[julia-users] I cant view Plots in Juno - Atom IDE

[Erick J Zagal]

I have this code:

using Plots

x = linspace(0, 10, 200)
y = sin(x)
plot(x, y, color=:blue, linewidth=2, label="sine")

when run this in the console , show the plot , but  trying in Juno only 
show [Plots.jl] Initializing backend:plotly
the plot is nothing 
Add a Screenshot

Help

Re: [julia-users] Is the master algorithm on the roadmap?

[Kevin Liu]

I'll try to build it, compare it, and show it to you guys. I offered to do 
this as work. I am waiting to see if they will accept it. 

On Sunday, August 7, 2016 at 6:15:50 PM UTC-3, Stefan Karpinski wrote:
>
> Kevin, as previously requested by Isaiah, please take this to some other 
> forum or maybe start a blog.
>
> On Sat, Aug 6, 2016 at 10:53 PM, Kevin Liu 
> > wrote:
>
>> Symmetry-based learning, Domingos, 2014 
>> https://www.microsoft.com/en-us/research/video/symmetry-based-learning/
>>
>> Approach 2: Deep symmetry networks generalize convolutional neural 
>> networks by tying parameters and pooling over an arbitrary symmetry group, 
>> not just the translation group. In preliminary experiments, they 
>> outperformed convnets on a digit recognition task. 
>>
>> On Friday, August 5, 2016 at 4:56:45 PM UTC-3, Kevin Liu wrote:
>>>
>>> Minsky died of a cerebral hemorrhage at the age of 88.[40] 
>>>  Ray Kurzweil 
>>>  says he was contacted by 
>>> the cryonics organization Alcor Life Extension Foundation 
>>>  seeking 
>>> Minsky's body.[41] 
>>>  
>>> Kurzweil 
>>> believes that Minsky was cryonically preserved by Alcor and will be revived 
>>> by 2045.[41] 
>>>  Minsky 
>>> was a member of Alcor's Scientific Advisory Board 
>>> .[42] 
>>>  In 
>>> keeping with their policy of protecting privacy, Alcor will neither confirm 
>>> nor deny that Alcor has cryonically preserved Minsky.[43] 
>>>  
>>>
>>> We better do a good job. 
>>>
>>> On Friday, August 5, 2016 at 4:45:42 PM UTC-3, Kevin Liu wrote:

 *So, I think in the next 20 years (2003), if we can get rid of all of 
 the traditional approaches to artificial intelligence, like neural nets 
 and 
 genetic algorithms and rule-based systems, and just turn our sights a 
 little bit higher to say, can we make a system that can use all those 
 things for the right kind of problem? Some problems are good for neural 
 nets; we know that others, neural nets are hopeless on them. Genetic 
 algorithms are great for certain things; I suspect I know what they're bad 
 at, and I won't tell you. (Laughter)*  - Minsky, founder of CSAIL MIT

 *Those programmers tried to find the single best way to represent 
 knowledge - Only Logic protects us from paradox.* - Minsky (see 
 attachment from his lecture)

 On Friday, August 5, 2016 at 8:12:03 AM UTC-3, Kevin Liu wrote:
>
> Markov Logic Network is being used for the continuous development of 
> drugs to cure cancer at MIT's CanceRX , on 
> DARPA's largest AI project to date, Personalized Assistant that 
> Learns (PAL) , progenitor of Siri. One of 
> Alchemy's largest applications to date was to learn a semantic network 
> (knowledge graph as Google calls it) from the web. 
>
> Some on Probabilistic Inductive Logic Programming / Probabilistic 
> Logic Programming / Statistical Relational Learning from CSAIL 
> 
>  (my 
> understanding is Alchemy does PILP from entailment, proofs, and 
> interpretation)
>
> The MIT Probabilistic Computing Project (where there is Picture, an 
> extension of Julia, for computer vision; Watch the video from Vikash) 
> 
>
> Probabilistic programming could do for Bayesian ML what Theano has 
> done for neural networks. 
>  - Ferenc Huszár
>
> Picture doesn't appear to be open-source, even though its Paper is 
> available. 
>
> I'm in the process of comparing the Picture Paper and Alchemy code and 
> would like to have an open-source PILP from Julia that combines the best 
> of 
> both. 
>
> On Wednesday, August 3, 2016 at 5:01:02 PM UTC-3, Christof Stocker 
> wrote:
>>
>> This sounds like it could be a great contribution. I shall keep a 
>> curious eye on your progress
>>
>> Am Mittwoch, 3. August 2016 21:53:54 UTC+2 schrieb Kevin Liu:
>>>
>>> Thanks for the advice Cristof. I am only interested in people 
>>> wanting to code it in Julia, from R by Domingos. The algo has been 
>>> successfully applied in many areas, even though there are many other 
>>> areas 
>>> remaining. 
>>>
>>> On Wed, Aug 3, 2016 at 4:45 PM, Christof Stocker <
>>> stocker@gmail.com> wrote:
>>>
>>>

Re: [julia-users] GlobalRef(Module, func) vs. :(Module.func)

[Yichao Yu]

On Mon, Aug 8, 2016 at 7:14 AM, Andrei Zh  wrote:

> Then maybe the whole approach is incorrect, so let me describe what I try
> to achieve.
>
> The general idea is to extract AST of a function and do some
>

Without knowing more higher level information, if this is what you want to
do then


> transformations on it. To do so, I use `Base.uncompressed_ast` (borrowed
> from ReverseDiffSource.jl
> ),
> iterate over it and
>

^^ this is the right way to do it.


> sometimes create new expressions using either `Expr(head, args...)` or
> plain :(expr) notation. Somewhere in this chain I get both -
> `GlobalRef(Module, func)` and `:(Module.func)`.
>
> 1. Should I use `Base.uncompressed_ast` for this task at all?
> 2. What is a set of nodes that I should work with? E.g. should I try to
> avoid `GlobalRef`?
>

It strongly depend on what you want to do and whether you care about what
they represent.


>
> I know that AST is (somewhat intentionally) poorly documented, but some
> guidelines would be very helpful.
>

The devdoc should have fairly complete description of what these nodes are.
Note that the internal AST is currently, well, internal and might change
very often. (we try to keep the surface AST relatively stable).


