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<maasha> good morning
<maasha> ?
<maasha> GOOD MORNING
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<maasha> .oO(Rude bastards)
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<yorickpeterse> wat
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<maasha> I'd appreciate some help wrapping my head around these two profiles on an app using MRI and Rubinius: https://gist.github.com/maasha/141580cdaedf1b47c187
<maasha> For some reason rbx is much slower - but reading these graphs is sort of confusing: what steps in the graphs indicate bottle necks?
<yorickpeterse> brixen: ping
<yorickpeterse> brixen: wait, in case internet shits itself at some point: lets meet outside next break, lets discuss evil plans
<yorickpeterse> now lets hope I can actually push my stuff
<yorickpeterse> yisss, pushed
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<heftig> maasha: looks IO-bound to me
<cremes> maasha: i was gonna say the same. in MRI it is IO bound. in rbx, the hot spot is the String#tr! path.
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<maasha> eh, String#tr! is extremely low level and evil fast?
<maasha> So the deal here is to make a Unix pipe lookalike in Ruby, so you do command1 | command2 | command3 | ... command1 is a parser and is probably the bottleneck limited by IO - but how to tell that form the prof graphs?
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<maasha> I three different implmentations: forks, threads and enumerables. I am timing some real data and it looks like in all cases rbx is 2-3 times slower than MRI - even for the threaded version.
<maasha> I have *
<cremes> maasha: let’s look at the rbx prof data first. check out line 129 which says that String#tr_trans is taking 82.7% of CPU.
<cremes> further, we see in the next columns over that tr_trans takes 15.47 seconds of time for itself and 4018.58 seconds for its children.
<cremes> that’s out of a 4878 second total run time.
<cremes> so, in this case, rbx doesn’t have an “evil fast” low level String#tr.
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<cremes> looking at lines 142-144 we see it broken down into even more detail. something inside String#tr_trans is quite slow. looks like there are two block forms… one is okay and the other is a slow beast.
<cremes> there might be an easy “win” here to do some String#tr_trans optimization.
<cremes> this is great for rbx because now we have some “real world” code (your code!) that shows a perf problem in rbx. we can fix it and everyone’s
<cremes> code that uses String#tr! gets faster.
<cremes> hmmm, breaking it down further, look at lines 152-153. looks like Hash#[] might not be fast in this case. lines 162-163 break it down even more.
<cremes> maybe it’s using a particularly slow path in Hash#[] that we don’t hit much. hard to say without looking at the code. but now we know where to concentrate our efforts.
<cremes> and since this is ruby (instead of C or C++) then probably anyone can try to fix it.
<cremes> maasha: i know it’s probably disappointing that your very first attempt at using rbx showed that it’s slower. don’t lose heart!
<cremes> maasha: this can be fixed!
<maasha> cremes: Is tr! implemented in rbx as a Ruby enumerator?
<cremes> maasha: i don’t know. download the source and take a look. i gotta run off to work… i’ll try and check in later.
<maasha> cremes: so for checking - what is fastes? Hash[obj] or Hash.has_key? obj (this seems confusing also in MRI)
<maasha> cremes: Right, appreciated it.
<cremes> maasha: whenever you wonder which one is fastest, write a benchmark and compare them. look at benchmark_suite for rubinius… it’s better than the stdlib ‘benchmark’
<maasha> cremes: would be nice if you could simultaneously benchmark across MRI and rbx
<maasha> Actually, I did benchmark hash[obj] vs hash.has_key? obj in MRI and the first won (Ruby 1.9.x) - Maybe I should try again.
<cremes> maasha: you can. take a look at benchmark_suite… you can bench across mri, rbx and jruby and compare them. really gotta run… hopefully someone else can give you some guidance this morning!
<maasha> Great. Thanks
<maasha> hash[obj] is slightly faster than hash.has_key? obj in MRI. Using rbx hash.has_key? obj is makedly faster thatn hash[obj].
<maasha> But clearly a premature optimerization thing
<maasha> yup, tr_trans is looking very slow
<maasha> bejeeesus, no wonder why it is running like a raped ape :o( - tr is supposed to be in C and the lookup table compiled before runtime.
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<maasha> OK, there is an issues on the subject already: https://github.com/rubinius/rubinius/issues/2522
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<headius> maasha: I'd expect those two Hash methods to either be the same for perf or has_key? should be a bit faster
<headius> actually they should still be the same...both have to hash the key, find the bucket, and ensure the right key is in there
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<headius> maasha: tr is pure Ruby in Rubinius
<headius> along with all of Hash
<maasha> headius: I would expect the same, but perhaps hash[] allocates a return value making it a tad slower?
<maasha> Slow tr is a show stopper for me.
<headius> it shouldn't add anything
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<headius> I mean allocate anything
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<headius> Hash#[] could be a bit slower because it does have to access the value, but that's just a hop or two after finding the bucket
<headius> not sure why has_key? would be much faster in rbx
<maasha> headius: and "much faster" is probably an exaggeration.
