind directoriessafer file sharing 191
  
• book reviewscientific books 320
  
• bucket sortfaster than quicksort 141
  
• C
• CC vs Fortran -- default array indexing 154 155
  calling C from Fortran -- portable interface 260
  comment blocks for documentation systems 367
  commenting out commented code, or, how to nest "comments" 339
  finding path of an executable 183
  linking gridinfo, gridinit, and FFT libraries with C/C++ code 233
  path to executable 183
  pointer pointer 394
  pointer reference 159 394
  preprocessor directives with make 326
  pretty-printer 295
  programming style question, how would you choose the minimum 264
  question-mark colon construct 127
  retaining the precision of output doubles using format specifiers 361
  trapping floating point errors using gcc feenableexcept 376
  using realloc 394
  viewing arrays in totalview 145
  
• C++confusion between "cpp" and "CC" commands 279
  copying values from a C style array to a STL vector 350
  linking to C libraries 308
  using the STL map class 399
  using the STL vector assign member function 350
  using the STL vector reserve member function 350
  using the stringstream class 373
  
• C/C++calling from python 344 349
  
• CDPATHjumping between directories 123
  
• CPUdetermine the core a process is using 396
  
• CVSalternative to diff 313
  version control and software maintenance 278
  
• Catch-22 257
  
• Co-Array Fortranarray bounds 154
  
• Collectivescollective nouns for supercomputer related terminology 384
  
• Compiler options-O3,aggress 166
  -g 166
  from the executable file, determine what compiler flags were used 368
  
• Cray Fortran(/ ... /) syntax -- array constructor 157
  -Fmacro expansion 174
  -Oinlinefrom 207
  -Rbarray bounds checking 129
  -Vversion 149
  -eIimplicit none 129
  -rxreport on variable usage and cross-references 221
  -s cf77typestype compatibility with Fortran 77 174
  -static 202
  ALLOCATE statement -- testing for success 135
  Directive for unwinding loops 292
  performance comparison of DO-IF vs WHERE 205
  
• cURLcommand-line retrieval of web pages 311
  
• carpal tunnel syndromeavoiding 113
  
• chgrp 192
  
• chmod-R go+rXintelligently add execute bit 147
  1770setting the sticky bit 109
  changing entire path to a selected file, but not recursively 220
  g=x ~blind home directory 191
  group/world executable directories put at risk all files within 298
  
• code-blindnesscures 271
  
• col-bxconverting man pages 118
  
• commusing the comm command to compare files 362
  
• commasreformatting long number strings with comma separators 329
  
• compilersdetermining version 149
  
• core filesdeterminine origin of 200
  limiting size 121
  managing files from many processes 403
  
• cp--parentspreserving parent directories (GNU cp) 377
  -i 187
  -pcopying modification time along with the file 231
  
• cpuUNICOS /etc/cpu command for control over caching 209
  
• cshfile name completion 176
  redirecting stderr and stdout 223
  
• csh/tcshcommand line editing 397
  extracting the extension from a filename using variable modifiers 347
  
• cutextracting columns of data from text files 272 337 356
  
• D
• DISPLAY environment variableIncorrect setting causes console session failure 243
  
• DMFFile compression and affect on DMF migration 188
  How to dmput files owned by other members of a group 222
  
• DoxygenFor code documentation 367
  
• DuplicatesFinding duplicate files 392
  
• date+%Y%m%dCreating file versions with a date stamp 310
  --dateTiming a series of jobs 393
  Generating a series of file names containing dates 398
  
• date stampCreating file versions with a date stamp 310
  
• dcdesktop calculator 167
  
• debuggingfinding problem in one of many source files 275
  
• deleting ^M characters in batch 139 287
  
• deleting the file "-i" 102
  
• development environmentsreader favorites 341
  
• diamond as conductor 120
  
• diff"modern" alternatives to diff (tkdiff, ediff, vimdiff, etc...) 313
  -D 124
  comparing a file to stdin 338
  comparing a remote file to a local file 338
  ndiff, numerical differences allowed and handled intelligently 378
  
• dirname/basename commandsreturns directory path or file name from a path/filename string 268 401
  
• dmgetmost efficient use 162
  
• dotfilesmaintaining consistent dotfiles across multiple systems 312
  
• du-minclude Cray DMF migrated files 164
  -skexcludes Cray DMF migrated files, under-estimates size of tar file 267
  -sktotaled disk usage in KBs 164
  -sktotal size of subdirectories 405
  
• E
• e-mailsending automatic vacation messages 143
  
• e-mail from NQS 138
  
• echofor shell preview of wild-card expansion 256
  in .bashrc causes scp failure 419
  
• editorsfavorite development environments 341
  using text editors to copy/paste rectangular blocks 272
  
• egrepadvanced filtering examples 161 168 337 389
  
• emacsdiff-like features 313
  getting colors to work on any platforms 297
  tramp to access remote files 314
  
• env/usr/bin/env searches PATH for binary 372
  
• environment variablesappending to $PATH, $LM_LICENSE_FILE, etc. 245
  available to running NQS jobs 198
  show environment of a running process 417
  testing if set 319
  
• escapescontrolling the interpretation of regular expressions 280
  
• evalevaluate variable as a perl program 406
  
• exsingle command line "ex" command prepends file A to file B 302
  
• execUnix exec command, for redirecting stdout to file for entire session 388
  
• exit statusof a pipeline 412
  
• expand commandreplacing tabs with spaces 203
  
• expectan expect script for ftp initialization 273
  timeout 411
  
• explainCray's "explain" command prints details on many warnings/errors 293
  
• exprdifferences 237
  using regular expression to extract a substring 347
  
• eye strainreducing 106
  
• F
• FFTlinking gridinfo, gridinit, and FFT libraries with C/C++ code 233
  
• FortranCYCLE and EXIT 248 249
  DO loop iterator exit value, formula for computing 325
  Fortran 90 INTEGER constants 215
  Fortran 90 MODULE replaces Fortran 77 COMMON 199
  Fortran 90 OPTIONAL subroutine args and effect on inlining 208
  Fortran 90 generic functions 215
  Fortran vs C -- default array indexing 154 155
  IO buffering problems caused out-of-order output, fixed with flush 386
  LOG10 vs ALOG10 158
  NAMELIST 213
  OPEN (RECL=1024) 144
  RESHAPE 228
  WRITE 144
  WRITE with implied DO incompatible with read with explicit DO 284
  calling C from Fortran -- portable interface 260
  calling from Python 421
  f90 type inconsistency 174
  free vs fixed format discussion 261
  header and include files 171
  intrinsic functions 158
  pretty-printer 295
  trapping floating point errors using gcc feenableexcept 376
  unformatted files and porting them 219
  using arbitrary array bounds 154 155
  