>
>
>
> On Monday, August 8, 2016 at 1:55:51 AM UTC+3, Yichao Yu wrote:
>>
>>
>>
>> On Mon, Aug 8, 2016 at 3:57 AM, Andrei Zh  wrote:
>>
>>> While parsing Julia expressions, I noticed that sometimes calls to
>>>
>>
>> This shouldn't happen.
>>
>>
>>> global functions resolve to `GloablRef` and sometimes to
>>>
>>
>> and GlobalRef should only happen during lowering.
>>
>>
>>> getfield(Module, func). Could somebody please clarify:
>>>
>>> 1. Why do we need both?
>>>
>>
>> GlobalRef is essentially an optimization. It's more restricted and easier
>> to interpret/codegen and is emitted by lowering/type inference when it is
>> legal to do so.
>>
>>
>>> 2. Is it safe to replace one by the other (assuming only modules and
>>> functions are involved)?
>>>
>>
>> Not always. There are certainly cases where a GlobalRef currently can't
>> be used (method definition for example) I'm not sure if there's cases the
>> other way around.
>>
>>

Re: [julia-users] GlobalRef(Module, func) vs. :(Module.func)

[Andrei Zh]

Then maybe the whole approach is incorrect, so let me describe what I try 
to achieve. 

The general idea is to extract AST of a function and do some 
transformations on it. To do so, I use `Base.uncompressed_ast` (borrowed 
from ReverseDiffSource.jl 
),
 
iterate over it and sometimes create new expressions using either 
`Expr(head, args...)` or plain :(expr) notation. Somewhere in this chain I 
get both - `GlobalRef(Module, func)` and `:(Module.func)`. 

1. Should I use `Base.uncompressed_ast` for this task at all? 
2. What is a set of nodes that I should work with? E.g. should I try to 
avoid `GlobalRef`? 

I know that AST is (somewhat intentionally) poorly documented, but some 
guidelines would be very helpful. 



On Monday, August 8, 2016 at 1:55:51 AM UTC+3, Yichao Yu wrote:
>
>
>
> On Mon, Aug 8, 2016 at 3:57 AM, Andrei Zh  > wrote:
>
>> While parsing Julia expressions, I noticed that sometimes calls to 
>>
>
> This shouldn't happen.
>  
>
>> global functions resolve to `GloablRef` and sometimes to 
>>
>
> and GlobalRef should only happen during lowering.
>  
>
>> getfield(Module, func). Could somebody please clarify:
>>
>> 1. Why do we need both? 
>>
>
> GlobalRef is essentially an optimization. It's more restricted and easier 
> to interpret/codegen and is emitted by lowering/type inference when it is 
> legal to do so.
>  
>
>> 2. Is it safe to replace one by the other (assuming only modules and 
>> functions are involved)? 
>>
>
> Not always. There are certainly cases where a GlobalRef currently can't be 
> used (method definition for example) I'm not sure if there's cases the 
> other way around.
>
>

Re: [julia-users] GlobalRef(Module, func) vs. :(Module.func)

[Yichao Yu]

On Mon, Aug 8, 2016 at 3:57 AM, Andrei Zh  wrote:

> While parsing Julia expressions, I noticed that sometimes calls to
>

This shouldn't happen.


> global functions resolve to `GloablRef` and sometimes to
>

and GlobalRef should only happen during lowering.


> getfield(Module, func). Could somebody please clarify:
>
> 1. Why do we need both?
>

GlobalRef is essentially an optimization. It's more restricted and easier
to interpret/codegen and is emitted by lowering/type inference when it is
legal to do so.


> 2. Is it safe to replace one by the other (assuming only modules and
> functions are involved)?
>

Not always. There are certainly cases where a GlobalRef currently can't be
used (method definition for example) I'm not sure if there's cases the
other way around.

[julia-users] Re: I get this error while trying to run *.jl file from Terminal ERROR: LoadError: UndefVarError: input not defined

[Kristoffer Carlsson]

Please include the file you are tying to run.

On Sunday, August 7, 2016 at 11:09:07 PM UTC+2, Rishabh Raghunath wrote:
>
>
>
> Hello,
> I am a beginner in the Julia language .. 
> I get this error while I try to run .jl Julia program file from the 
> terminal. However It works perfectly fine in the Juno IDE. This following 
> is the error message I receive while trying to run the program from the 
> Linux terminal:
>
>
> ERROR: LoadError: UndefVarError: input not defined
> in legacy at /home/rishabh/Desktop/ProjectJulia/juliatest.jl:120
> while loading /home/rishabh/Desktop/ProjectJulia/juliatest.jl, in 
> expression starting on line 138
>
> How do I resolve this and run .jl file in the terminal rather than in Juno 
> ?
> Thanks In advance
>

Re: [julia-users] Is the master algorithm on the roadmap?

[Stefan Karpinski]

Kevin, as previously requested by Isaiah, please take this to some other
forum or maybe start a blog.

On Sat, Aug 6, 2016 at 10:53 PM, Kevin Liu  wrote:

> Symmetry-based learning, Domingos, 2014 https://www.microsoft.com/en-
> us/research/video/symmetry-based-learning/
>
> Approach 2: Deep symmetry networks generalize convolutional neural
> networks by tying parameters and pooling over an arbitrary symmetry group,
> not just the translation group. In preliminary experiments, they
> outperformed convnets on a digit recognition task.
>
> On Friday, August 5, 2016 at 4:56:45 PM UTC-3, Kevin Liu wrote:
>>
>> Minsky died of a cerebral hemorrhage at the age of 88.[40]
>>  Ray Kurzweil
>>  says he was contacted by
>> the cryonics organization Alcor Life Extension Foundation
>>  seeking
>> Minsky's body.[41]
>>  Kurzweil
>> believes that Minsky was cryonically preserved by Alcor and will be revived
>> by 2045.[41]
>>  Minsky
>> was a member of Alcor's Scientific Advisory Board
>> .[42]
>>  In
>> keeping with their policy of protecting privacy, Alcor will neither confirm
>> nor deny that Alcor has cryonically preserved Minsky.[43]
>> 
>>
>> We better do a good job.
>>
>> On Friday, August 5, 2016 at 4:45:42 PM UTC-3, Kevin Liu wrote:
>>>
>>> *So, I think in the next 20 years (2003), if we can get rid of all of
>>> the traditional approaches to artificial intelligence, like neural nets and
>>> genetic algorithms and rule-based systems, and just turn our sights a
>>> little bit higher to say, can we make a system that can use all those
>>> things for the right kind of problem? Some problems are good for neural
>>> nets; we know that others, neural nets are hopeless on them. Genetic
>>> algorithms are great for certain things; I suspect I know what they're bad
>>> at, and I won't tell you. (Laughter)*  - Minsky, founder of CSAIL MIT
>>>
>>> *Those programmers tried to find the single best way to represent
>>> knowledge - Only Logic protects us from paradox.* - Minsky (see
>>> attachment from his lecture)
>>>
>>> On Friday, August 5, 2016 at 8:12:03 AM UTC-3, Kevin Liu wrote:

