Re: [julia-users] Base.Threads user feedback: it's great. please keep it. anyone tried hybrid (addprocs + Threads)?

2016-11-15 Thread Florian Oswald
ok, thanks for that. do you think this is going to change already in v0.6 or will that have to wait until a future release? On 14 November 2016 at 23:59, Yichao Yu <yyc1...@gmail.com> wrote: > On Mon, Nov 14, 2016 at 5:08 PM, Florian Oswald > <florian.osw...@gmail.com> wrote

[julia-users] Base.Threads user feedback: it's great. please keep it. anyone tried hybrid (addprocs + Threads)?

2016-11-14 Thread Florian Oswald
I'm not sure how many people are using Base.Threads out there, I came across it by accident and think it works great. It's under the heading "experimental" in the manual, so I just wanted to encourage the developers that this is a great feature, please don't drop it. I just wrote @threads in

Re: [julia-users] Unit Testing: should I use Base.Test instead of FactCheck?

2016-10-31 Thread Florian Oswald
e lack of indentation for nested testsets is a regression that > hit 0.5 (BaseTestNext on 0.4 indents nested testsets), and there’s > currently an issue filed: https://github.com/JuliaLang/julia/issues/18611 > > so they should get re-prettified soon enough. > > -s > > > On Fri,

Re: [julia-users] Unit Testing: should I use Base.Test instead of FactCheck?

2016-10-29 Thread Florian Oswald
D'oh. Thanks! On Saturday, 29 October 2016, Steven G. Johnson <stevenj@gmail.com> wrote: > > > On Friday, October 28, 2016 at 10:30:28 AM UTC-4, Florian Oswald wrote: >> >> There is 1 thing I sorely miss from Base.Test coming from FactCheck, and >> that

[julia-users] Gallium: how to remove a breakpoint?

2016-10-29 Thread Florian Oswald
hi all, i have got a rather simple question but can't figure it out: https://github.com/Keno/Gallium.jl/issues/166 thanks

[julia-users] Re: [ANNOUNCE] TestSetExtensions.jl

2016-10-29 Thread Florian Oswald
Good stuff! I like the idea of extending Base.Test anyway you could easily integrate printing messages after failed tests? https://groups.google.com/d/msg/julia-users/_cZ8y_-JAVA/8EcTWdxcAQAJ cheers On Thursday, 27 October 2016 17:27:38 UTC+2, Spencer Russell wrote: > > Hey All, > > I just

[julia-users] Unit Testing: should I use Base.Test instead of FactCheck?

2016-10-28 Thread Florian Oswald
I know there are many testing packages out there. I have been using FactCheck, but have seen it's been relegated to the JuliaArchive. I take that as a sign it's a good moment to use something else. There is 1 thing I sorely miss from Base.Test coming from FactCheck, and that is the ability to

Re: [julia-users] use macros like a preprocessor directive?

2016-10-24 Thread Florian Oswald
Ok. any suggestions how to get close to the C preprocessor behaviour though? On Monday, 24 October 2016 11:13:18 UTC+2, Mauro wrote: > > On Mon, 2016-10-24 at 10:37, Florian Oswald <florian...@gmail.com > > wrote: > > I have something that this in C++ I would write li

[julia-users] use macros like a preprocessor directive?

2016-10-24 Thread Florian Oswald
I have something that this in C++ I would write like double f(double x){ // do something with x #ifdef MACROVAR // do something else with x #endif return(x) } I was trying to understand how i could use julia macro's to achieve something similar. I have seen how the Logging.jl

[julia-users] Interpolations.jl: how to use the scale function?

2016-10-15 Thread Florian Oswald
Hi folks, I have question on SO that needs some attention. thanks! http://stackoverflow.com/questions/40045208/how-to-use-scale-in-interpolations-jl

Re: [julia-users] help with @generated function call please?

2016-10-15 Thread Florian Oswald
don't need to write `$N` in your code; using `N` > directly has the same effect here. > > I'm not saying that generated functions should be avoided at all costs, > but if it isn't necessary here you might as well skip the associated > complications. > > -erik > > On Fri, Oc

[julia-users] help with @generated function call please?

2016-10-14 Thread Florian Oswald
hi all, I want to evaluate a function at each index of an array. There is a N dimensional function, and I want to map it onto an N-dimensional array: fpoly(x::Array{Real,5}) = x[1] + x[2]^2 + x[3] + x[4]^2 + x[5] want to do a = rand(2,2,2,2,2); b = similar(a) for i1 in indices(a,1) for i2

Re: [julia-users] How to debug julia v0.5 code? Debug.jl is down, how to use Gallium.jl

2016-10-13 Thread Florian Oswald
Oh! Sorry I didn't get that. Thanks! On Thursday, 13 October 2016, Michele Zaffalon <michele.zaffa...@gmail.com> wrote: > From ASTInterpreter's README: > >- `stuff runs stuff in the current frame's context > > > On Thu, Oct 13, 2016 at 5:47 PM, Florian Oswald &

Re: [julia-users] How to debug julia v0.5 code? Debug.jl is down, how to use Gallium.jl