<headius> you want to run that bench a couple times in a loop...it's too short for rbx to optimize anything
<headius> because Hash is pure Ruby, rbx needs time to warm it up
<headius> there's a rubinius-benchmark project with some core class benchmarks in it
<maasha> Hm, the core of MRI is some hash implementation presumably in C - which is also used for Hash AFAIK.
<headius> yes, Hash is all C in MRI
<maasha> Hm slow Hash is another show stopper for me :o(
<maasha> Hey all! Drop what you are doing at get started working on tr and Hash !!! :o)
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<headius> you may be able to help optimize them
<headius> I'm not the one to help, though...I don't know what rbx does fast and what it doesn't do fast anymore
<yorickpeterse> maasha: might be worth reporting this as an issue of some sort, both me and brixen are currently at Baruco so we're a bit offline
<yorickpeterse> (I'll be gone again in a few minutes)
<headius> yeah, might as well report it
<headius> and then help fix it :-)
<maasha> tr is reported
<maasha> and Hash too
<maasha> There are "performance" issues on both on github.
<yopp> hash = {foo: "bar"}
<yopp> is it real case?
<yopp> have you tried with bigger hash, as well as trying to run it with bmbm?
<yopp> to warmup VM
<yopp> things are muuuch faster when JITed
<yopp> benchmarking jruby and rbx is kinda tricky
<maasha> yopp: OK, so I didn't do a realistic benchmark, but thing is that Hash is slowish compared to MRI.
<headius> I never thought I'd see the day that tr performance mattered to someone
<headius> I think I implemented that in jruby
<yopp> hash[] 5386950.8 (±7.6%) i/s - 26762148 in 4.999343s
<yopp> hash[] 7221757.4 (±15.4%) i/s - 35279608 in 5.013160s
<yopp> 25%
<maasha> headius: so in bioinformatics we deal a lot with strings of DNA which quality scores encoded in ASCII. tr is very handy for switching between the different quality score encoding types.
<headius> yopp: 25% what?
<headius> maasha: I think that's the first time someone's given me a good example of using tr, too :-)
<headius> I know some others using Ruby for bioinformatics
<maasha> headius: yeah, converting DNA to RNA is tr/Tt/Uu/ as an example
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<maasha> headius: also reverse-complementing DNA is done with tr.
<maasha> headius: and as mentioned - converting quality score encodings, but also truncating out of bounds scores.
<maasha> I luve tr because it is so damned fast - until now!
<yopp> headius, slower
<headius> yopp: rbx is slower or MRI os slower?
<yopp> rbx slower ;)
<headius> maasha: that's pretty cool...do you have any isolated tr use I could try running?
<maasha> headius: so a chunk of real life data and a small test script?
<headius> yopp: ahh
<headius> maasha: yeah sure
<maasha> I can cook that up.
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<headius> cool
<headius> I can't use JRuby if it has inline C of course :-) mostly interested in how you're using tr
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<yopp> huh
<yopp> that's fun
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<yopp> maasha, in your real life example, you have strings as keys?
<yopp> uh lol
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<maasha> symbols as keys and strings as values.
<maasha> oh, champagne! brb
<yopp> so in fact rbx is not really slower in real world
<yopp> 5.7m vs 6.1m
<yopp> headius, jruby is why so fast here?
<yopp> also, it's funny why strings keys are slower everywhere
<yopp> isn't keys are hashed to strings?
<headius> string keys need to be duped and frozen
<headius> so there's allocation involved
<headius> jruby is fast because...I dunno, jruby is fast
<headius> JVM black magic
<headius> (and maybe a little hard work from us)
<maasha> headius: so test data: ftp://ftp_20140912_7772:+d3EFt+n-nGH@ftp.dna.ku.dk
<headius> whose genome am I downloading?
<maasha> headius: its is a collection of bacteria
<headius> anything interesting?
<maasha> headius: so for some real life code as well try this:
<maasha> ruby -rbiopieces -e 'BP.new.read_fastq(input: "in1.fq").trim_seq.write_fastq(encoding: :base_64, output: "out.fq", force: true).run(progress: true)'
<maasha> implies installing the biopieces gem
<headius> figured
<maasha> headius: this particular test data I have no idea what the project is about. But I have plenty of other interesting stuff: locate bacteria that gives asthma, novel bacteria form the Mariana Trench etc.
<headius> very nice
<headius> sigh...I need to port narray to jruby one of these days
<headius> that will prevent me from running this on JRuby in any case, and I suppose you have MRI numbers already
<maasha> And this Biopieces thing is actually a Biopieces2.0 -> https://docs.google.com/document/d/1Uo3bNsevbEEvs9xTKqS0m2JlAxFg5dWLSqYRJKOo3Uc/edit
<maasha> narray is great
<maasha> And what do you mean by MRI numbers?
<headius> MRI perf
<headius> curiousity
<headius> I'll try it on MRI
<maasha> I have MRI perf for a slighly more complex biopieces pipeline: https://gist.github.com/maasha/141580cdaedf1b47c187
<headius> you mean rbx?
<maasha> both MRI and rbx for this script: https://gist.github.com/maasha/0b512afcb3ab512ef08d
<headius> maybe I should port narray today instead of working on JRuby's new JIT
<headius> yeesh, twitter storm
<headius> maasha: is biopieces the library that uses inline C?