 Markov Logic Network is being used for the continuous development of
 drugs to cure cancer at MIT's CanceRX , on
 DARPA's largest AI project to date, Personalized Assistant that Learns
 (PAL) , progenitor of Siri. One of Alchemy's
 largest applications to date was to learn a semantic network (knowledge
 graph as Google calls it) from the web.

 Some on Probabilistic Inductive Logic Programming / Probabilistic Logic
 Programming / Statistical Relational Learning from CSAIL
 
  (my
 understanding is Alchemy does PILP from entailment, proofs, and
 interpretation)

 The MIT Probabilistic Computing Project (where there is Picture, an
 extension of Julia, for computer vision; Watch the video from Vikash)
 

 Probabilistic programming could do for Bayesian ML what Theano has done
 for neural networks. 
 - Ferenc Huszár

 Picture doesn't appear to be open-source, even though its Paper is
 available.

 I'm in the process of comparing the Picture Paper and Alchemy code and
 would like to have an open-source PILP from Julia that combines the best of
 both.

 On Wednesday, August 3, 2016 at 5:01:02 PM UTC-3, Christof Stocker
 wrote:
>
> This sounds like it could be a great contribution. I shall keep a
> curious eye on your progress
>
> Am Mittwoch, 3. August 2016 21:53:54 UTC+2 schrieb Kevin Liu:
>>
>> Thanks for the advice Cristof. I am only interested in people wanting
>> to code it in Julia, from R by Domingos. The algo has been successfully
>> applied in many areas, even though there are many other areas remaining.
>>
>> On Wed, Aug 3, 2016 at 4:45 PM, Christof Stocker <
>> stocker@gmail.com> wrote:
>>
>>> Hello Kevin,
>>>
>>> Enthusiasm is a good thing and you should hold on to that. But to
>>> save yourself some headache or disappointment down the road I advice a
>>> level head. Nothing is really as bluntly obviously solved as it may 
>>> seems
>>> at first glance after listening to brilliant people explain things. A
>>> physics professor of mine once told me that on

Re: [julia-users] @animate @gif using plots

[Tom Breloff]

Something like 'legend = :topright' might work.

On Sunday, August 7, 2016, digxx  wrote:

> Is it possible to position the legend manually in a plot(x,y,leg_pos=???)
>

Re: [julia-users] @animate @gif using plots

[digxx]

Is it possible to position the legend manually in a plot(x,y,leg_pos=???)

Re: [julia-users] Re: chol() more strict in v0.5?

[Andreas Noack]

It would be great with an entry for this in Compat.jl, e.g. something like

cholfact(A::HermOrSym, args...) = cholfact(A.data, A.uplo, args...)

On Sun, Aug 7, 2016 at 2:44 PM, Chris <7hunderstr...@gmail.com> wrote:

> mmh, could you explain your comment a little more?
>
> David, thanks for the tip.

Re: [julia-users] @animate @gif using plots

[digxx]

Sorry again, not quite the same error:
He was using ffmpeg apparently. Though I got it working with convert now 
(after removing all the imagemagick packages from julia and with the 
manually installed stuff) what is remaining is the jumping legend also seen 
in the above uploaded gif.

[julia-users] GlobalRef(Module, func) vs. :(Module.func)

[Andrei Zh]

While parsing Julia expressions, I noticed that sometimes calls to global 
functions resolve to `GloablRef` and sometimes to getfield(Module, func). 
Could somebody please clarify:

1. Why do we need both? 
2. Is it safe to replace one by the other (assuming only modules and 
functions are involved)? 

Re: [julia-users] @animate @gif using plots

[digxx]

>
> I just manually installed imagemagick and got the error:
>
> julia> 
gif(anim,"C:\\Users\\Diger\\Documents\\Julia\\Plotting\\anim2.gif",fps=15)
Unzul▒ssiger Parameter - 7
WARNING: Tried to create gif using convert (ImageMagick), but got error: 
ErrorException("failed process: Process(`convert -delay 7 -loop 0 
'C:\\cygwin64\\tmp\\jul20EA.tmp\\*.png' -alpha off 
'C:\\Users\\Diger\\Documents\\Julia\\Plotting\\anim2.gif'`, 
ProcessExited(4)) [4]")
ImageMagick can be installed by executing `Pkg.add("ImageMagick")`
Will try ffmpeg, but it's lower quality...)
INFO: Saved animation to C:\Users\Diger\Documents\Julia\Plotting\anim2.gif
Plots.AnimatedGif("C:\\Users\\Diger\\Documents\\Julia\\Plotting\\anim2.gif")


So same error as before but apparent afterwards he still is able to use the 
installed version to convert it?
The .gifs look pretty weird though:
http://fs5.directupload.net/images/160807/odlvopvt.gif 

[julia-users] Re: chol() more strict in v0.5?

[Chris]

mmh, could you explain your comment a little more? 

David, thanks for the tip.

Re: [julia-users] @animate @gif using plots

[digxx]

Yes I did and it still persists :-(
I added and removed various Packages to see if sth is missing (comparing to 
before)
but nothing works :-(
I removed and readded Imagemagick but that also didnt help.

