[#311132] Haskell GHC : parallel regex-dna : using pcre

Date:
2008-09-22 19:38 Priority:
3

State:
Closed

Submitted by:
Don Stewart (dons-guest) Assigned to:
Nobody (None)

Category:
Haskell GHC Group:
regex-dna

Resolution:
Accepted

Summary:
Haskell GHC : parallel regex-dna : using pcre

Detailed description
This is a variant of the current regex-dna Haskell GHC entry, parallelised using parMap, but importing Text.Regex.PCRE instead of Text.Regex.Posix. To use the haskell-regex-pcre library, either find and install your native package, or just build it from hackage: $ wget http://hackage.haskell.org/packages/archive/regex-pcre-builtin/0.94.2.0.7.7/regex-pcre-builtin-0.94.2.0.7.7.tar.gz $ tar xzf regex-pcre-builtin-0.94.2.0.7.7.tar.gz $ cd regex-pcre-builtin-0.94.2.0.7.7 $ runhaskell Setup.hs configure --prefix=$HOME $ runhaskell Setup.hs build $ sudo runhaskell Setup.hs install The program should be compiled with: ghc B.hs --make -O2 -fglasgow-exts -package regex-posix -optc-O3 -threaded And run with: +RTS -N4 -qw -RTS Observered parallelism: $ time ./B +RTS -N4 -qw < /tmp/data agggtaaa\|tttaccct 356 [cgt]gggtaaa\|tttaccc[acg] 1250 a[act]ggtaaa\|tttacc[agt]t 4252 ag[act]gtaaa\|tttac[agt]ct 2894 agg[act]taaa\|ttta[agt]cct 5435 aggg[acg]aaa\|ttt[cgt]ccct 1537 agggt[cgt]aa\|tt[acg]accct 1431 agggta[cgt]a\|t[acg]taccct 1608 agggtaa[cgt]\|[acg]ttaccct 2178 50833411 50000000 66800214 ./B +RTS -N4 -qw < /tmp/data 27.45s user 0.19s system 284% cpu 9.711 total Note that this is significantly faster than using Text.Regex.Posix, although the code is identical, only an import changes.

Followup

Message
Date: 2008-09-30 01:09 Sender: Isaac Gouy Ho hum installed from hackage.
Date: 2008-09-23 05:23 Sender: Don Stewart I will chase up the debian and ubuntu (if any) developers. In the coming year, we'll be pushing distros to adopt the standard Haskell platform, so this won't occur again, http://www.cse.unsw.edu.au/~dons/papers/CPJS08.html Till the, the hackage->debian->ubuntu pipeline will continue to have holes, sadly.
Date: 2008-09-23 01:58 Sender: Isaac Gouy I'm making a lot of typos today! libghc6-regex-pcre-dev doesn't seem to exist - can you find out why? (I have this vain hope of getting maintainers to fix problems rather than doing my own workarounds.)
Date: 2008-09-23 01:10 Sender: Isaac Gouy libghc6-regex-posix-dev doesn't seem to exist
Date: 2008-09-23 00:58 Sender: Don Stewart > libghc6-regex-base-dev That is the core interface. It uses one of the backend engines, * regex-posix * regex-pcre * regex-tdfa and some others. I imagine you already have the posix library installed, libghc6-regex-posix-dev and now you'll need: libghc6-regex-pcre-dev if that's available on Ubuntu, otherwise, it can be built from hackage as above.
Date: 2008-09-23 00:54 Sender: Isaac Gouy > either find and install your native package libghc6-regex-base-dev "A library containing the interface API for the Haskell regular expressions library packages regex-posix, regex-pcre, regex-parsec, regex-tdfs, regex-dfa." Except it doesn't seem to know about pcre?

Attachments:

B.hs

Field	Old Value	Date	By
Resolution	None	2008-09-30 01:09	igouy-guest
status_id	Open	2008-09-30 01:09	igouy-guest
close_date	2008-09-30 01:09	2008-09-30 01:09	igouy-guest
File Added	2844: B.hs	2008-09-22 19:38	dons-guest