2016-10-13 Thread Florian Oswald
> of commands. The documentation seems to be spread across the two packages. > > > On Thu, Oct 13, 2016 at 5:15 PM, Florian Oswald <florian...@gmail.com > > wrote: > >> hi, >> >> i usually used Debug.jl to debug code, which is great, but errors on >>

Re: [julia-users] How to debug julia v0.5 code? Debug.jl is down, how to use Gallium.jl

2016-10-13 Thread Florian Oswald
er.jl>'s README which gives the list > of commands. The documentation seems to be spread across the two packages. > > > On Thu, Oct 13, 2016 at 5:15 PM, Florian Oswald <florian.osw...@gmail.com> > wrote: > >> hi, >> >> i usually used Debug.jl to d

[julia-users] How to debug julia v0.5 code? Debug.jl is down, how to use Gallium.jl

2016-10-13 Thread Florian Oswald
hi, i usually used Debug.jl to debug code, which is great, but errors on julia 0.5: https://github.com/toivoh/Debug.jl/issues/80 I have no idea how to use Gallium.jl just from looking at the examples. Anyone? thanks.

[julia-users] Re: why do we have Base.isless(a, ::NAtype) but not Base.isless(a, ::Nullable)?

2016-10-13 Thread Florian Oswald
ok i found the conversation here: https://groups.google.com/d/topic/julia-users/W6yyV4i_W_k/discussion On Thursday, 13 October 2016 15:45:23 UTC+2, Florian Oswald wrote: > > I mean, do I have to cycle through the array and basically clean it of > #NULL before findign the

Re: [julia-users] Re: What's the status of SIMD instructions from a user's perspective in v0.5?

2016-10-13 Thread Florian Oswald
ithout measuring performance before > and after. Given the low-level nature if the changes, looking at the > generated assembler code via `@code_native` is usually also insightful. > > I'll be happy to help if you have a specific problem on which you're > working. > > -erik &g

[julia-users] Re: What's the status of SIMD instructions from a user's perspective in v0.5?

2016-10-13 Thread Florian Oswald
t/SIMD.jl it is builds on top of > VecElement. > > In many cases we can perform automatic vectorisation, but you have to > start Julia with -O3 > > On Thursday, 13 October 2016 22:15:00 UTC+9, Florian Oswald wrote: >> >> i see on the docs >> http://docs.j

[julia-users] Re: why do we have Base.isless(a, ::NAtype) but not Base.isless(a, ::Nullable)?

2016-10-13 Thread Florian Oswald
I mean, do I have to cycle through the array and basically clean it of #NULL before findign the maximium or is there another way? On Thursday, 13 October 2016 15:42:02 UTC+2, Florian Oswald wrote: > > i'm trying to understand why we don't have something similar in terms of > c

[julia-users] why do we have Base.isless(a, ::NAtype) but not Base.isless(a, ::Nullable)?

2016-10-13 Thread Florian Oswald
i'm trying to understand why we don't have something similar in terms of comparison for Nullable as we have for DataArrays NAtype (below). point me to the relevant github conversation, if any, is fine. How would I implement methods to find the maximium of an Array{Nullable{Float64}}? like so?

[julia-users] What's the status of SIMD instructions from a user's perspective in v0.5?

2016-10-13 Thread Florian Oswald
i see on the docs http://docs.julialang.org/en/release-0.5/stdlib/simd-types/?highlight=SIMD that there is a vecElement that is build for SIMD support. I don't understand if as a user I should construct vecElement arrays and hope for some SIMD optimization? thanks.

[julia-users] Re: problem when building julia 0.5 on plattform without indirect linking

2016-09-25 Thread Florian Oswald
see https://github.com/JuliaLang/julia/issues/18666 On Sunday, 25 September 2016 15:54:30 UTC+2, Florian Oswald wrote: > > hi, > > i am trying to build the julia release on a remote unix system and get > until this step: > > [uctpfos@jake julia]$ make > > *LINK*

[julia-users] problem when building julia 0.5 on plattform without indirect linking

2016-09-25 Thread Florian Oswald
hi, i am trying to build the julia release on a remote unix system and get until this step: [uctpfos@jake julia]$ make *LINK* *usr/bin/julia* /opt/rh/devtoolset-3/root/usr/libexec/gcc/x86_64-redhat-linux/4.9.1/ld:

[julia-users] Re: Julia v0.5.0 always killed on a memory limited cluster

2016-09-23 Thread Florian Oswald
This is affecting my work in exactly the same way. my jobs have been down on an SGE managed cluster since I upgraded to v0.5-xxx for other reasons. Some support on this would be very good. On Thursday, 22 September 2016 11:26:16 UTC+2, Alan Crawford wrote: > > I am using Julia v0.5.0 on a

Re: [julia-users] v0.5 deprecates :call. so how do you :call now?

2016-09-19 Thread Florian Oswald
erm... yes. sorry that was a stupid question. thanks anyway! On Monday, 19 September 2016 10:48:44 UTC+2, Bart Janssens wrote: > > > > On Mon, Sep 19, 2016 at 10:11 AM Florian Oswald <florian...@gmail.com > > wrote: > >> >> So I read somewhere that my

Re: [julia-users] v0.5 deprecates :call. so how do you :call now?