Am Sonntag, 7. August 2016 19:56:23 UTC+2 schrieb Tom Breloff:
>
> Did you restart julia after adding ImageMagick?  The errors are because it 
> can't find either ImageMagick or ffmpeg, one of which is required to make 
> gifs. 
>
> On Sunday, August 7, 2016, digxx > 
> wrote:
>
>> Hey I reinstalled Julia and am now wondering why the animation part of 
>> plots doesnt work anymore. It did before...
>> I presume I'm lacking dependencies though which ones?
>>
>> The following produces an error.
>>
>> x=linspace(0,pi,100)
>> anim=@animate for i=0:100
>> y=sin(x*exp(i/50))
>> plot(x,y,xlims=(0,pi),ylims=(-1,1))
>> end
>> gif(anim, dirname(@__FILE__)*"\\anim.gif", fps=30)
>>
>> and the error is :
>>
>> Unzul▒ssiger Parameter - 3
>> WARNING: Tried to create gif using convert (ImageMagick), but got error: 
>> ErrorException("failed process: Process(`convert -delay 3 -loop 0 
>> 'C:\\cygwin64\\tmp\\jul28E7.tmp\\*.png' -alpha off 
>> 'C:\\Users\\Diger\\Documents\\Julia\\Plotting\\anim.gif'`, 
>> ProcessExited(4)) [4]")
>> ImageMagick can be installed by executing `Pkg.add("ImageMagick")`
>> Will try ffmpeg, but it's lower quality...)
>> ERROR: LoadError: could not spawn `ffmpeg -v 0 -framerate 30 -i 
>> 'C:\cygwin64\tmp\jul28E7.tmp/%06d.png' -y 
>> 'C:\Users\Diger\Documents\Julia\Plotting\anim.gif'`: no such file or 
>> directory (ENOENT)
>>  in _jl_spawn at process.jl:262
>> while loading C:\Users\Diger\Documents\Julia\Plotting\animation.jl, in 
>> expression starting on line 6
>>
>> When I first used the animation thingy I also had this error. But this 
>> was fixed after adding ImageMagick...
>>
>> Also now I do have ImageMagick installed and it seemed to have run 
>> through without any problems, still the error persists...
>>
>

Re: [julia-users] @animate @gif using plots

[Tom Breloff]

Did you restart julia after adding ImageMagick?  The errors are because it
can't find either ImageMagick or ffmpeg, one of which is required to make
gifs.

On Sunday, August 7, 2016, digxx  wrote:

> Hey I reinstalled Julia and am now wondering why the animation part of
> plots doesnt work anymore. It did before...
> I presume I'm lacking dependencies though which ones?
>
> The following produces an error.
>
> x=linspace(0,pi,100)
> anim=@animate for i=0:100
> y=sin(x*exp(i/50))
> plot(x,y,xlims=(0,pi),ylims=(-1,1))
> end
> gif(anim, dirname(@__FILE__)*"\\anim.gif", fps=30)
>
> and the error is :
>
> Unzul▒ssiger Parameter - 3
> WARNING: Tried to create gif using convert (ImageMagick), but got error:
> ErrorException("failed process: Process(`convert -delay 3 -loop 0
> 'C:\\cygwin64\\tmp\\jul28E7.tmp\\*.png' -alpha off
> 'C:\\Users\\Diger\\Documents\\Julia\\Plotting\\anim.gif'`,
> ProcessExited(4)) [4]")
> ImageMagick can be installed by executing `Pkg.add("ImageMagick")`
> Will try ffmpeg, but it's lower quality...)
> ERROR: LoadError: could not spawn `ffmpeg -v 0 -framerate 30 -i
> 'C:\cygwin64\tmp\jul28E7.tmp/%06d.png' -y 
> 'C:\Users\Diger\Documents\Julia\Plotting\anim.gif'`:
> no such file or directory (ENOENT)
>  in _jl_spawn at process.jl:262
> while loading C:\Users\Diger\Documents\Julia\Plotting\animation.jl, in
> expression starting on line 6
>
> When I first used the animation thingy I also had this error. But this was
> fixed after adding ImageMagick...
>
> Also now I do have ImageMagick installed and it seemed to have run through
> without any problems, still the error persists...
>

[julia-users] @animate @gif using plots

[digxx]

Hey I reinstalled Julia and am now wondering why the animation part of 
plots doesnt work anymore. It did before...
I presume I'm lacking dependencies though which ones?

The following produces an error.

x=linspace(0,pi,100)
anim=@animate for i=0:100
y=sin(x*exp(i/50))
plot(x,y,xlims=(0,pi),ylims=(-1,1))
end
gif(anim, dirname(@__FILE__)*"\\anim.gif", fps=30)

and the error is :

Unzul▒ssiger Parameter - 3
WARNING: Tried to create gif using convert (ImageMagick), but got error: 
ErrorException("failed process: Process(`convert -delay 3 -loop 0 
'C:\\cygwin64\\tmp\\jul28E7.tmp\\*.png' -alpha off 
'C:\\Users\\Diger\\Documents\\Julia\\Plotting\\anim.gif'`, 
ProcessExited(4)) [4]")
ImageMagick can be installed by executing `Pkg.add("ImageMagick")`
Will try ffmpeg, but it's lower quality...)
ERROR: LoadError: could not spawn `ffmpeg -v 0 -framerate 30 -i 
'C:\cygwin64\tmp\jul28E7.tmp/%06d.png' -y 
'C:\Users\Diger\Documents\Julia\Plotting\anim.gif'`: no such file or 
directory (ENOENT)
 in _jl_spawn at process.jl:262
while loading C:\Users\Diger\Documents\Julia\Plotting\animation.jl, in 
expression starting on line 6

When I first used the animation thingy I also had this error. But this was 
fixed after adding ImageMagick...

Also now I do have ImageMagick installed and it seemed to have run through 
without any problems, still the error persists...

[julia-users] Re: new installation of julia

[Uwe Fechner]

The informations, that you give are not precise enough.
Which Windows version do you have?
How do you launch julia?
Are you sure, that you do not have to versions of julia on your computer?

On Linux, for me the following was sufficient to upgrade julia 0.4 to  
0.4.7-pre+3:

git pull
git checkout v0.4.6
make -j4
./julia

If I type git checkout again, I get the same message:
HEAD ist jetzt bei 2e358ce... Tag v0.4.6

Sometimes it is needed to do 
make clean
make distclean
make -j4

For details on Windows look here:
https://github.com/JuliaLang/julia/blob/master/README.windows.md

Good luck!

