Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-04-23

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All times shown according to UTC.

Time Nick Message
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14:17 rbennacer <rbennacer> hey guys how can i install a specific perl module from CPAN ex: Sphinx-Search-0.11
14:18 leont You type «cpan Sphinx::Search» in your shell
14:18 leont or cpanm instead of cpan, if you've got that installed
14:19 leont (I'm assuming you've got a setup that allows you to install stuff, otherwise you might need to install local::lib first: https://metacpan.org/module/local​::lib#The-bootstrapping-technique)
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14:30 pyrimidine leont++
14:44 rbuels i find cpanm is the best way to get people started with local::lib
14:45 rbuels curl http://cpanmin.us | perl -  -L path/to/new/local/lib local::lib
14:45 rbuels installs local::lib in a local::lib  o_O
14:45 leont That is a nice one
14:45 leont But one would need cpanm first, and still need to setup the env-vars
14:45 rbuels no
14:46 rbuels that's what the curl is for
14:46 leont Right
14:46 leont But then you still need to use that to install cpanm itself
14:46 rbuels no
14:46 rbuels cpanm runs from the wire.
14:46 leont I know, you don't want to keep doing that, or at least I wouldn't
14:47 rbuels you can add cpanm itself to the command if they need to install it too, then
14:47 rbuels curl http://cpanmin.us | perl -  -L path/to/new/local/lib local::lib App::cpanminus
14:47 rbuels and you're done.
14:48 rbuels to get the local::lib env vars, perl -Ipath/to/new/local/lib -Mlocal::lib=path/to/new/local/lib
14:48 rbuels i *think* that works anyway
14:48 * rbuels tries it
14:48 leont You need to put something like that in your .bashrc though
14:49 leont cpanm needs properly set up env-vars, unless you want to keep doing the -L thing
14:49 pyrimidine yes, there is a line to source the necessary env
14:49 leont (and perl needs $PERL5LIB, unless you want to keep doing use lib)
14:49 pyrimidine well, there is for perlbrew at least
14:49 pyrimidine also, perlbrew install-cpanm'
14:50 pyrimidine *'perlbrew install-cpanm'
14:50 leont eval $(perl -I$HOME/foo/lib/perl5 -Mlocal::lib=$LOCATION)
14:51 pyrimidine funny, but I end up using perlbrew over local::lib, just for the flexibility of switching out the perl version if I need to
14:51 leont (erm, almost, -I should be $LOCATION/lib/perl5)
14:51 leont Yeah, me too, usually
14:51 pyrimidine even when running on a cluster/HPC resource
14:53 pyrimidine s/even/especially/
14:53 leont It's not like it takes a lot of time to compile perl on an 8 core
14:54 leont (or more)
15:07 pyrimidine 96-core
15:08 pyrimidine but it tops out at 18
15:08 pyrimidine (I only use 6, running the compile jobs interactively with PBS)
15:09 leont Yeah, I noticed that compiling it on a 12 core was hardly faster than on an 8 core, so I can imagine even more doesn't make sense
15:10 leont Some steps are rather serial (including I think generating the unicode database)
15:24 kai pyrimidine: wellm then do yourself a favour and don't run blast on that multithreaded ;)
15:35 pyrimidine kai: haven't tried BLAST on it actually.  Mainly assembly jobs (SGI-Altix w/ 8TB RAM)
15:37 kai pyrimidine: blast+ seems to have some really nasty locking issues, my quad-core easily outperforms a 24 core system we've got in the server room
15:37 kai on the 24 core box, most threads keep spinning idly waiting for locks
15:38 kai so I guess there's contention about a single ressource, which would make the possibilities of locking grow exponentially
15:39 leont Sounds like a failing architecture
15:39 leont Rule #1 of locking, avoid doing anything that requires it
15:40 leont Though I can easily imagine the bottleneck being malloc
15:41 leont kai: have you tried using intel's multi-threading malloc? It can increase performance in such use-cases
15:42 kai no, I didn't.
15:43 kai I've created a script wrapper to start 24 blast instances running on a single thread ;)
15:44 leont It's part of Intel's Thread Building Blocks, I've heard good stuff about it, though I haven't tried it on anything larger than 8 core myself (performance did increase compared to glibc malloc, but not by an order of magnitude)
15:45 leont See http://software.intel.com/en-us/article​s/optimizing-without-breaking-a-sweat/
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