• file commandprobe file type and other info 112 200 332
  
• filesaccess time 178
  batch editing in place 126
  compression and its affect on DMF migration 188
  determining source or type of 112
  generating unique file names in C/C++/Fortran programs 229
  remote access 402
  sharing with your group without compromising home directory 191
  
• find-ctimeto find recently changed files 405
  -execusing with grep 283
  -execusing with tar 331
  -exec and -typeusing -exec with chmod and -type 332
  -mminto find recently modified files (GNU find) 346
  -mtimeto find recently modified files 346
  -pruneprevent descending into subdirectory 181 187
  -sizefinding large files to help stay under quota 259
  -type mfinding migrated files 162
  examples 147 187 230 283 331 332 357 405
  preserving files which match a wildcard expression, deleting the rest 301
  removing core and mppcore files 107
  
• ftpautomating ftp sessions with batch scripts and initialization macdef macros 273
  how to "more" remote and local files 105
  mget/mput a batch of files without prompting 277
  
• G
• gccinline assembly 396
  
• gdbstack traces from many files 403
  
• grep--signifies end of options 226
  -llisting file names 103
  -oShow only the part of a matching line that matches the pattern 358
  -vexcluding grep itself from ps output 224
  list files not containing certain text, using find -exec 230
  list lines before search pattern 345
  listing file names even when only one file searched 283
  searching for multi-line patterns 371
  
• grmview-deqdetermining memory usage at runtime 134
  -l 134
  
• groupgroup/world executable directories put at risk all files within 298
  what determines group ownership of a new file 192
  
• gzipDetermining if a zipped file is okay without unzipping it 321
  
• H
• Haskellexamples 375 410
  
• hexidecimalconverting decimal to hex and back in Unix 282
  
• hidden characters in file names 180
  
• I
• ImageMagick for postscript to png image conversion 374
  
• Initializing program parametersavoiding recompilation 213
  
• implicit none 129
  adding implicit none and explicit declarations to legacy codes 221
  
• inliningimpeded by Fortran 90 OPTIONAL arguments and one workaround 208
  inlinefrom required by Cray Fortran if source in separate files 207
  
• interprocess communicationcommunicating Perl processes 407
  
• J
• jajob accounting command 190
  
• K
• kdestroyremoving Kerberos tickets 288
  
• kerberoskerberos skew too great 189
  next token mode 169
  
• keyboard keys"enlarging" a too-small key on the keyboard by remapping it 352
  
• killaborting MPP jobs 125
  
• krcpcopying directories recursively 343
  
• ksh"_" environment variable 183
  CDPATH environment variable 123
  PS1, favorite settings for your shell prompt 349
  command line editing 397
  file name completion 176
  history file environment variable, HISTFILE 317
  integer keyword 354
  loops in ksh 354 370
  prompt, favorite settings for your shell prompt 349
  redirecting stderr and stdout 223
  typeset declaration 385
  
• L
• Linuxcommands for beginners 408
  
• Loadlevelergetting number of nodes and procs 316
  
• ldusing ld or ar to combine .o files and reduce over-sized argument string 300
  
• librariesdetermining which used 168
  show which shared library each symbol in an executable is provided by 383
  
• limit-d dlimlimiting size of core files 121
  setting maximum stack frame size when your code won't compile 202
  
• listserverproblems unsubscribing 218
  
• llsubmitstarting batch job in directory from which it was submitted 289
  
• ln-spreventing core file creation 114
  
• lock filecommunicating Perl processes 407
  
• ls-Ssort by file size 405
  -boctal codes for nongraphic characters 180
  -dlisting directories only 391
  -qquestion marks for nongraphic characters 180
  -tsort by last time file was modified 405
  -usort by last time file was accessed 405
  colorized output 415
  when directory is not "executable" 244
  
• ls *listing two subdirectory levels 128
  
• lslppgetting XLF version numbers 318
  
• M
• MFLOP/Smeasuring on T3E 153
  
• MPIMPI_Abort for aborting MPP jobs 125
  MPI_Bcast vs SHMEM_BROADCAST 195
  MPI_Comm_dup and creating your own MPI libraries 232
  MPI_Rsend, synchronizing with MPI_Recv 291
  displaying system information from an MPI program 399
  how to preface stdout with task number 255
  message tags, coordinating sends and recvs 210
  using PMPI to build custom MPI subroutine timers 382
  
• MPI compilershow the flags the MPI compiler passes to the system compiler 390
  
• Minneapolisbest restaurants 170
  
• make.PHONY target 400
  Makefile style advice 418
  dependency for Makefile itself 111
  parallel 148
  passing macro definitions from "make" compile line through to compilers 297
  preprocessor directives with make 326
  unconditional make 400
  
• man pagesadding personal man pages to search path 186
  stripping format chars 118
  
• md5sumusing to find duplicate files 392
  
• memorizationhow to remember numbers 305
  
• memory for T3E compilergetting (or not) more of it 251
  
• memory utilizationdetermining at run-time with ja command 190
  
• merging source code versions 124
  
• mkdir-pmaking complete tree 172
  
• modules (Fortran 90)initializing variables 199
  
• modules (UNICOS environment)"module load pghpf" command 151
  creating custom Cray Programming Environment modules 186
  listing compilers, libs, tools, etc. and versions 117
  trouble calling "module" in qsub script 206
  