And: Installing the binary distribution as explained in the link above (no 
installer,
just extracting the downloaded file) is probably the easiest way to go.


On Sunday, August 7, 2016 at 3:59:11 PM UTC+2, digxx wrote:
>
> Hey thx for ur answer. Somewhere I read it is recommended more to compile 
> it urself than using the precompiled binaries.
> Apart from that I tried once using them and it didnt work somehow.
> Or are u talking about the windows installer for me?
>
> Btw, does it have any effect after compiling and installing Julia to git 
> checkout v0.4.6 coz it still tells me
> HEAD is now at 2e358ce... Tag v0.4.6
> and I'm not sure what it means
>

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

[Henri Girard]

Every thing works fine now. I had to change python version, only 3 works 
now (I don't know why ?), I work with ubuntu 16.04 repos and compiled 
julia-0.5 RC+1 with a symlink in /usr/bin/julia5.
I still have ubuntu julia version 0.4.5 but unusable at the moment.
Regards
Henri

Le lundi 1 août 2016 16:37:09 UTC+2, Chris Rackauckas a écrit :
>
> I am pleased to announce the first release of DifferentialEquations.jl 
> .
>
> An accompanying blog post explains the motivation and philosophy of the 
> package in more detail. 
> 
>
> DifferentialEquations.jl is a library of methods for solving various 
> differential equations. DifferentialEquations.jl makes it easy to access 
> many different methods for solving equations and plot the results. This 
> v0.1 release marks that the core of DifferentialEquations.jl is complete, 
> which includes:
>
>
>- The standard ODE, SDE, and PDE (Heat and Poisson) solvers 
>
> 
>.
>- Plot recipes for all the basic types.
>- Tests for convergence of every algorithm.
>- Extensive documentation 
>and 
>tutorials 
>
> 
>.
>
> DifferentialEquations.jl also has many special features not seen in other 
> differential equation libraries, which includes (but is not limited to):
>
>
>- A simple interface via multiple-dispatch (see the blog post 
>
>).
>- Implementations of Feagin's Order 10, 12, and 14 Runge-Kutta methods 
>
> 
>.
>- Compatibility with Julia-defined number types 
>
> .
>  This 
>has been tested to work with Bigs, DecFP, and ArbFloats, and is actively 
>being tested with ArbReals and DoubleDouble.
>- Wrappers to ODE.jl and ODEInterface.jl 
>
> ,
>  
>giving you instant access to tons of different solver methods just by 
>changing the `alg` keyword.
>- State-of-the-art stochastic differential equation solvers 
>
> .
>  Implemented 
>are results from recent papers, and many other algorithms (including fast 
>adaptivity and highly-stable explicit methods) are waiting on a private 
>branch until papers are published.
>- Finite element solvers for some common stochastic PDEs 
>
> 
>  including 
>the Reaction-Diffusion equation used to describe Turing Morphogenesis 
>
> 
>.
>- An algorithm design and testing suite 
>
> 
>.
>
> For more information, check out the documentation 
> or the 
> IJulia 
> tutorial notebooks 
> .
>  If 
> you're interested in contributing, please see the Contributor's Guide 
> 
>  
> and/or chat with me on the Gitter channel 
> .
>

Re: [julia-users] Re: eigs fails silently

[Ralph Smith]

Right, ARPACK only enforces the projection for the generalized problem. I 
think your example relies on roundoff error in the orthogonalization step 
to populate the null space.

With regard to semi-definite B (or C in the OP), the shifted version of the 
algorithm (mode 3 in ARPACK) will work for this case, but does require ncv 
<= rank(B). Here one needs to solve (A - sigma * B) x = y instead of B x = 
y, with only a nonsingularity requirement.  I got this to work by 
suppressing the isposdef() check in arnoldi.jl; passing sigma=0 selects the 
right mode.  The disadvantage is that when B is *indefinite* the algorithm 
produces nonsense without complaint. Do you know of a simple test for 
semi-definiteness?

Just for the record, the logic in arnoldi.jl is not tricky.  If one has a 
really large problem where the factorizations are impractical, one could 
readily adapt the arnoldi.jl code to invoke iterative linear solvers.

On Saturday, August 6, 2016 at 6:07:58 PM UTC-4, Andreas Noack wrote:
>
> Ralph, ARPACK seems to be okay with the singularity (of A) in the 
> non-generalized case. In the problem here B=I so it's only a generalized 
> problem by algorithm, not by math and 
>
> julia> eigs(A)[1]
> 6-element Array{Float64,1}:
>  -100.0
>   100.0
> 4.44392e-15
>-3.0281e-18
> 3.5842e-33
> 1.69212e-33
>
> so here ARPACK is doing something different. Maybe expanding with vectors 
> from the null space which I guess is fine as long the αs and βs are zeroed 
> and you reorthogonalize.
>
> On Saturday, August 6, 2016 at 5:02:42 PM UTC-4, Ralph Smith wrote:
>>
>> The 0.5 behavior is the same as Fortran, and is technically correct. 
>>  ARPACK cannot create more (orthogonal) Krylov vectors than the rank of the 
>> matrix A,
>> so your example needs the additional keyword ncv=2. This doesn't seem to 
>> be adequately documented in arpack-ng either. The 0.4 behavior looks 
>> unreliable.
>>
>> On Saturday, August 6, 2016 at 2:03:21 AM UTC-4, Madeleine Udell wrote:
>>>
>>> Actually: I'm not sure we should chalk the error up to ARPACK. Julia 0.4 
>>> is able to produce a (correct, I think) answer to
>>>
>>> eigs(A, C)
>>>
>>> but 0.5 gives an ARPACK error. I don't suppose ARPACK changed between 
>>> Julia versions...!?
>>>
>>> On Sat, Aug 6, 2016 at 1:54 AM, Madeleine Udell  
>>> wrote:
>>>
 Andreas, thanks for the investigation. I'll use 0.5 for now, and hope 
 the real problems I encounter are within the capabilities of ARPACK.

 It's embarrassing to be bested by Matlab...