2016-09-19 Thread Florian Oswald
Cheers, > > Bart > > On Mon, Sep 19, 2016 at 9:32 AM Florian Oswald <florian...@gmail.com > > wrote: > >> i was trying to make sense of the final outcome of the discussion here >> https://github.com/JuliaLang/julia/pull/13412, but no way. Also I'm not &

[julia-users] v0.5 deprecates :call. so how do you :call now?

2016-09-19 Thread Florian Oswald
i was trying to make sense of the final outcome of the discussion here https://github.com/JuliaLang/julia/pull/13412, but no way. Also I'm not sure what to search for in the documentation (?Base.call tells me it's deprecated.) So: if up to now I programmatically evaluate a function f like

[julia-users] can someone help me read julia's memory footprint on this cluster? [SGE]

2016-09-12 Thread Florian Oswald
hi all, i get the following output from the SGE command `qstat -j jobnumber` of a julia job that uses 30 workers. I am confused by the mem column. am I using more memory than what I asked for? I asked for max 4G on each processor. job-array tasks:1-30:1 usage1:

[julia-users] Re: @profile does not allow variable assignment on v0.5

2016-09-09 Thread Florian Oswald
end > 125 > > > If you think it is a regression file a bug report for profile. > > > On Friday, September 9, 2016 at 1:04:21 PM UTC+3, Florian Oswald wrote: >> >> hi all, >> >> on v0.5-rc3, I see this >> >> *julia> **f(x)=x^3* >

[julia-users] @profile does not allow variable assignment on v0.5

2016-09-09 Thread Florian Oswald
hi all, on v0.5-rc3, I see this *julia> **f(x)=x^3* *f (generic function with 1 method)* *julia> **@profile y = f(5)* *125* *julia> **y* *ERROR: UndefVarError: y not defined* which used to work in previous versions. Is that intended behaviour?

Re: [julia-users] how to set the maximal waiting time for ClusterManagers.addprocs_sge()?

2016-06-01 Thread Florian Oswald
) call? On Thursday, 2 June 2016, David van Leeuwen <david.vanleeu...@gmail.com> wrote: > Could this be related to this > <https://github.com/JuliaParallel/ClusterManagers.jl/issues/4#event-677794220> > ? > > On Wednesday, June 1, 2016 at 7:26:50 PM UTC+2, Florian Osw

[julia-users] how to set the maximal waiting time for ClusterManagers.addprocs_sge()?

2016-06-01 Thread Florian Oswald
i'm having a problem on a cluster where setting up the connections via ClusterManagers.addprocs_sge() takes longer than the 60 second limit. how can I extend that limit? thanks!

[julia-users] Re: installing nlopt.jl on unix with manually installed NLopt?

2015-05-19 Thread Florian Oswald
figured it out: https://github.com/JuliaOpt/NLopt.jl/issues/36 On Monday, 18 May 2015 15:23:57 UTC+1, Florian Oswald wrote: Hi all, I'm working on a scienfitic unix cluster where the NLopt.jl provided build.jl fails. I paste the error output in the end. I installed NLopt manually

[julia-users] installing nlopt.jl on unix with manually installed NLopt?

2015-05-18 Thread Florian Oswald
Hi all, I'm working on a scienfitic unix cluster where the NLopt.jl provided build.jl fails. I paste the error output in the end. I installed NLopt manually into ~/local. How can I build NLopt.jl such that it takes my ~/local/lib/libnlopt.a? I have done push!(Sys.DL_LOAD_PATH,

[julia-users] Re: 4D interpolation from scattered points

2015-05-18 Thread Florian Oswald
Hi there, xdata (or any other grid) does not need to be on a grid, that's just the way the example is written. but no extrapolation, that's right. On Thursday, 14 May 2015 01:05:55 UTC+1, Yakir Gagnon wrote: Thanks a ton people!!! ExtremelyRandomizedTrees.jl: Might be really good, but

[julia-users] Lexicon.jl Index() function?

2015-05-12 Thread Florian Oswald
Hi all, I'm trying to follow the steps outline in the Lexicon documentation http://lexiconjl.readthedocs.org/en/latest/api/Lexicon/ and I am stuck with this: using Lexicon, Docile, Docile.Interface index = Index() update!(index, save(docs/api/Lexicon.md, Lexicon)); update!(index,

[julia-users] Re: Lexicon.jl Index() function?

2015-05-12 Thread Florian Oswald
? -- Mike On Tuesday, 12 May 2015 12:29:17 UTC+2, Florian Oswald wrote: Hi all, I'm trying to follow the steps outline in the Lexicon documentation http://lexiconjl.readthedocs.org/en/latest/api/Lexicon/ and I am stuck with this: using Lexicon, Docile, Docile.Interface index = Index() update

[julia-users] problem with dataframes.Index when loading JLD dataset

2014-10-06 Thread Florian Oswald
Hi all, I'm currently trying to work out why I get an error when trying to load a dict with several dataframes in it with HDF5, JLD, see https://github.com/timholy/HDF5.jl/issues/158 which results in this error: *ERROR: stored type DataFrames.Index does not match currently loaded type* I just

Re: [julia-users] ANN: QuantEcon.jl

2014-10-06 Thread Florian Oswald
If I may, I've got an implementation of linear interpolation that I'm quite happy with. It uses a GSL kind of accelerator that remembers the index position of the last evaluation. the binary search for the correct bracket of x in the grid is the main bottleneck in my experience. So taking

[julia-users] How to print a StatsBase.CoefTable / other table object to latex?