• mosquitosrepellents, traps, and head nets 250
  
• mpirun-ffor complex argument lists 211
  timing a series of mpirun commands to evaluate performance changes 393
  
• mpixx, mpicc, mpixlf90show the flags the MPI compiler passes to the system compiler 390
  
• mppcore filesdeleting 107
  storing on /tmp 114
  
• mppsize command 112
  
• mppview-tdetermining memory usage at runtime 134
  
• mppwidthfetching core count within a job 404
  
• mv-i 187
  moving a directory into itself 225
  pitfalls 177
  
• N
• NQS daemon 175
  
• NQS jobautomatically creating unique directory for output 269
  checking stdout/stderr while still running 217
  determining if checkpointed 140
  preventing rerun 119
  vanishes 138
  
• NetCDFnetCDF Operators (NCO) 378
  testing the equivalence of netCDF files while allowing for differences in precision 378
  viewing netCDF data 327 378
  
• New Years Computing Resolutions 236
  
• ndiffdiff of files, but with numerical differences allowed and handled intelligently 378
  
• nmshow which shared library each symbol in an executable is provided by 383
  
• numeric constantsdeclaring in Fortran 90 to be of a particular type 215
  
• numerical precisionnumerical precision and roundoff error summing real numbers 366
  
• O
• OBJECT_MODErunning ar command on 32 and 64 bit libraries on IBM systems 333
  
• OS version numberdiscover using "uname" command 204
  
• OpenMPPermissible C/C++ "for" loops 253
  SINGLE vs MASTER comparison 212
  
• od-cviewing files 180 287 337
  -tdisplay binary data converted to standard types 365
  
• optimization level defaultsCray, SGI, IBM compilers 235
  
• P
• PATT3E performance analysis tools 153
  
• PATHlisting one path per line in a colon-delimited list of paths 265
  
• PBSscript generation 395
  testing if PBS_O_WORKDIR set 319
  
• PEvers (programming environment components) 117
  
• PIPESTATUScapture pipeline exit status 412
  
• Pigetting machine precision value for Pi in C/C++ and Fortran programs 263
  
• parallel make 148
  
• parallel random number generation 133
  
• passwordsinvent and remember 131
  remembering 324
  
• pathhow-compiledPathscale compiler option to determine, from the executable, what compiler flags were used 368
  
• performance improvementgeneral advice 166
  timing a series of MPI jobs 393
  
• perl".." (ranging operator) many nifty uses 163
  -eentering script on command line 163 265
  -p -iedit files in-place, assumed loop 126 208 274 304
  Algorithm::Permute module 410
  File::Basename module 401
  FindBin module 401
  Schwartzian transform 375
  Time::Local module 398
  alarm 411
  checking number of inputs per line 409
  evaluating math expressions found in a text file, and s///e 285
  examples 241 262 265 287 304 322 329 356 357 358 370 375 409
  extracting fields from ls output 356
  map 358
  recovering from an untar in the wrong place 357
  script for condensing a file 116
  slurp mode 371
  
• perl regular expressionslook-ahead assertion 358
  minimal, or non-greedy, matching 262 358
  
• perl xdumpread binary files and convert 365
  
• permissionssetting for a directory tree 416
  
• pghpfaccessing man pages 151
  
• pgreplist processes that meet criteria 407
  
• pipefailcapture pipeline failure status 412
  
• postscript to png image conversionImageMagick, gs, gimp, Netpbm, pstopnm, and ps2png 374
  
• preprocessingcpp examples 260 339
  
• program memory usagehow to determine 134 137
  
• ps-e option to show environment of a process 417
  -p $$to determine which shell I'm using 294
  extracting grep process from grepped output 224
  
• python"/usr/bin/env python" searches PATH for python binary 372
  calling C/C++ from 344 349
  calling Fortran from 421
  evaluating math expressions found in a text file 285
  examples 375 392
  extracting matched patterns from lines of input 358
  glob module 385
  itertools module 410
  os.path.walk 392
  set type in python 362
  
• Q
• qalteraltering NQS requests at run-time 150
  
• qdeldeleting a list of jobs 381
  
• qsub-jjob log 140
  -l mpp_tMPP time 136
  -l p_mpp_tMPP time per process 136
  -nrno restart 119
  -rocheck stdout while job still running 217
  chaining a sequence of jobs 150
  specifying shell to use 206
  starting batch job in directory from which it was submitted 198
  
• quotahow to locate all your big files so you can move or delete them 259
  
• quotescontrolling the interpretation of regular expressions 280
  
• R
• readexample of shell read construct 356
  
• redirecting stdoutUnix exec command, for redirecting stdout to file for entire session 388
  
• remap keyboard"enlarging" a too-small key on the keyboard by remapping it 352
  
• renamerenaming files 322 385
  
• resetcommand for rescuing corrupted terminal session 361
  
• rm-i and -fusing together 270
  deleting a file named "-i" 102
  disabling "rm *" (while otherwise allowing "*") 355 356
  preserving files which match a wildcard expression, deleting the rest 179 301
  
• rmdir-pdeleting directory tree 172
  
• roundoff errornumerical precision and roundoff error summing real numbers 366
  
• rsynccheck for differences in a remote file 413
  preserve file ownership and group settings during file transfer 364
  
• rubypermutation library 410
  
• S
• SHMEMSHMEM_BROADCAST vs MPI_Bcast 195
  shmem_fence vs shmem_quiet 194
  
• SV1disabling caching 209
  
• SWIGconnecting C/C++ to python 344 349
  
• SecurID Cardgenerating a sequence of valid codes w/out reentering PIN 196
  handling & storing 160
  obtainin a new PIN 201
  
• Sourdough Sam Math contest 165
  
• Stack frame size too largeSGI f90 warning 202
  
• scp-pto preserve dates during transfer 314
  copying directories recursively 343
  echo command in .bashrc causes failure 419
  using remote environments with scp 340
  
• scurvy, avoidingTips for impoverished students 369
  
• search and replaceas smart as you want, across many directories and files 208
  removing unwanted octal and extended ASCII codes from text files 287
  