 On Fri, Aug 5, 2016 at 9:23 PM, Andreas Noack  
 wrote:

> I've looked a bit into this. I believe there is a bug in the Julia 
> wrappers on 0.4. The good news is that the bug appears to be fixed on 
> 0.5. 
> The bad news is the ARPACK seems to have a hard time with the problem. I 
> get
>
> julia> eigs(A,C,nev = 1, which = :LR)[1]
> ERROR: Base.LinAlg.ARPACKException("unspecified ARPACK error: -")
>  in aupd_wrapper(::Type{T}, 
> ::Base.LinAlg.#matvecA!#67{Array{Float64,2}}, ::Base.LinAlg.##64#71{Array
> {Float64,2}}, ::Base.LinAlg.##65#72, ::Int64, ::Bool, ::Bool, 
> ::String, ::Int64, ::Int64, ::String, :
> :Float64, ::Int64, ::Int64, ::Array{Float64,1}) at 
> ./linalg/arpack.jl:53
>  in #_eigs#60(::Int64, ::Int64, ::Symbol, ::Float64, ::Int64, ::Void, 
> ::Array{Float64,1}, ::Bool, ::B
> ase.LinAlg.#_eigs, ::Array{Float64,2}, ::Array{Float64,2}) at 
> ./linalg/arnoldi.jl:271
>  in (::Base.LinAlg.#kw##_eigs)(::Array{Any,1}, ::Base.LinAlg.#_eigs, 
> ::Array{Float64,2}, ::Array{Floa
> t64,2}) at ./:0
>  in #eigs#54(::Array{Any,1}, ::Function, ::Array{Float64,2}, 
> ::Array{Float64,2}) at ./linalg/arnoldi.
> jl:80
>  in (::Base.LinAlg.#kw##eigs)(::Array{Any,1}, ::Base.LinAlg.#eigs, 
> ::Array{Float64,2}, ::Array{Float6
> 4,2}) at ./:0
>
> and since SciPy ends up with the same conclusion I conclude that the 
> issue is ARPACK. Matlab is doing something else because they are able to 
> handle this problem.
>
> Given that 0.5 is almost release, I'll not spend more time on the 
> issue on 0.4. Thought, if anybody is able to figure out what is going on, 
> please let us know.
>
> On Friday, August 5, 2016 at 8:47:26 AM UTC-4, Madeleine Udell wrote:
>>
>> Setting `which=:LR, nev=1` does not return the generalized eigenvalue 
>> with the largest real parts, and does not give a warning or error:
>>
>> n = 10
>> C = eye(n)
>> A = zeros(n,n)
>> A[1] = 100
>> A[end] = -100
>> @assert eigs(A, C, nev=1, which=:LR)[1][1] == maximum(eigs(A, C)[1])
>>
>> Am I expected to set nev greater than the number of eigenvalues I 
>> truly desire, based on my intuition as a numerical analyst? Or has eigs 
>> broken its implicit guarantee?
>>
>>


 -- 
 Madeleine Udell
 Assistant Professor, 

[julia-users] Pkg.status()

[digxx]

When calling Pkg.status() the first time it's telling me:
julia> Pkg.status()
INFO: Initializing package repository C:\cygwin64\home\Diger\.julia\v0.4
INFO: Cloning METADATA from git://github.com/JuliaLang/METADATA.jl
error: could not lock config file 
C:\cygwin64\home\Diger\.julia\v0.4\julF320.tmp\METADATA\.git/config: No 
such file or directory
ERROR: failed process: Process(`git 
'--work-tree=C:\cygwin64\home\Diger\.julia\v0.4\julF320.tmp\METADATA' 
'--git-dir=C:\cygwin64\home\Diger\.julia\v0.4\julF320.tmp\METADATA\.git' 
config remote.origin.url git://github.com/JuliaLang/METADATA.jl`, 
ProcessExited(255)) [255]
 in pipeline_error at process.jl:555


What's the issue here?

Re: [julia-users] Re: Apparently I need to rebuild Julia?

[Daniel Carrera]

Ah, sorry.

- Ubuntu 16.04 LTS, the one that just came out.

- Julia 0.4.6, the current stable release.

- Hmm... I couldn't remember how I installed Julia, so I decided to try
with the package manager... I found it, uninstalled it, then re-installed
it and now I seem to have been downgraded to 0.4.5 but now there is no
error... So I'm not sure what happened. I looked at my
/etc/apt/sources.list file and I don't see any Julia repository. So I
figure that I must have installed Julia using a PPA, so I found the PPA:

https://launchpad.net/~staticfloat/+archive/ubuntu/juliareleases


This time, instead of the PPA, I edited /etc/apt/sources.list and ran
`apt-get update && apt-get upgrade`. This upgraded Julia again to 0.4.6 and
*now* it doesn't show any errors.

So... I guess we figured out and fixed the issue. Thanks for your help!

Cheers,
Daniel.




On 7 August 2016 at 15:40, Uwe Fechner  wrote:

> Could you give some more information:
> - which Ubuntu version
> - which version of Julia
> - how did you install Julia?
>
> Regards, Uwe
>
> On Sunday, August 7, 2016 at 12:43:39 PM UTC+2, Daniel Carrera wrote:
>>
>> Hello,
>>
>> I just upgraded my Ubuntu install and now I get this message:
>>
>> % julia
>> WARNING: Error during initialization of module GMP:
>> ErrorException("The dynamically loaded GMP library (version 6.1.0 with
>> __gmp_bits_per_limb == 64)
>> does not correspond to the compile time version (version 5.1.3 with
>> __gmp_bits_per_limb == 64).
>> Please rebuild Julia.")
>>
>>
>>
>> I tried Googling but I can't figure out what I need to do. Help?
>>
>> Cheers,
>> Daniel.
>>
>

[julia-users] Re: new installation of julia

[digxx]

Hey thx for ur answer. Somewhere I read it is recommended more to compile 
it urself than using the precompiled binaries.
Apart from that I tried once using them and it didnt work somehow.
Or are u talking about the windows installer for me?

Btw, does it have any effect after compiling and installing Julia to git 
checkout v0.4.6 coz it still tells me
HEAD is now at 2e358ce... Tag v0.4.6
and I'm not sure what it means

[julia-users] Re: Apparently I need to rebuild Julia?

[Uwe Fechner]

Could you give some more information:
- which Ubuntu version
- which version of Julia
- how did you install Julia?