2014-09-19 Thread Florian Oswald
just wondering if anyone has a way to print for example a GLM regression output table to tex? I think I'm looking for something like [http://cran.r-project.org/web/packages/texreg/index.html], although maybe that's not the best way to achieve this in julia. right now I'm converting the

[julia-users] unexpected domain error for ^(float,float)

2014-09-18 Thread Florian Oswald
# define a variable gamma: gamma = 1.4 mgamma = 1.0-gamma julia mgamma -0.3999 # this works: julia -0.3999^2.5 -0.10119288512475567 # this doesn't: julia mgamma^2.5 ERROR: DomainError in ^ at math.jl:252

Re: [julia-users] unexpected domain error for ^(float,float)

2014-09-18 Thread Florian Oswald
guess it is not possible to give binary minus a lower precedence than ^ and unary minus of higher precedence, since these are just different methods of the same function/operator. Op donderdag 18 september 2014 14:54:26 UTC+2 schreef Florian Oswald: yes - not sure why -0.4 and (-0.4) are any

Re: [julia-users] unexpected domain error for ^(float,float)

2014-09-18 Thread Florian Oswald
september 2014 14:54:26 UTC+2 schreef Florian Oswald: yes - not sure why -0.4 and (-0.4) are any different. On 18 September 2014 13:52, Patrick O'Leary patrick...@gmail.com wrote: Seems like the literal -0.4^2.5 should throw the same error, though? On Thursday, September 18, 2014 6:42:56

Re: [julia-users] unexpected domain error for ^(float,float)

2014-09-18 Thread Florian Oswald
and told the author to clarify the ambiguity. On Thursday, September 18, 2014, Florian Oswald florian.osw...@gmail.com wrote: well, I guess most computer scientists would be surprised. writing on a piece of paper -10^2 and -(10^2) I think most people are going to say the first

[julia-users] how to push!(::DataFrame,::DataFrameRow) or append!(::DataFrame,::DataFrameRow) ?

2014-09-12 Thread Florian Oswald
i'm trying to do this: using DataFrames df = DataFrame(a=[hi,there],x = rand(2)) df2 = DataFrame(a=[oh,yeah],x = rand(2)) for e in eachrow(df) append!(df2,e) end ERROR: `append!` has no method matching append!(::DataFrame, ::DataFrameRow{DataFrame}) in anonymous at no file:2 or julia for i

Re: [julia-users] how to push!(::DataFrame,::DataFrameRow) or append!(::DataFrame,::DataFrameRow) ?

2014-09-12 Thread Florian Oswald
| 0.0222873 | julia append!(df2,df) 4x2 DataFrame |---|-|| | Row # | a | x | | 1 | oh| 0.00803615 | | 2 | yeah | 0.0222873 | | 3 | hi| 0.862957 | | 4 | there | 0.101378 | ~~~ On Fri, Sep 12, 2014 at 7:57 AM, Florian

Re: [julia-users] how to push!(::DataFrame,::DataFrameRow) or append!(::DataFrame,::DataFrameRow) ?

2014-09-12 Thread Florian Oswald
Leah: yeah that works. but i think i almost prefer my previous solution, instead of this push!(df2,[v for (_,v) in e]) that: push!(df2,array(e)) not sure about the performance implications though. On 12 September 2014 22:18, Gray Calhoun gcalh...@iastate.edu wrote: Oh, I wasn't

Re: [julia-users] how to push!(::DataFrame,::DataFrameRow) or append!(::DataFrame,::DataFrameRow) ?

2014-09-12 Thread Florian Oswald
to an existing DataFrame, so this seems like it's either a mechanism for transferring rows from one DataFrame to another very slowly or a mechanism for inserting duplicate rows. -- John On Sep 12, 2014, at 3:37 PM, Florian Oswald florian.osw...@gmail.com wrote: I'll submit a PR

[julia-users] how to turn off redirect_stdout() ?

2014-09-02 Thread Florian Oswald
hi! this works fine: julia rdstdout, wrstdout = redirect_stdout() (Pipe(open, 0 bytes waiting),Pipe(open, 0 bytes waiting)) *run(`date`)**julia * *s = readavailable(rdstdout)**Tue 2 Sep 2014 17:11:33 BST\n* *but now I want to turn the redirection off again. how do I do this?* thanks!

Re: [julia-users] Re: how to turn off redirect_stdout() ?

