# Specific Domains

**URL:** https://discourse.julialang.org/c/domain/10.md?no_subcategories=false&page=514

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**Page:** 515

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## [Support for cancer data in GeneticVariation?](https://discourse.julialang.org/t/support-for-cancer-data-in-geneticvariation/18601)

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**Author:** [@aalexandersson](https://discourse.julialang.org/u/aalexandersson)\
**Replies:** 3\
**Last updated:** [December 13, 2018, 9:20am UTC](https://discourse.julialang.org/t/support-for-cancer-data-in-geneticvariation/18601 "2018-12-13T09:20:48Z")

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I want to try to use Julia for analyzing cancer genomics data but I am not sure how. BioJulia seems to cover the basics, and I have contacted Julia Computing for info about JuliaRun and JuliaDB. Genomics data are increa…

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## [PSA: Convex.jl default solver deprecation](https://discourse.julialang.org/t/psa-convex-jl-default-solver-deprecation/18570)

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**Author:** [@Rory-Finnegan](https://discourse.julialang.org/u/Rory-Finnegan)\
**Replies:** 4\
**Last updated:** [December 12, 2018, 11:37pm UTC](https://discourse.julialang.org/t/psa-convex-jl-default-solver-deprecation/18570 "2018-12-12T23:37:44Z")

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Support for default solvers in Convex.jl is about to be dropped. For the most part this’ll just require you to explicitly pass a MathProgBase.AbstractMathProgSolver as the second argument to solve!, if you aren’t already…

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## [How do I use MATLAB.jl and vpa?](https://discourse.julialang.org/t/how-do-i-use-matlab-jl-and-vpa/18595)

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**Author:** [@Noel\_Araujo](https://discourse.julialang.org/u/Noel_Araujo)\
**Replies:** 6\
**Last updated:** [December 12, 2018, 10:21pm UTC](https://discourse.julialang.org/t/how-do-i-use-matlab-jl-and-vpa/18595 "2018-12-12T22:21:22Z")

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Hello everyone, I am want to do something conceptually simple using MATLAB.jl package. I have a BigFloat matrix in Julia, and I want to send to Matlab to compute its inverse/determinant/eigenvalues with arbitrary-precis…

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## [Timing square function in CUDA](https://discourse.julialang.org/t/timing-square-function-in-cuda/18440)

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**Author:** [@cuchxq](https://discourse.julialang.org/u/cuchxq)\
**Replies:** 4\
**Last updated:** [December 11, 2018, 9:19pm UTC](https://discourse.julialang.org/t/timing-square-function-in-cuda/18440 "2018-12-11T21:19:32Z")

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I am trying to compare if there is any speed benefit to use Nvidia’s math pow function than my own square kernel. Here is the code. using CuArrays, CUDAnative, CUDAdrv function square(a, ndrange) i = (blockIdx().…

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## [DistributedArrays: basic example from doc fails](https://discourse.julialang.org/t/distributedarrays-basic-example-from-doc-fails/18551)

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**Author:** [@samo](https://discourse.julialang.org/u/samo)\
**Replies:** 5\
**Last updated:** [December 11, 2018, 7:46pm UTC](https://discourse.julialang.org/t/distributedarrays-basic-example-from-doc-fails/18551 "2018-12-11T19:46:23Z")

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Hi all, I am new to Julia and would like to try out DistributedArrays. However, the basic example from the Julia documentation fails for me. Trying to make sure that there is no issue with the installation, I completely…

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## [Flux gradient clipping](https://discourse.julialang.org/t/flux-gradient-clipping/18544)

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**Author:** [@Fart](https://discourse.julialang.org/u/Fart)\
**Replies:** 2\
**Last updated:** [December 11, 2018, 7:21pm UTC](https://discourse.julialang.org/t/flux-gradient-clipping/18544 "2018-12-11T19:21:04Z")

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Does anyone have a working implementation of gradient clipping in Flux? I’ve tried directly modifying the param.grad field but get LoadError: type TrackedArray is immutable

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## [How to use CachingPool?](https://discourse.julialang.org/t/how-to-use-cachingpool/18498)

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**Author:** [@MaximilianJHuber](https://discourse.julialang.org/u/MaximilianJHuber)\
**Replies:** 4\
**Last updated:** [December 10, 2018, 11:55pm UTC](https://discourse.julialang.org/t/how-to-use-cachingpool/18498 "2018-12-10T23:55:19Z")