Regards, Uwe

On Sunday, August 7, 2016 at 12:43:39 PM UTC+2, Daniel Carrera wrote:
>
> Hello,
>
> I just upgraded my Ubuntu install and now I get this message:
>
> % julia
> WARNING: Error during initialization of module GMP:
> ErrorException("The dynamically loaded GMP library (version 6.1.0 with 
> __gmp_bits_per_limb == 64)
> does not correspond to the compile time version (version 5.1.3 with 
> __gmp_bits_per_limb == 64).
> Please rebuild Julia.")
>
>
>
> I tried Googling but I can't figure out what I need to do. Help?
>
> Cheers,
> Daniel.
>

[julia-users] Re: new installation of julia

[Uwe Fechner]

Is there a reason, why you want to compile Julia yourself? 
It might be easier to use a precompiled version, that you can download from 
http://julialang.org/downloads/ .

ln -s creates a symbolic link to the executable, such that is in the search 
path. This is the way to go 
on Linux, but I don't know if it works with mingw on Windows, that you are 
using.

On Linux, you can check with
which julia
in which directory the julia executable is found. Perhaps you have two 
versions on your computer
and you execute the old version because it is in the search path before 
your new version?

On Sunday, August 7, 2016 at 3:14:24 PM UTC+2, digxx wrote:
>
> hey thx,
> So i did git checkout v0.4.6 and compiled and in julia versioninfo() still 
> says 0.4.0 ??!
> u sure I need to do git checkout 0.4.6 or git checkout v0.4.6
>
> About this sudo In -s:
> I dont quite understand, so I write
>
> make sudo In -s /julia/usr/bin/julia4.6 ???
>
> What does the In or ln ( is it i or l ) stand for?
>

[julia-users] Re: chol() more strict in v0.5?

[David van Leeuwen]

I ran into the same problems.  In order to keep compatible with 0.4 I had 
to wrap the call to `chol()` into

forcesymmetric(c::Matrix) = full(Symmetric(c))

On Wednesday, August 3, 2016 at 3:02:52 PM UTC+2, Andreas Noack wrote:
>
> Yes. We are stricter now. LAPACK doesn't check for symmetry at all which 
> we used to mimic. It might seem pedantic but it will capture programming 
> errors and it is more in line with how check things elsewhere and it's in 
> line with the behavior for the sparse Cholesky. For now, you'd need to use 
> the Symmetric wrapper but ideally we'd have more operations returning 
> Symmetric in the future, e.g. cov.
>
> On Tuesday, August 2, 2016 at 8:49:22 AM UTC-4, Chris wrote:
>>
>> I ran into this issue when some of my unit tests failed on the v0.5 
>> release candidate. This example illustrates it:
>>
>> v0.4:
>>_   _ _(_)_ |  A fresh approach to technical computing
>>   (_) | (_) (_)|  Documentation: http://docs.julialang.org
>>_ _   _| |_  __ _   |  Type "?help" for help.
>>   | | | | | | |/ _` |  |
>>   | | |_| | | | (_| |  |  Version 0.4.6 (2016-06-19 17:16 UTC)
>>  _/ |\__'_|_|_|\__'_|  |  Official http://julialang.org/ release
>> |__/   |  x86_64-w64-mingw32
>>
>> julia> a = cov(rand(1000,6));
>>
>> julia> chol(inv(a))
>> 6x6 UpperTriangular{Float64,Array{Float64,2}}:
>>  3.58638  -0.0476413  -0.208862   0.0448371  -0.1271090.163736
>>  0.0   3.5431 -0.0297272  0.1167 -0.0598619  -0.105655
>>  0.0   0.0 3.456670.0493362   0.0118136  -0.00615045
>>  0.0   0.0 0.03.36366 0.0491131   0.146946
>>  0.0   0.0 0.00.0 3.52767-0.0148549
>>  0.0   0.0 0.00.0 0.0 3.52757
>>
>> v0.5:
>>_   _ _(_)_ |  A fresh approach to technical computing
>>   (_) | (_) (_)|  Documentation: http://docs.julialang.org
>>_ _   _| |_  __ _   |  Type "?help" for help.
>>   | | | | | | |/ _` |  |
>>   | | |_| | | | (_| |  |  Version 0.5.0-rc0+0 (2016-07-26 20:22 UTC)
>>  _/ |\__'_|_|_|\__'_|  |  Official http://julialang.org/ release
>> |__/   |  x86_64-w64-mingw32
>>
>> julia> a = cov(rand(1000,6));
>>
>> julia> chol(inv(a))
>> ERROR: ArgumentError: matrix is not symmetric/Hermitian. This error can 
>> be avoided by calling chol(Hermitian(A)) which will ignore either the upper 
>> or lower triangle of the matrix.
>>  in chol(::Array{Float64,2}) at .\linalg\cholesky.jl:156
>>
>> julia> b = inv(a);
>>
>> julia> maximum(b'-b)
>> 1.1102230246251565e-16
>>
>> I know an example using rand() is not ideal, but the behavior is pretty 
>> consistent. I tracked the difference down to here 
>> :
>>  
>> basically, in v0.5 there is an explicit check for a Hermitian matrix using 
>> ishermitian(), whereas in v0.4, chol() just uses the `info` output 
>> parameter from LAPACK.potrf!(). Calling potrf!() on the matrix `b` above 
>> returns a zero for info, meaning the execution completed successfully. So, 
>> it seems the ishermtian check for symmetry is stricter than LAPACK's.
>>
>> This is not necessarily a problem, but I run into this kind of issue 
>> frequently in my code, and I'm wondering what the best way forward is. I 
>> could wrap every chol() argument with Hermitian to ensure it's exactly 
>> symmetric, but then I lose a guard against more sinister bugs, since it 
>> will force any matrix to be Hermitian. Thoughts? Is the explicit 
>> ishermitian check necessary?
>>
>

[julia-users] Re: new installation of julia

[digxx]

hey thx,
So i did git checkout v0.4.6 and compiled and in julia versioninfo() still 
says 0.4.0 ??!
u sure I need to do git checkout 0.4.6 or git checkout v0.4.6

About this sudo In -s:
I dont quite understand, so I write

make sudo In -s /julia/usr/bin/julia4.6 ???

What does the In or ln ( is it i or l ) stand for?