2014-09-02 Thread Florian Oswald
) readline(rd) redirect_stdout(oldout) println(hello world) (with the last line outputting to screen normally) On Tuesday, September 2, 2014 7:25:05 PM UTC+3, Florian Oswald wrote: hi! this works fine: julia rdstdout, wrstdout = redirect_stdout() (Pipe(open, 0 bytes waiting),Pipe(open, 0 bytes

Re: [julia-users] what is Julia for R cut()

2014-08-30 Thread Florian Oswald
White johnmyleswh...@gmail.com wrote: DataArrays has a cut function. -- John On Aug 29, 2014, at 11:17 AM, Florian Oswald florian.osw...@gmail.com wrote: hi what's the julia equivalent of this R call? i don't need the levels and labels, just some kind of grouping index. cut(sample(1

[julia-users] Re: best way to run parallel julia in batch mode?

2014-08-30 Thread Florian Oswald
sorry correct my call to julia -p 32 exper.jl myout.out (without the first , not sure that makes a difference) On Saturday, 30 August 2014 12:58:57 UTC+1, Florian Oswald wrote: @require should work for what you want. i usually run batch jobs like this julia -p 32 exper.jl myout.out

[julia-users] Re: Logging output in batch mode

2014-08-30 Thread Florian Oswald
try standard unix cat julia script.jl output.txt On Friday, 29 August 2014 17:12:37 UTC+1, Thomas Covert wrote: Suppose I wanted to run a julia script in batch mode, like this bash$ julia script.jl How would I tell julia to save the visual output of this to a text file? As far as I

[julia-users] Re: Installing Julia on Mac

2014-08-30 Thread Florian Oswald
any reason you are using homebrew to install julia? both the build and precompiled binary are straightforward to install, I would go with that. On Saturday, 30 August 2014 10:26:34 UTC+1, idontgetoutmuch wrote: I am trying to install Julia using brew brew install --HEAD --64bit julia and

Re: [julia-users] what is Julia for R cut()

2014-08-30 Thread Florian Oswald
=0Ai9cmDERDCGgdDJ6VDQtQjBGWm5LTzh6R0lRNHY1RVEusp=sharing I’d prefer setting up a special website (possibly using Github Pages) that houses information for R users coming to Julia. That way we’d be able to house more than just spreadsheets. — John On Aug 30, 2014, at 4:35 AM, Florian Oswald florian.osw

[julia-users] what is Julia for R cut()

2014-08-29 Thread Florian Oswald
hi what's the julia equivalent of this R call? i don't need the levels and labels, just some kind of grouping index. cut(sample(1:10,10,TRUE),c(0,3,6,10)) [1] (3,6] (6,10] (0,3] (6,10] (3,6] (6,10] (0,3] (0,3] (3,6] (3,6] Levels: (0,3] (3,6] (6,10]

Re: [julia-users] Sharing success: running Julia on PBS cluster across compute nodes

2014-08-28 Thread Florian Oswald
:-) On Wed, Aug 27, 2014 at 6:38 PM, Florian Oswald florian.osw...@gmail.com wrote: Dear All, after bugging this list long enough with questions about how to get Julia running in parallel on a Torque/PBS managed cluster I thought I'd share my experience with the list. I realise that by julia

Re: [julia-users] Sharing success: running Julia on PBS cluster across compute nodes

2014-08-28 Thread Florian Oswald
I'm mentioning this because we there's a dangling issue on the topic since 24 of May: https://github.com/nlhepler/ClusterManagers.jl/issues/13 On 28 August 2014 10:53, Florian Oswald florian.osw...@gmail.com wrote: no problem about adding this to clustermanagers.jl. just one question

[julia-users] Sharing success: running Julia on PBS cluster across compute nodes

2014-08-27 Thread Florian Oswald
Dear All, after bugging this list long enough with questions about how to get Julia running in parallel on a Torque/PBS managed cluster I thought I'd share my experience with the list. I realise that by julia standards this is a rather modest achievement, but I'd been happy to come across

[julia-users] question about performance hit because of build options on unix HPC

2014-08-24 Thread Florian Oswald
Hi! I'm running julia release 0.3 on an hpc system that features two 6-core 2.4GHz Intel Westmere processors (a total of 12 processor cores) per node. I noticed my program is significantly slower on that machine than on my mac, where I run this on 1 core (2.4GHz Intel Core i5). (runtime is 60

Re: [julia-users] Suggestion: Start using Julia 0.3-RC4

2014-08-19 Thread Florian Oswald
hey! yeah no worries! when I overcame my impatience (which led me to abort the download after 2 seconds because of the wrong name), I found out that the package had the correct content. cheers On 19 August 2014 16:54, Elliot Saba staticfl...@gmail.com wrote: Whoops, sorry about that Florian!