• sedexamples 139 216 241 283 290 304 315 322 323 329 349
  search replace on slew of files 304
  
• sequsing seq to generate a range of dates 398
  using seq with ksh 354
  
• shellappending to the settings of existing environment variables, like PATH 245
  command line editing 397
  expansion of wildcard characters 216 225 256
  how to determine which shell I'm using 294
  prompt and PS1, favorite settings for your shell prompt 349
  sh script to reformatting number strings with commas 329
  shell aliases -- reader favorites 146
  syntax for conditional tests, "[" versus "[[" versus "test" 348
  
• sort-nnumeric sort 405
  Unix sort examples 281 316 337 389
  
• sort methods compared 141
  
• sortingsorting when the key field can be pattern matched, but isn't normally delimited 375
  sorting words on one line 152
  
• squeezing text 116
  
• ssh-c arcfourfaster, but less secure, transfers 414
  known_hosts file 402
  piping input/output to/from 414
  searching a list of machines 402
  using a ssh configuration file to create machine aliases 353
  
• statdetailed inode listins 356
  
• static memory allocationdetermining 137
  
• stderrpiping both stderr and stdout with csh and ksh 335
  
• sticky bit 109
  
• stringsUnix command 168
  
• stty erase <BACKSPACE> 110
  
• T
• table of squaresusing recurrence to compute quickly 286
  
• tabsreplacing with spaces 203
  
• taradding selected files only 377
  archiving specific files only 331
  extracting specific files only 323
  moving everything accidentally untarred in the wrong directory somewhere else 357
  piping input/output to/from 414
  relative untar (remove leading "/'s") 184
  transferring directories between systems using tar with stdin and stdout 343
  using tar to preserve file ownership and group settings during file transfer 364
  why is tar file 3x expected size from "du -sk" 267
  
• tcshcommand completion in tcsh 353
  command line editing 397
  disabling "rm *" with "set rmstar=1" 355
  
• teepiping stderr and stdout to a file and displaying on the screen 335
  
• terminalcolorized output 415
  
• testshell syntax for conditional tests, "/usr/bin/[" versus "/usr/bin/test" versus "[[" 348
  
• tips for lifefrom readers 185 306
  warming your car when it's cold 334
  
• tips for studentsmilk crates 369
  paying bills 369
  
• tmp and scratch purgers 177
  
• totalviewexpanding fortran automatic arrays 243
  viewing C arrays 145
  
• touch-rcopying file access and mod time 231
  
• trtranslate command, example 140 152 316 337 356 375
  
• U
• Unixfinding path of an executable 183
  path to parent script 401
  
• Unix commandsLinux commands for beginners 408
  giving arguments that start with "-" and could be construed as options 226
  
• Unix vacation programautomatic e-mail reply 143
  
• ualsextracting fields from ls output 356
  finding files newer than a specified age 377
  
• ulimit-tset a hard limit on CPU time 411
  
• ulpWhat's an ulp? Or, Unit of Least Precision 254
  
• unameprint system info (hostname nodename release version hardware) 204
  
• uniqUnix uniq command, examples 316 362
  
• unique directory namegenerating automatically in scripts 269
  
• V
• version controlmaintaining software in collaborations 278
  
• vi"!" and ":" commands, how to use registers to edit, save, and execute again 173 379
  "yank" from file 1 and "put" into file 2 252
  "|" jump to column 115
  :%s,/lib ,/usr/lib ,using characters other than "/" to delimit search/replace 266
  :%s/^M//gremoving CTRL-M characters 139
  :.,'m s/^/Ccommenting-out blocks of Fortran code 104
  :10,30s/.\{25\}/&|/inserting vertical lines 142
  :frenaming file buffer 193
  :rusing file insertion to prepend a file to current file 302
  ex commands 104 302 379
  finding cursor column 115
  generating and loading a list of files from grep 103
  noautoindentfixing staggering paste 122
  regular expresion to switch order of element within a line 274
  
• vim"&" repeats last ":s" command 379
  autocmd, remember cursor position and other state between sessions 336
  making color schemes 328
  register ":" contains last ":" (or ex) command. "@:" executes it again 379
  replace 330
  setting highlight colors 328
  
• vimdiffcheck for differences in remote file 413
  
• W
• WHERE construct in Fortran 90 205
  
• web browsersobtaining URL of a frame in Netscape, IE, Lynx 227
  
• wgetcommand-line retrieval of web pages 311
  
• what commandprobing executable 108 168
  
• X
• xargs-lusing with find and grep 283
  examples 283 301 304 322
  preserving files which match a wildcard expression, deleting the rest 301
  
• xlf-qreport -qlistloop, optimization, and other listings 309
  -qsuffixIBM Fortran compiler, recognizing .f90 files as Fortran 90 246 303
  -qsuffixRunning the preprocessor on files with arbitrary suffix 303
  getting XLF version numbers 318
  
• Z
• zshcommand completion in zsh 353
  command line editing 397
  disabling "rm *" 355
  loops in zsh 354
  

Selected Category: "Programming"

• A
• AutotoolsMakefile style advice 418
  
• apportioning K tasks among M PEs 132
  
• B
• BLACSglobal reductions with BLACS, coding from communication primitives 351
  
• babelconnecting C/C++ to python 344
  
• C
• CC vs Fortran -- default array indexing 154 155
  calling C from Fortran -- portable interface 260
  comment blocks for documentation systems 367
  commenting out commented code, or, how to nest "comments" 339
  finding path of an executable 183
  linking gridinfo, gridinit, and FFT libraries with C/C++ code 233
  path to executable 183
  pointer pointer 394
  pointer reference 159 394
  preprocessor directives with make 326
  pretty-printer 295
  programming style question, how would you choose the minimum 264
  question-mark colon construct 127
  retaining the precision of output doubles using format specifiers 361
  trapping floating point errors using gcc feenableexcept 376
  using realloc 394
  viewing arrays in totalview 145
  
• C++confusion between "cpp" and "CC" commands 279
  copying values from a C style array to a STL vector 350
  linking to C libraries 308
  using the STL map class 399
  using the STL vector assign member function 350
  using the STL vector reserve member function 350
  using the stringstream class 373
  