[julia-users] Apparently I need to rebuild Julia?

[Daniel Carrera]

Hello,

I just upgraded my Ubuntu install and now I get this message:

% julia
WARNING: Error during initialization of module GMP:
ErrorException("The dynamically loaded GMP library (version 6.1.0 with 
__gmp_bits_per_limb == 64)
does not correspond to the compile time version (version 5.1.3 with 
__gmp_bits_per_limb == 64).
Please rebuild Julia.")



I tried Googling but I can't figure out what I need to do. Help?

Cheers,
Daniel.

[julia-users] Re: new installation of julia

[Henri Girard]

Make -j9 (number of core) compile le version git you have installed (by the 
way git is dev version 0.6, as I needed version 0.5 RC  i did git checkout 
0.5 , for you it's git checkout 0.4.6)
Make install : Install in the path you prefix it for example I put it in 
/usr/share/julia on ubuntu
But I prefer do a symlink :
sudo ln -s /your path to julia/julia /usr/bin/julia (you could even put 
other julia /usr/bin/julia4.6 ... etc...
and you call the bin by it's name.
 

Le dimanche 7 août 2016 10:55:39 UTC+2, digxx a écrit :
>
> So, now I freshly compiled julia again from the source after I specified:
> git checkout release-0.4 but then inside Julia I get by typing 
> versioninfo() 
>
> Julia Version 0.4.0
> Commit 0ff703b* (2015-10-08 06:20 UTC)
> Platform Info:
>   System: Windows (x86_64-w64-mingw32)
>   CPU: Intel(R) Core(TM) i5 CPU 750  @ 2.67GHz
>   WORD_SIZE: 64
>   BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Nehalem)
>   LAPACK: libopenblas64_
>   LIBM: libopenlibm
>   LLVM: libLLVM-3.3
>
> So why doesnt it install 0.4.6 automatically?
> git checkout release-0.4.6 doesnt work...
>

Re: [julia-users] new installation of julia

[digxx]

>
> Oh and what is the difference between make / make install
>
What do u need a make.user file for since I dont have it  

Re: [julia-users] new installation of julia

[digxx]

>
> Thx 


Do you know what these commands do:

git reset --hard #Forcibly remove any changes to any files under version 
control 

git clean -x -f -d #Forcibly remove any file or directory not under version 
control

I do not really get what that version control means?!?

In what cases/situations do u use this for example? 

Re: [julia-users] new installation of julia

[Bart Janssens]

Hi,

I think you need to do:
git checkout v0.4.6

You can also list the tags with git tag.

Cheers,

Bart

On Sun, Aug 7, 2016 at 10:55 AM digxx  wrote:

> So, now I freshly compiled julia again from the source after I specified:
> git checkout release-0.4 but then inside Julia I get by typing
> versioninfo()
>
> Julia Version 0.4.0
> Commit 0ff703b* (2015-10-08 06:20 UTC)
> Platform Info:
>   System: Windows (x86_64-w64-mingw32)
>   CPU: Intel(R) Core(TM) i5 CPU 750  @ 2.67GHz
>   WORD_SIZE: 64
>   BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Nehalem)
>   LAPACK: libopenblas64_
>   LIBM: libopenlibm
>   LLVM: libLLVM-3.3
>
> So why doesnt it install 0.4.6 automatically?
> git checkout release-0.4.6 doesnt work...
>

[julia-users] new installation of julia

[digxx]

So, now I freshly compiled julia again from the source after I specified:
git checkout release-0.4 but then inside Julia I get by typing 
versioninfo() 

Julia Version 0.4.0
Commit 0ff703b* (2015-10-08 06:20 UTC)
Platform Info:
  System: Windows (x86_64-w64-mingw32)
  CPU: Intel(R) Core(TM) i5 CPU 750  @ 2.67GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Nehalem)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.3

So why doesnt it install 0.4.6 automatically?
git checkout release-0.4.6 doesnt work...

Re: [julia-users] One month later...

[Henri Girard]

Sorry, now julia-0.4.5 kernel dies. I won't use it any more, as long as 
julia-0.5 works with my file. It's time to go over...



Le 07/08/2016 à 09:06, Yichao Yu a écrit :



On Sun, Aug 7, 2016 at 12:10 PM, Henri Girard > wrote:


I can't get it working, all my julia/ijulia files give me error
and I can't get any solution, ijulia freezes


your script start giving errors with nothing changed? What are the 
errors you see?



Le 06/08/2016 à 23:54, Yichao Yu a écrit :



On Sun, Aug 7, 2016 at 12:56 AM, Henri Girard
mailto:henri.gir...@gmail.com>> wrote:

Hi,
I went in holliday for a month. Julia/ijulia was working fine...
Trying again today, I got a lot of warning and errors.
I was on ubuntu v0.4.5, so seeing things where going bad I


What do you mean by "going bad"? What error/warning do you see on
0.4.5?

compile 0.5 RC, which gives less error and warning messages.
This RC work fine in console but I can't get it working in
ijulia always error at the end and very very long (even
without ending) time to do the thing.
Does it happen only with me ? Or is there a julia adaptation
time at the moment ?
Best regards
Henri

Re: [julia-users] One month later...

[Yichao Yu]

On Sun, Aug 7, 2016 at 12:10 PM, Henri Girard 
wrote:

> I can't get it working, all my julia/ijulia files give me error and I
> can't get any solution, ijulia freezes
>

your script start giving errors with nothing changed? What are the errors
you see?


>
> Le 06/08/2016 à 23:54, Yichao Yu a écrit :
>
>
>
> On Sun, Aug 7, 2016 at 12:56 AM, Henri Girard 
> wrote:
>
>> Hi,
>> I went in holliday for a month. Julia/ijulia was working fine...
>> Trying again today, I got a lot of warning and errors.
>> I was on ubuntu v0.4.5, so seeing things where going bad I
>>
>
> What do you mean by "going bad"? What error/warning do you see on 0.4.5?
>
>
>> compile 0.5 RC, which gives less error and warning messages. This RC work
>> fine in console but I can't get it working in ijulia always error at the
>> end and very very long (even without ending) time to do the thing.
>> Does it happen only with me ? Or is there a julia adaptation time at the
>> moment ?
>> Best regards
>> Henri
>>
>
>
>