[julia-users] help with improving performance of nested loops

2014-08-18 Thread Florian Oswald
Hi all, i'm trying to improve the performance of this function: https://gist.github.com/floswald/9e79f6f51c276becbd74 In a nutshell, I have got a high-dimensional array vbar (in this instance it is 9D), and I want to obtain another array EV (also 9D), by matrix-multiplying several dimensions

Re: [julia-users] help with improving performance of nested loops

2014-08-18 Thread Florian Oswald
* ((ip1-1) + p.np * (ij-1 ] * Gs[is + p.ns * (is1-1)] * Gtau[itau1] On 18 August 2014 19:13, Kevin Squire kevin.squ...@gmail.com wrote: Have you run it through the profiler already? On Monday, August 18, 2014, Florian Oswald florian.osw...@gmail.com wrote: Hi all, i'm trying

Re: [julia-users] help with improving performance of nested loops

2014-08-18 Thread Florian Oswald
augustus 2014 22:35:25 UTC+2 schreef Florian Oswald: Hi! yes. I find that 37 % of time spent at line 26 51 % of time spent at line 29 in the gist. line 26 is idx1 = idx9(is1,iz1,iy1,ip1,itau1,ia,ih,ij,age,p) line 29 is @inbounds tmp += m.vbar[idx1] * Gz[iz + p.nz * (iz1 + p.nz * (ij-1

[julia-users] Re: what's the best way to do R table() in julia? (why does StatsBase.count(x,k) need k?)

2014-08-17 Thread Florian Oswald
17, 2014 4:45:21 PM UTC+3, Florian Oswald wrote: Hi I'm looking for the best way to count how many times a certain value x_i appears in vector x, where x could be integers, floats, strings. In R I would do table(x). I found StatsBase.counts(x,k) but I'm a bit confused by k (where k goes

Re: [julia-users] Re: help with improving performance of a matrix multiplication

2014-08-08 Thread Florian Oswald
:n v1[m*(j-1) + i] = stemp * v0[n*(i-1) + j] end --Tim On Friday, August 08, 2014 03:43:26 AM Florian Oswald wrote: thanks for all your tips guys - sad to report that none of them worked out so far. Andrei: I checked I'm using Blas. called gemv directly as well. Stefan

[julia-users] Re: Run Julia job on several workers on a cluster

2014-08-02 Thread Florian Oswald
Hi Ken, sorry can i just ask you a question on this? Thibaut (post below) was actually able to use your function to set Julia up on our departmental SGE cluster and it works fine. That facility is down with a disk failure for the time being though, so I have been trying to get going on a

Re: [julia-users] git SSL problems with METADATA.jl

2014-08-01 Thread Florian Oswald
that does sound worrying. I doubt the admin wants to know what I'm downloading but rather get (temporarily) rid of a problem. Does that compromise the security of the hpc system or does it mean someone could hack my github account? On 1 August 2014 08:02, gael.mc...@gmail.com wrote: Sounds

Re: [julia-users] git SSL problems with METADATA.jl

2014-08-01 Thread Florian Oswald
verifies signatures and who does not. Ivar kl. 12:45:48 UTC+2 fredag 1. august 2014 skrev Florian Oswald følgende: that does sound worrying. I doubt the admin wants to know what I'm downloading but rather get (temporarily) rid of a problem. Does that compromise the security of the hpc system

[julia-users] addprocs(machinefile) on a cluster with N nodes and ppn processors per node

2014-08-01 Thread Florian Oswald
Hi, I'm trying to setup a cluster across machines on a PBS managed cluster. I parse the PBS_NODEFILE, which for the case of a submit script with option #PBS -l nodes=2:ppn=12 looks like this: node001 node001 node001 ... node002 ... node002 I am unsure about what exactly I have to give to

[julia-users] Re: addprocs(machinefile) on a cluster with N nodes and ppn processors per node

2014-08-01 Thread Florian Oswald
here is the parsing function in case that helps: https://github.com/floswald/mpitest/blob/removeMaster/julia/iridis/sge.jl On Friday, 1 August 2014 15:03:49 UTC+1, Florian Oswald wrote: Hi, I'm trying to setup a cluster across machines on a PBS managed cluster. I parse the PBS_NODEFILE

[julia-users] Re: addprocs(machinefile) on a cluster with N nodes and ppn processors per node

2014-08-01 Thread Florian Oswald
and here is the error message I get. there is something wrong with the ssh_exchange_identification? https://gist.github.com/floswald/236da440fb717c683e37 On Friday, 1 August 2014 15:18:07 UTC+1, Florian Oswald wrote: here is the parsing function in case that helps: https://github.com

Re: [julia-users] git SSL problems with METADATA.jl

2014-07-31 Thread Florian Oswald
to the README (especially for hpc and similar environments with tricky network configs). Temporarily renaming your ~/.julia folder is a safe way to do such a test. On Wed, Jul 30, 2014 at 5:01 PM, Florian Oswald florian.osw...@gmail.com wrote: Very helpful, thanks! I resorted to manually

[julia-users] git SSL problems with METADATA.jl

2014-07-30 Thread Florian Oswald
i'm working on a remote server that has git version 1.7.4.1 I could use this git to build julia and clone a host of other repos, but when I want to do Pkg.status() it fails with error: SSL certificate problem, verify that the CA cert is OK. Details: error:14090086:SSL

[julia-users] Re: git SSL problems with METADATA.jl

2014-07-30 Thread Florian Oswald
, 30 July 2014 18:06:03 UTC+1, Ivar Nesje wrote: Do you clone the other repositories over https or the ssh based git protocol? kl. 19:03:06 UTC+2 onsdag 30. juli 2014 skrev Florian Oswald følgende: i'm working on a remote server that has git version 1.7.4.1 I could use this git to build