• C/C++calling from python 344 349
  
• CVSalternative to diff 313
  version control and software maintenance 278
  
• Co-Array Fortranarray bounds 154
  
• Collectivescollective nouns for supercomputer related terminology 384
  
• Compiler options-O3,aggress 166
  -g 166
  from the executable file, determine what compiler flags were used 368
  
• Cray Fortran(/ ... /) syntax -- array constructor 157
  -Fmacro expansion 174
  -Oinlinefrom 207
  -Rbarray bounds checking 129
  -Vversion 149
  -eIimplicit none 129
  -rxreport on variable usage and cross-references 221
  -s cf77typestype compatibility with Fortran 77 174
  -static 202
  ALLOCATE statement -- testing for success 135
  Directive for unwinding loops 292
  performance comparison of DO-IF vs WHERE 205
  
• F
• FFTlinking gridinfo, gridinit, and FFT libraries with C/C++ code 233
  
• FortranCYCLE and EXIT 248 249
  DO loop iterator exit value, formula for computing 325
  Fortran 90 INTEGER constants 215
  Fortran 90 MODULE replaces Fortran 77 COMMON 199
  Fortran 90 OPTIONAL subroutine args and effect on inlining 208
  Fortran 90 generic functions 215
  Fortran vs C -- default array indexing 154 155
  IO buffering problems caused out-of-order output, fixed with flush 386
  LOG10 vs ALOG10 158
  NAMELIST 213
  OPEN (RECL=1024) 144
  RESHAPE 228
  WRITE 144
  WRITE with implied DO incompatible with read with explicit DO 284
  calling C from Fortran -- portable interface 260
  calling from Python 421
  f90 type inconsistency 174
  free vs fixed format discussion 261
  header and include files 171
  intrinsic functions 158
  pretty-printer 295
  trapping floating point errors using gcc feenableexcept 376
  unformatted files and porting them 219
  using arbitrary array bounds 154 155
  
• G
• gccinline assembly 396
  
• gdbstack traces from many files 403
  
• H
• Haskellexamples 375 410
  
• I
• Initializing program parametersavoiding recompilation 213
  
• implicit none 129
  adding implicit none and explicit declarations to legacy codes 221
  
• inliningimpeded by Fortran 90 OPTIONAL arguments and one workaround 208
  inlinefrom required by Cray Fortran if source in separate files 207
  
• interprocess communicationcommunicating Perl processes 407
  
• L
• lock filecommunicating Perl processes 407
  
• M
• MPIMPI_Abort for aborting MPP jobs 125
  MPI_Bcast vs SHMEM_BROADCAST 195
  MPI_Comm_dup and creating your own MPI libraries 232
  MPI_Rsend, synchronizing with MPI_Recv 291
  displaying system information from an MPI program 399
  how to preface stdout with task number 255
  message tags, coordinating sends and recvs 210
  using PMPI to build custom MPI subroutine timers 382
  
• MPI compilershow the flags the MPI compiler passes to the system compiler 390
  
• make.PHONY target 400
  Makefile style advice 418
  dependency for Makefile itself 111
  parallel 148
  passing macro definitions from "make" compile line through to compilers 297
  preprocessor directives with make 326
  unconditional make 400
  
• man pagesadding personal man pages to search path 186
  stripping format chars 118
  
• memory for T3E compilergetting (or not) more of it 251
  
• merging source code versions 124
  
• modules (Fortran 90)initializing variables 199
  
• modules (UNICOS environment)"module load pghpf" command 151
  creating custom Cray Programming Environment modules 186
  listing compilers, libs, tools, etc. and versions 117
  trouble calling "module" in qsub script 206
  
• mpirun-ffor complex argument lists 211
  timing a series of mpirun commands to evaluate performance changes 393
  
• mpixx, mpicc, mpixlf90show the flags the MPI compiler passes to the system compiler 390
  
• N
• NetCDFnetCDF Operators (NCO) 378
  testing the equivalence of netCDF files while allowing for differences in precision 378
  viewing netCDF data 327 378
  
• numeric constantsdeclaring in Fortran 90 to be of a particular type 215
  
• numerical precisionnumerical precision and roundoff error summing real numbers 366
  
• O
• OpenMPPermissible C/C++ "for" loops 253
  SINGLE vs MASTER comparison 212
  
• optimization level defaultsCray, SGI, IBM compilers 235
  
• P
• PATT3E performance analysis tools 153
  
• Pigetting machine precision value for Pi in C/C++ and Fortran programs 263
  
• parallel make 148
  
• parallel random number generation 133
  
• pathhow-compiledPathscale compiler option to determine, from the executable, what compiler flags were used 368
  
• performance improvementgeneral advice 166
  timing a series of MPI jobs 393
  
• pghpfaccessing man pages 151
  
• preprocessingcpp examples 260 339
  
• program memory usagehow to determine 134 137
  
• R
• roundoff errornumerical precision and roundoff error summing real numbers 366
  
• S
• SHMEMSHMEM_BROADCAST vs MPI_Bcast 195
  shmem_fence vs shmem_quiet 194
  
• SV1disabling caching 209
  
• SWIGconnecting C/C++ to python 344 349
  
• Stack frame size too largeSGI f90 warning 202
  
• sort methods compared 141
  
• sortingsorting when the key field can be pattern matched, but isn't normally delimited 375
  sorting words on one line 152
  
• T
• totalviewexpanding fortran automatic arrays 243
  viewing C arrays 145
  
• W
• WHERE construct in Fortran 90 205
  
• X
• xlf-qreport -qlistloop, optimization, and other listings 309
  -qsuffixIBM Fortran compiler, recognizing .f90 files as Fortran 90 246 303
  -qsuffixRunning the preprocessor on files with arbitrary suffix 303
  getting XLF version numbers 318
  

Selected Category: "Unix"

