85 lines
2.7 KiB
Plaintext
85 lines
2.7 KiB
Plaintext
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(Message inbox:135)
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Date: Mon, 17 Oct 88 16:53:33 PDT
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To: mike@wheaties.ai.mit.edu
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cc: darin%pioneer@eos.arc.nasa.gov, luzmoor@violet.berkeley.edu
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From: James A. Woods <jaw@eos.arc.nasa.gov>
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Subject: README.cray for GNU e?grep
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I just sent this out to comp.unix.cray:
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-------------------------------------------------------------------
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From: jaw@eos.UUCP (James A. Woods)
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Newsgroups: comp.unix.cray
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Subject: GNU e?grep on Cray machines
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Message-ID: <1750@eos.UUCP>
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Date: 17 Oct 88 23:47:29 GMT
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Organization: NASA Ames Research Center, California
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Lines: 66
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# "What comes after silicon? Oh, gallium arsenide, I'd guess. And after
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that, there's a thing called indium phosphide."
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-- Seymour Cray, Datamation interview, circa 1980
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Now that most Cray software development is done on Crays themselves,
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thanks to Unix, GNU e?grep should come in handy. Of course, if you're
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scanning GENBANK for the Human Genome Project at 10 MB/second (the raw
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X/MP Unix I/O rate), you really do need the speed.
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Sample, from one of the Ames Cray 2 machines:
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stokes> time ./egrep astrian web2 # GNU egrep
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alabastrian
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Lancastrian
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Zoroastrian
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Zoroastrianism
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0.5980u 0.0772s 0:01 35%
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stokes> time /usr/bin/egrep astrian web2 # ATT egrep
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alabastrian
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Lancastrian
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Zoroastrian
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Zoroastrianism
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7.6765u 0.1373s 0:15 49%
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(web2 is a 2.4 MB wordlist, standard on BSD Unix.)
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To bring up GNU E?GREP, ftp Mike Haertel's version 1.1 package from
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'prep.ai.mit.edu' or 'ames.arc.nasa.gov'. Mention -DUSG in the Makefile,
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and specify
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#define SIGN_EXTEND_CHAR(c) ((c)>(char)127?(c)-256:(c))
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in regex.c. [Cray characters, like MIPS chars, are unsigned, but the
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compiler won't allow ... #define SIGN_EXTEND_CHAR(c) ((signed char) (c))]
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However, at least on the Cray 2, there's a compiler bug involving the
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increment operator in complex expressions, which requires the following
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modification (also in regex.c):
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change
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m->elems[m->nelem++].constraint |= s2->elems[j++].constraint;
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to
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m->elems[m->nelem].constraint |= s2->elems[j].constraint;
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m->nelem++;
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j++;
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Thanks go to Darin Okuyama of NASA ARC for providing this workaround.
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-- James A. Woods (ames!jaw)
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NASA Ames Research Center
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P.S.
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Though Crays are not at their best pushing bytes, the timing difference
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is even more exaggerated with heavier regexpr processing, to wit:
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time ./egrep -i 'as.*Trian' web2
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...
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0.7677u 0.0769s 0:01 44%
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vs.
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time /usr/bin/egrep -i 'as.*Trian' web2
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...
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16.1327u 0.1379s 0:32 49%
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which is a mite unfair given a known System 5 egrep -i gaffe. You get
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extra credit for vectorizing the inner loop of the Boyer/Moore/Gosper
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code, though changing all chars to ints might help also.
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