Re: [julia-users] Re: git SSL problems with METADATA.jl

2014-07-30 Thread Florian Oswald
or https in the readme. On Wed, Jul 30, 2014 at 1:11 PM, Florian Oswald florian.osw...@gmail.com wrote: hmm, I don't know. but - this works: git clone g...@github.com:tlamadon/Utils.git and this does not git clone git://github.com/JuliaLang/METADATA.jl but that does git clone g

Re: [julia-users] git SSL problems with METADATA.jl

2014-07-30 Thread Florian Oswald
] https://www.kernel.org/pub/software/scm/git/docs/git-push.html#URLS [2] http://stackoverflow.com/questions/3777075/ssl-certificate-rejected-trying-to-access-github-over-https-behind-firewall On Wed, Jul 30, 2014 at 1:47 PM, Florian Oswald florian.osw...@gmail.com javascript:_e(%7B%7D,'cvml

Re: [julia-users] git SSL problems with METADATA.jl

2014-07-30 Thread Florian Oswald
and similar environments with tricky network configs). Temporarily renaming your ~/.julia folder is a safe way to do such a test. On Wed, Jul 30, 2014 at 5:01 PM, Florian Oswald florian.osw...@gmail.com wrote: Very helpful, thanks! I resorted to manually cloning all my packages, completely bypassing

[julia-users] help with improving performance of a matrix multiplication

2014-07-29 Thread Florian Oswald
Hi all, I've got an algorithm that hinges critically on fast matrix multiplication. I put up the function on this gist https://gist.github.com/floswald/6dea493417912536688d#file-tensor-jl-L45 indicating the line (45) that takes most of the time, as you can see in the profile output that is

[julia-users] help with improving performance of a matrix multiplication

2014-07-29 Thread Florian Oswald
which is the bottleneck: getindex or matrix multiplication. Dahua On Tuesday, July 29, 2014 4:22:32 PM UTC-5, Florian Oswald wrote: Hi all, I've got an algorithm that hinges critically on fast matrix multiplication. I put up the function on this gist https://gist.github.com/floswald

Re: [julia-users] iterate over rows of sparse matrix and get index of nonzeros?

2014-07-22 Thread Florian Oswald
. They will be convenient to use for sure, but may not give the best performance. -viral On Monday, July 21, 2014 12:15:46 PM UTC+5:30, Florian Oswald wrote: Transposing is fine! Thanks for that! On Sunday, 20 July 2014, Odd Andersen odd.ander...@gmail.com wrote: Sparse matrices in Julia are to my

Re: [julia-users] iterate over rows of sparse matrix and get index of nonzeros?

2014-07-21 Thread Florian Oswald
Transposing is fine! Thanks for that! On Sunday, 20 July 2014, Odd Andersen odd.ander...@gmail.com wrote: Sparse matrices in Julia are to my understanding stored as compressed sparse columns. So it is very easy to get the nonzero elements for a given column, but not so easy for rows. To

[julia-users] Pkg.update() fails: Key not found: Sampling

2014-07-19 Thread Florian Oswald
i'm getting this error here. any idea? I can't do Pkg.rm(GLM) - assuming that's where the problem is. *julia **Pkg.update()* *INFO: Updating METADATA...* *INFO: Updating MOpt...* *INFO: Updating StatsBase...* *INFO: Updating Copulas...* *INFO: Updating DataFrames...* *INFO: Updating

Re: [julia-users] Re: Pkg.update() fails: Key not found: Sampling

2014-07-19 Thread Florian Oswald
: I'm getting the same error. This is making it really tough to get any work done, since I can't seem to add, remove or update packages now. On Saturday, July 19, 2014 7:47:05 AM UTC-4, Florian Oswald wrote: i'm getting this error here. any idea? I can't do Pkg.rm(GLM) - assuming that's where

[julia-users] iterate over rows of sparse matrix and get index of nonzeros?

2014-07-19 Thread Florian Oswald
i am looking for a way to do something like *s=sprand(3,5,0.6)* *for i in 1:size(s,1)* * mySparseRowFunction(s[i, ])* *end* I guess I'm looking for an iterator over the nonzero elements, ideally by row. Does something like this exist? I know julia uses a different format, but I'm

Re: [julia-users] Re: ways to improve performance of a non-integer power?

2014-07-17 Thread Florian Oswald
hi simon, very interesting to know indeed! I'll keep that in mind. thanks! On 17 July 2014 13:10, Simon Byrne simonby...@gmail.com wrote: On Wednesday, 16 July 2014 20:39:39 UTC+1, Florian Oswald wrote: myexp(parameter * mylog(x) ) and it does make a sizeable difference. I'll try your

[julia-users] question about GSL.jl package usage

2014-07-16 Thread Florian Oswald
Hi! I want to use the function interpolation suite from the GSL library. I came across the GSL.jl package which wraps the entire GSL library (which is awesome). I am stuck with setting up the interpolation object and wanted to reach out for help. my issue is described here in greater detail:

[julia-users] ways to improve performance of a non-integer power?