• Symbol
• .netrc fileauto-initialize ftp sessions and define ftp macros 273
  
• /dev/stdinaccessing stdin as a file 338
  
• A
• aliasesreader favorites 146 290 363
  using within scripts 342
  
• arrunning ar command on 32 and 64 bit libraries on IBM systems 333
  using ar or ld to combine .o files and reduce over-sized argument string 300
  
• argument list too longwhen the shell can't handle wildcard expansion 216 300
  
• assign commandtranslating unformatted files 219
  
• B
• basename/dirname commandsreturn file name or directory path from a path/filename string 268
  
• bashcommand completion in bash 353
  command line editing 397
  extracting the extension from a filename using pattern matching operators 347
  
• batchsubmitting batch jobs in IRIX 249
  
• batch removeusing Unix commands 179
  
• bcevaluating math expressions found in a text file 285 406
  
• blind directoriessafer file sharing 191
  
• C
• CDPATHjumping between directories 123
  
• cURLcommand-line retrieval of web pages 311
  
• chgrp 192
  
• chmod-R go+rXintelligently add execute bit 147
  1770setting the sticky bit 109
  changing entire path to a selected file, but not recursively 220
  g=x ~blind home directory 191
  group/world executable directories put at risk all files within 298
  
• col-bxconverting man pages 118
  
• commusing the comm command to compare files 362
  
• commasreformatting long number strings with comma separators 329
  
• compilersdetermining version 149
  
• core filesdeterminine origin of 200
  limiting size 121
  managing files from many processes 403
  
• cp--parentspreserving parent directories (GNU cp) 377
  -i 187
  -pcopying modification time along with the file 231
  
• cshfile name completion 176
  redirecting stderr and stdout 223
  
• csh/tcshcommand line editing 397
  extracting the extension from a filename using variable modifiers 347
  
• cutextracting columns of data from text files 272 337 356
  
• D
• DISPLAY environment variableIncorrect setting causes console session failure 243
  
• date+%Y%m%dCreating file versions with a date stamp 310
  --dateTiming a series of jobs 393
  Generating a series of file names containing dates 398
  
• date stampCreating file versions with a date stamp 310
  
• dcdesktop calculator 167
  
• deleting ^M characters in batch 139 287
  
• deleting the file "-i" 102
  
• development environmentsreader favorites 341
  
• diff"modern" alternatives to diff (tkdiff, ediff, vimdiff, etc...) 313
  -D 124
  comparing a file to stdin 338
  comparing a remote file to a local file 338
  ndiff, numerical differences allowed and handled intelligently 378
  
• dirname/basename commandsreturns directory path or file name from a path/filename string 268 401
  
• dotfilesmaintaining consistent dotfiles across multiple systems 312
  
• du-minclude Cray DMF migrated files 164
  -skexcludes Cray DMF migrated files, under-estimates size of tar file 267
  -sktotaled disk usage in KBs 164
  -sktotal size of subdirectories 405
  
• E
• echofor shell preview of wild-card expansion 256
  in .bashrc causes scp failure 419
  
• egrepadvanced filtering examples 161 168 337 389
  
• env/usr/bin/env searches PATH for binary 372
  
• environment variablesappending to $PATH, $LM_LICENSE_FILE, etc. 245
  available to running NQS jobs 198
  show environment of a running process 417
  testing if set 319
  
• execUnix exec command, for redirecting stdout to file for entire session 388
  
• exit statusof a pipeline 412
  
• expand commandreplacing tabs with spaces 203
  
• exprdifferences 237
  using regular expression to extract a substring 347
  
• F
• file commandprobe file type and other info 112 200 332
  
• filesaccess time 178
  batch editing in place 126
  compression and its affect on DMF migration 188
  determining source or type of 112
  generating unique file names in C/C++/Fortran programs 229
  remote access 402
  sharing with your group without compromising home directory 191
  
• find-ctimeto find recently changed files 405
  -execusing with grep 283
  -execusing with tar 331
  -exec and -typeusing -exec with chmod and -type 332
  -mminto find recently modified files (GNU find) 346
  -mtimeto find recently modified files 346
  -pruneprevent descending into subdirectory 181 187
  -sizefinding large files to help stay under quota 259
  -type mfinding migrated files 162
  examples 147 187 230 283 331 332 357 405
  preserving files which match a wildcard expression, deleting the rest 301
  removing core and mppcore files 107
  
• G
• grep--signifies end of options 226
  -llisting file names 103
  -oShow only the part of a matching line that matches the pattern 358
  -vexcluding grep itself from ps output 224
  list files not containing certain text, using find -exec 230
  list lines before search pattern 345
  listing file names even when only one file searched 283
  searching for multi-line patterns 371
  
• groupgroup/world executable directories put at risk all files within 298
  what determines group ownership of a new file 192
  
• H
• hexidecimalconverting decimal to hex and back in Unix 282
  
• hidden characters in file names 180
  
• K
• killaborting MPP jobs 125
  
• krcpcopying directories recursively 343
  
• ksh"_" environment variable 183
  CDPATH environment variable 123
  PS1, favorite settings for your shell prompt 349
  command line editing 397
  file name completion 176
  history file environment variable, HISTFILE 317
  integer keyword 354
  loops in ksh 354 370
  prompt, favorite settings for your shell prompt 349
  redirecting stderr and stdout 223
  typeset declaration 385
  
• L
• Linuxcommands for beginners 408
  
• Loadlevelergetting number of nodes and procs 316
  
• ldusing ld or ar to combine .o files and reduce over-sized argument string 300
  
• librariesdetermining which used 168
  show which shared library each symbol in an executable is provided by 383
  
• limit-d dlimlimiting size of core files 121
  setting maximum stack frame size when your code won't compile 202
  
• ln-spreventing core file creation 114
  
• ls-Ssort by file size 405
  -boctal codes for nongraphic characters 180
  -dlisting directories only 391
  -qquestion marks for nongraphic characters 180
  -tsort by last time file was modified 405
  -usort by last time file was accessed 405
  colorized output 415
  when directory is not "executable" 244
  
• ls *listing two subdirectory levels 128
  
• lslppgetting XLF version numbers 318
  
• M
• mkdir-pmaking complete tree 172
  
• mv-i 187
  moving a directory into itself 225
  pitfalls 177
  
• N
• ndiffdiff of files, but with numerical differences allowed and handled intelligently 378
  