<headius> yay, it ran in MRI... 5 seconds
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<headius> maasha: rbx did finish this, yes?
<headius> weird, it ran for maybe 10s and then exited without any output
<headius> the little command line, not the script
<headius> oh well, back to jit
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<headius> maasha: I think it would be possible to use inline_java on JRuby in your gem...this doesn't look too complicated
<headius> not that you can use jruby without narray anyway, but I have never seen a real-world use of ruby_inline either
<headius> etc
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<maasha> headius: yes, biopieces uses inline_C. I have no idea about java, so inline_java is not going to happen.
<headius> yeah, I didn't think so :-)
<maasha> inline_c is very handy.
<maasha> no need to worry about compilation and you have the ruby api at your hands.
<maasha> and for certain speed critical things you get your 1000 fold speedup
<headius> yes, it's unfortunate that the Ruby API is so invasive...makes it very hard to support on modern VMs
<maasha> invasive?
<maasha> you mean stay away form the API because your code will break stuff else-where?
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<headius> I mean it depends on being able to access pointers directly...VMs like rbx and jvm can't do that because they move objects for more efficient GC
<headius> rbx supports C exts by giving you a pointer to a separately-managed handle that can always find the object on the heap
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<maasha> oh, I think I will just stick with my DNA
<headius> probably easier than implementing a VM :-)
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<yopp> btw, maasha, can you recommend any good literature, like dunno "Build you own monster using DNA in 21 days" from PragProg?
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<|jemc|> is there any reason why a Module#dynamic_method would not be JIT'd?
<headius> you're using dynamic_method?
<|jemc|> it doesn't seem to me like it would make a difference, but - I may be missing something
<|jemc|> headius: yes, well, I'm playing around with using it anyway
<|jemc|> it may or may nto remain
<|jemc|> *not
<headius> I'm pretty sure evan did no optimization of dynamic_method
<headius> not that you're concerned about that
<|jemc|> can you elaborate on what you mean by 'no optimization'?
<headius> oh, maybe I'm thinking of something else
<headius> he had a dynamic call site thingy where you could define your own call site logic
<|jemc|> (and you're right that performance isn't my number one priority but the more little good decisions I can make along the way means less optimization I'm having to do later)
<headius> yeah, ignore me, I found it
<|jemc|> dynamic_method is just a convenient way to define a method in terms of bytecode instead of ruby
<headius> this is just a way to define a method on the fly using the rbx generator
<headius> yeah
<|jemc|> yeah
<headius> as for jitting...dunno why it wouldn't
<headius> maybe it's not hot enough
<|jemc|> (I don't have any data to suggest that it is or isn't JIT-ing, just trying to make sure I wasn't missing some obvious reason why it wouldn't before I commit this up)
<headius> that's not something you'd be hitting on a hot path, right?
<|jemc|> oh, it's going to be hot :P
<|jemc|> it's part every method call in my language
<|jemc|> err... *part of
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<headius> you define a dynamic_method for every call?
<headius> that doesn't seem efficient :-)
<headius> or are you referring to methods generated via dynamic_method?
<|jemc|> oh, the definition itself is not part of every call
<|jemc|> but each call passes through a method generated via dynamic method, yes
<|jemc|> that does some extra things like deciding whether to actually invoke the real method body or use a cached value, for instance
<headius> yeah I'd be surprised if they wouldn't JIT
<headius> hmmm...not that JRuby has its own bytecode-like representation, maybe we should add something like this
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<tarcieri> _____ ____ ___ ____ _ __ ___ _ _
<tarcieri> | ___| _ \|_ _| _ \ / \\ \ / / | | |
<|jemc|> FRIDAY
<tarcieri> | |_ | |_) || || | | |/ _ \\ V /| | | |
<tarcieri> | _| | _ < | || |_| / ___ \| | |_|_|_|
<tarcieri> |_| |_| \_\___|____/_/ \_\_| (_|_|_)
<tarcieri>
<headius> FR-FRIDAY-IDAY
<chrisseaton> headius: no more bytecode!
<|jemc|> headius: more bytecode!
<headius> chrisseaton: that should be the truffle motto
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<maasha> yopp: DNA monster is already taken: http://www.nature.com/news/handle-with-care-1.13505
<maasha> yopp: someone already took the bird flu virus and made it truly deadly in the name of science.
<maasha> It was published earlier this year.
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<GitHub27> [rubinius] gustavotemple opened pull request #3131: PowerPC64 support for LLVM and Atomic (master...support-llvm-ppc64) http://git.io/t9Sbng
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<headius> neat
<headius> does the JIT work on ppc?
<headius> I thought I heard rbx would need to move to MCJIT for non-x86
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<|jemc|> headius: that's true for arm, dunno about ppc
<headius> yeah I knew ARM for sure
<headius> oh, looks like ppc and ppc64 are in the old jit too, that's good
<headius> hmm, third hit in my search says it's not really maintained
<headius> but it's an oldish post
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<headius> *shrugs*
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<postmodern> thinking about splitting the md5s/version files out of ruby-install and into a separate git repo
<postmodern> would anyone be interested in maintaing the rbx files?
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