2014-07-16 Thread Florian Oswald
i'm looking for ways to improve the performance of ^ as in f(x) = x^1.4 I found this thread on integer powers, and it seems there are some benefits of calling system pow() functions (sometimes). https://github.com/JuliaLang/julia/issues/2741 is there anything related for non-integer powers or

Re: [julia-users] Re: ways to improve performance of a non-integer power?

2014-07-16 Thread Florian Oswald
. To be honest I'm not sure if the manual is the right place for things like that - but it would be good to have them in *some* place. cheers florian On Wednesday, 16 July 2014 21:47:58 UTC+1, Stefan Karpinski wrote: On Wed, Jul 16, 2014 at 12:39 PM, Florian Oswald florian...@gmail.com javascript

Re: [julia-users] how to use searchsortedlast(v::AbstractArray{T,1},x,lo::Int64,hi::Int64,o::Ordering)

2014-07-15 Thread Florian Oswald
of `Base.lt` (less than) defined. It's also possible to define your own orderings for special circumstances. For example, DataFrames has it's own ordering for sorting the columns of a DataFrame. Cheers, Kevin On Mon, Jul 14, 2014 at 12:50 PM, Florian Oswald florian.osw...@gmail.com wrote

[julia-users] how to use searchsortedlast(v::AbstractArray{T,1},x,lo::Int64,hi::Int64,o::Ordering)

2014-07-14 Thread Florian Oswald
hi all, i'm looking for ways to speed up an operation where i have an ordered array v, and to each index i of v I want to apply searchsortedlast(a,v[i]), where a is another array. obviously i know from v being increasingly ordererd that if searchsortedlast(a,v[i]) returns k then

Re: [julia-users] GLM DataFrameRegressionModel gives InexactError()

2014-07-06 Thread Florian Oswald
hi guys, sorry for not closing this thread earlier: @simonster pushed exactly the patch suggested by Milan yesterday evening. haven't tried yet, but should be all good. cheers florian On 5 July 2014 23:26, Milan Bouchet-Valat nalimi...@club.fr wrote: Le samedi 05 juillet 2014 à 15:06 -0700,

Re: [julia-users] GLM DataFrameRegressionModel gives InexactError()

2014-07-06 Thread Florian Oswald
here's the closed issue. https://github.com/JuliaStats/GLM.jl/issues/80 On 6 July 2014 10:55, Florian Oswald florian.osw...@gmail.com wrote: hi guys, sorry for not closing this thread earlier: @simonster pushed exactly the patch suggested by Milan yesterday evening. haven't tried yet

[julia-users] how to convert several DataFrame columns to type PooledDataArray for GLM regression

2014-07-04 Thread Florian Oswald
Hi, say I want to use the GLM package to run a regression that contains several categorical variables. My understanding is that I need the equivalent of an R factor, which is a PooledDataArray. Suppose I take this dataset using RDatasets *data = dataset(Ecdat,Benefits)* and I want columns

[julia-users] GLM DataFrameRegressionModel gives InexactError()

2014-07-04 Thread Florian Oswald
HI, in this example, why do I get an InexactError() when showing the fit summary? (I even converted :age to a Float) *data = dataset(Ecdat,Benefits)**d2 = DataFrame(age = convert(DataArray{Float64},data[:Age]), StateUR = data[:StateUR], sex = convert(PooledDataArray,data[:Sex]))* *julia

[julia-users] Re: how to convert several DataFrame columns to type PooledDataArray for GLM regression

2014-07-04 Thread Florian Oswald
ok - got it. the pool!() function worked after a restart. not sure what happened. On Friday, 4 July 2014 20:46:17 UTC+1, Florian Oswald wrote: Hi, say I want to use the GLM package to run a regression that contains several categorical variables. My understanding is that I need

Re: [julia-users] Re: build from source modifying Make.user on hpc cluster

2014-07-02 Thread Florian Oswald
UTC+1, Florian Oswald wrote: Hi all, I've got some very basic questions about building Julia from source on an hpc cluster. I got it to build fine a month ago, but now the makefile changed. I was partially succesful this time as well (my test runs), but some strange things happen and there's

Re: [julia-users] build from source modifying Make.user on hpc cluster

2014-07-01 Thread Florian Oswald
. On Monday, June 30, 2014 3:50:58 PM UTC-7, Florian Oswald wrote: thanks tony, just giving this a try from scratch. to be honest, I dont' know the exact age of those processors. Let me see how far I get without those newer binutils. On Monday, 30 June 2014 23:17:00 UTC+1, Tony Kelman wrote

[julia-users] Building 35 day old master and get DataFrames and Distributions to run

2014-07-01 Thread Florian Oswald
I'm having trouble building the current master on a unix cluster, see https://github.com/JuliaLang/julia/issues/7482 I was able to build it some time ago, so this commit builds: https://github.com/JuliaLang/julia/commit/ac46d58c5a23a8020c666789ca80614f5cda4d8f that version: Julia Version

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