• nmshow which shared library each symbol in an executable is provided by 383
  
• O
• OBJECT_MODErunning ar command on 32 and 64 bit libraries on IBM systems 333
  
• OS version numberdiscover using "uname" command 204
  
• od-cviewing files 180 287 337
  -tdisplay binary data converted to standard types 365
  
• P
• PATHlisting one path per line in a colon-delimited list of paths 265
  
• permissionssetting for a directory tree 416
  
• ps-e option to show environment of a process 417
  -p $$to determine which shell I'm using 294
  extracting grep process from grepped output 224
  
• Q
• quotahow to locate all your big files so you can move or delete them 259
  
• R
• redirecting stdoutUnix exec command, for redirecting stdout to file for entire session 388
  
• renamerenaming files 322 385
  
• resetcommand for rescuing corrupted terminal session 361
  
• rm-i and -fusing together 270
  deleting a file named "-i" 102
  disabling "rm *" (while otherwise allowing "*") 355 356
  preserving files which match a wildcard expression, deleting the rest 179 301
  
• rmdir-pdeleting directory tree 172
  
• rsynccheck for differences in a remote file 413
  preserve file ownership and group settings during file transfer 364
  
• S
• scp-pto preserve dates during transfer 314
  copying directories recursively 343
  echo command in .bashrc causes failure 419
  using remote environments with scp 340
  
• sequsing seq to generate a range of dates 398
  using seq with ksh 354
  
• shellappending to the settings of existing environment variables, like PATH 245
  command line editing 397
  expansion of wildcard characters 216 225 256
  how to determine which shell I'm using 294
  prompt and PS1, favorite settings for your shell prompt 349
  sh script to reformatting number strings with commas 329
  shell aliases -- reader favorites 146
  syntax for conditional tests, "[" versus "[[" versus "test" 348
  
• sort-nnumeric sort 405
  Unix sort examples 281 316 337 389
  
• squeezing text 116
  
• ssh-c arcfourfaster, but less secure, transfers 414
  known_hosts file 402
  piping input/output to/from 414
  searching a list of machines 402
  using a ssh configuration file to create machine aliases 353
  
• statdetailed inode listins 356
  
• static memory allocationdetermining 137
  
• stderrpiping both stderr and stdout with csh and ksh 335
  
• sticky bit 109
  
• stringsUnix command 168
  
• stty erase <BACKSPACE> 110
  
• T
• taradding selected files only 377
  archiving specific files only 331
  extracting specific files only 323
  moving everything accidentally untarred in the wrong directory somewhere else 357
  piping input/output to/from 414
  relative untar (remove leading "/'s") 184
  transferring directories between systems using tar with stdin and stdout 343
  using tar to preserve file ownership and group settings during file transfer 364
  why is tar file 3x expected size from "du -sk" 267
  
• tcshcommand completion in tcsh 353
  command line editing 397
  disabling "rm *" with "set rmstar=1" 355
  
• teepiping stderr and stdout to a file and displaying on the screen 335
  
• terminalcolorized output 415
  
• testshell syntax for conditional tests, "/usr/bin/[" versus "/usr/bin/test" versus "[[" 348
  
• touch-rcopying file access and mod time 231
  
• trtranslate command, example 140 152 316 337 356 375
  
• U
• Unixfinding path of an executable 183
  path to parent script 401
  
• Unix commandsLinux commands for beginners 408
  giving arguments that start with "-" and could be construed as options 226
  
• Unix vacation programautomatic e-mail reply 143
  
• ualsextracting fields from ls output 356
  finding files newer than a specified age 377
  
• ulimit-tset a hard limit on CPU time 411
  
• unameprint system info (hostname nodename release version hardware) 204
  
• uniqUnix uniq command, examples 316 362
  
• W
• what commandprobing executable 108 168
  
• X
• xargs-lusing with find and grep 283
  examples 283 301 304 322
  preserving files which match a wildcard expression, deleting the rest 301
  
• Z
• zshcommand completion in zsh 353
  command line editing 397
  disabling "rm *" 355
  loops in zsh 354
  

Selected Category: "Utility"

• C
• cpuUNICOS /etc/cpu command for control over caching 209
  
• D
• DMFFile compression and affect on DMF migration 188
  How to dmput files owned by other members of a group 222
  
• dmgetmost efficient use 162
  
• E
• e-mailsending automatic vacation messages 143
  
• e-mail from NQS 138
  
• editorsfavorite development environments 341
  using text editors to copy/paste rectangular blocks 272
  
• emacsdiff-like features 313
  getting colors to work on any platforms 297
  tramp to access remote files 314
  
• expectan expect script for ftp initialization 273
  timeout 411
  
• explainCray's "explain" command prints details on many warnings/errors 293
  
• F
• ftpautomating ftp sessions with batch scripts and initialization macdef macros 273
  how to "more" remote and local files 105
  mget/mput a batch of files without prompting 277
  
• G
• grmview-deqdetermining memory usage at runtime 134
  -l 134
  
• gzipDetermining if a zipped file is okay without unzipping it 321
  
• I
• ImageMagick for postscript to png image conversion 374
  
• J
• jajob accounting command 190
  
• K
• kdestroyremoving Kerberos tickets 288
  
• kerberoskerberos skew too great 189
  next token mode 169
  
• L
• llsubmitstarting batch job in directory from which it was submitted 289
  
• M
• memory utilizationdetermining at run-time with ja command 190
  
• mppcore filesdeleting 107
  storing on /tmp 114
  
• mppsize command 112
  
• mppview-tdetermining memory usage at runtime 134
  
• mppwidthfetching core count within a job 404
  
• N
• NQS daemon 175
  
• NQS jobautomatically creating unique directory for output 269
  checking stdout/stderr while still running 217
  determining if checkpointed 140
  preventing rerun 119
  vanishes 138
  
• P
• PBSscript generation 395
  testing if PBS_O_WORKDIR set 319
  
• PEvers (programming environment components) 117
  
• pgreplist processes that meet criteria 407
  
• postscript to png image conversionImageMagick, gs, gimp, Netpbm, pstopnm, and ps2png 374
  
• Q
• qalteraltering NQS requests at run-time 150
  
• qdeldeleting a list of jobs 381
  
• qsub-jjob log 140
  -l mpp_tMPP time 136
  -l p_mpp_tMPP time per process 136
  -nrno restart 119
  -rocheck stdout while job still running 217
  chaining a sequence of jobs 150
  specifying shell to use 206
  starting batch job in directory from which it was submitted 198
  
• V
• vi"!" and ":" commands, how to use registers to edit, save, and execute again 173 379
  "yank" from file 1 and "put" into file 2 252
  "|" jump to column 115
  :%s,/lib ,/usr/lib ,using characters other than "/" to delimit search/replace 266
  :%s/^M//gremoving CTRL-M characters 139
  :.,'m s/^/Ccommenting-out blocks of Fortran code 104
  :10,30s/.\{25\}/&|/inserting vertical lines 142
  :frenaming file buffer 193
  :rusing file insertion to prepend a file to current file 302
  ex commands 104 302 379
  finding cursor column 115
  generating and loading a list of files from grep 103
  noautoindentfixing staggering paste 122
  regular expresion to switch order of element within a line 274
  
• vim"&" repeats last ":s" command 379
  autocmd, remember cursor position and other state between sessions 336
  making color schemes 328
  register ":" contains last ":" (or ex) command. "@:" executes it again 379
  replace 330
  setting highlight colors 328
  
• vimdiffcheck for differences in remote file 413
  
• W
• web browsersobtaining URL of a frame in Netscape, IE, Lynx 227
  
• wgetcommand-line retrieval of web pages 311
  

Selected Category: "Scripting"

• Symbol
• [shell syntax for conditional tests, "/usr/bin/[" versus "/usr/bin/test" versus "[[" 348
  
• A
• awkchecking number of inputs per line 409
  examples 272 316 337 356 370 375 391 409
  extracting fields from ls output 356
  
• D
• DoxygenFor code documentation 367
  
• DuplicatesFinding duplicate files 392
  
• E
• escapescontrolling the interpretation of regular expressions 280
  
• evalevaluate variable as a perl program 406
  
• exsingle command line "ex" command prepends file A to file B 302
  
• M
• md5sumusing to find duplicate files 392
  
• P
• PIPESTATUScapture pipeline exit status 412
  
• perl".." (ranging operator) many nifty uses 163
  -eentering script on command line 163 265
  -p -iedit files in-place, assumed loop 126 208 274 304
  Algorithm::Permute module 410
  File::Basename module 401
  FindBin module 401
  Schwartzian transform 375
  Time::Local module 398
  alarm 411
  checking number of inputs per line 409
  evaluating math expressions found in a text file, and s///e 285
  examples 241 262 265 287 304 322 329 356 357 358 370 375 409
  extracting fields from ls output 356
  map 358
  recovering from an untar in the wrong place 357
  script for condensing a file 116
  slurp mode 371
  
• perl regular expressionslook-ahead assertion 358
  minimal, or non-greedy, matching 262 358
  
• perl xdumpread binary files and convert 365
  
• pipefailcapture pipeline failure status 412
  
• python"/usr/bin/env python" searches PATH for python binary 372
  calling C/C++ from 344 349
  calling Fortran from 421
  evaluating math expressions found in a text file 285
  examples 375 392
  extracting matched patterns from lines of input 358
  glob module 385
  itertools module 410
  os.path.walk 392
  set type in python 362
  
• Q
• quotescontrolling the interpretation of regular expressions 280
  
• R
• readexample of shell read construct 356
  
• rubypermutation library 410
  
• S
• sedexamples 139 216 241 283 290 304 315 322 323 329 349
  search replace on slew of files 304
  
• T
• tabsreplacing with spaces 203
  
• U
• unique directory namegenerating automatically in scripts 269
  

Selected Category: "Technical"

• A
• AMD Opterondetermine the core a process is using 396
  
• B
• base conversionconverting numbers between bases in Unix 282
  
• book reviewscientific books 320
  
• bucket sortfaster than quicksort 141
  
• C
• CPUdetermine the core a process is using 396
  
• D
• debuggingfinding problem in one of many source files 275
  
• K
• keyboard keys"enlarging" a too-small key on the keyboard by remapping it 352
  
• L
• listserverproblems unsubscribing 218
  
• M
• MFLOP/Smeasuring on T3E 153
  
• P
• passwordsinvent and remember 131
  remembering 324
  
• R
• remap keyboard"enlarging" a too-small key on the keyboard by remapping it 352
  
• S
• SecurID Cardgenerating a sequence of valid codes w/out reentering PIN 196
  handling & storing 160
  obtainin a new PIN 201
  
• search and replaceas smart as you want, across many directories and files 208
  removing unwanted octal and extended ASCII codes from text files 287
  
• T
• table of squaresusing recurrence to compute quickly 286
  
• tmp and scratch purgers 177
  
• U
• ulpWhat's an ulp? Or, Unit of Least Precision 254
  
• V
• version controlmaintaining software in collaborations 278
  

Selected Category: "General"

• A
• automobile engine heaterunplugging 156
  
• B
• bearsdefense against 197
  
• blankets on your carwarming your car when it's cold out 334
  
• C
• Catch-22 257
  
• carpal tunnel syndromeavoiding 113
  
• code-blindnesscures 271
  
• D
• diamond as conductor 120
  
• E
• eye strainreducing 106
  
• M
• Minneapolisbest restaurants 170
  
• memorizationhow to remember numbers 305
  
• mosquitosrepellents, traps, and head nets 250
  
• N
• New Years Computing Resolutions 236
  
• S
• Sourdough Sam Math contest 165
  
• scurvy, avoidingTips for impoverished students 369
  
• T
• tips for lifefrom readers 185 306
  warming your car when it's cold 334
  
• tips for studentsmilk crates 369
  paying bills 369