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Do I used the CachingPool incorrectly, or is this a bug? On Julia 1.0.2: using Distributed addprocs(2) @everywhere f\_passall(a,x) = length(x) + a its = 1:20 bigarr = ones(10^8) pool = CachingPool(workers()) pmap(pool, …

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## [Performance of log in nonlinear optimization](https://discourse.julialang.org/t/performance-of-log-in-nonlinear-optimization/18450)

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**Author:** [@danielcas](https://discourse.julialang.org/u/danielcas)\
**Replies:** 6\
**Last updated:** [December 10, 2018, 9:30pm UTC](https://discourse.julialang.org/t/performance-of-log-in-nonlinear-optimization/18450 "2018-12-10T21:30:06Z")

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I’m having some trouble with the function “log” in an optimization problem. For instance: I create a variable, and then the following constraint: @NLconstraint(ModelName, log(x) \<=100), I use Ipopt to solve it (a fea…

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## [How to use FFTW MPI routines with MPI.jl](https://discourse.julialang.org/t/how-to-use-fftw-mpi-routines-with-mpi-jl/18533)

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**Author:** [@favba](https://discourse.julialang.org/u/favba)\
**Replies:** 2\
**Last updated:** [December 10, 2018, 7:33pm UTC](https://discourse.julialang.org/t/how-to-use-fftw-mpi-routines-with-mpi-jl/18533 "2018-12-10T19:33:37Z")

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I’d like to use FFTW’s distributed memory routines and I have several doubts on how to achieve this. I guess one should be able to build that on top of MPI.jl and FFTW.jl, right? I’m still stuck in very conceptual doubt…

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## [Different parametrizations of probability distributions in Distributions.jl](https://discourse.julialang.org/t/different-parametrizations-of-probability-distributions-in-distributions-jl/18435)

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**Author:** [@alejandromerchan](https://discourse.julialang.org/u/alejandromerchan)\
**Replies:** 5\
**Last updated:** [December 10, 2018, 5:23pm UTC](https://discourse.julialang.org/t/different-parametrizations-of-probability-distributions-in-distributions-jl/18435 "2018-12-10T17:23:21Z")

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In R there are several probability distributions that allow keywords for different parametrizations of the same distribution. For example, I use the Negative Binomial distribution a lot in my simulations of some biologic…

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## [JuMP and Julia 0.7/1.0](https://discourse.julialang.org/t/jump-and-julia-0-7-1-0/12964)

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**Author:** [@miles.lubin](https://discourse.julialang.org/u/miles.lubin)\
**Replies:** 15\
**Last updated:** [December 9, 2018, 6:58pm UTC](https://discourse.julialang.org/t/jump-and-julia-0-7-1-0/12964 "2018-12-09T18:58:59Z")

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Updated Oct 1: tl;dr: Thanks mostly to the persistence of @ExpandingMan, JuMP 0.18.3 was released today supporting Julia 0.6, 0.7, and 1.0. Upgrade away! If you are using JuMP 0.18 on Julia 0.6, we do recommend upgradin…

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## [Using JuMP to pick winners of a tournament](https://discourse.julialang.org/t/using-jump-to-pick-winners-of-a-tournament/18476)

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**Author:** [@tyleransom](https://discourse.julialang.org/u/tyleransom)\
**Replies:** 2\
**Last updated:** [December 9, 2018, 2:11pm UTC](https://discourse.julialang.org/t/using-jump-to-pick-winners-of-a-tournament/18476 "2018-12-09T14:11:48Z")

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Hi, I’m using JuMP to pick winners of games of a single-elimination tournament. I have everything running fine except for the fact that I can’t seem to figure out how to impose a constraint that eliminated teams not be …

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## [MIQP: How does Pavito treat convex quadratic functions?](https://discourse.julialang.org/t/miqp-how-does-pavito-treat-convex-quadratic-functions/18400)

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**Author:** [@Olegg](https://discourse.julialang.org/u/Olegg)\
**Replies:** 6\
**Last updated:** [December 8, 2018, 1:19pm UTC](https://discourse.julialang.org/t/miqp-how-does-pavito-treat-convex-quadratic-functions/18400 "2018-12-08T13:19:43Z")

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Some Integer Programming solvers, e.g. CPLEX, provide specialised algorithms for convex quadratic constraints and objectives. Does Pavito enable such algorithms for a quadratic objective, or is it treated as a general…

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## [Taking Fitting Seriously](https://discourse.julialang.org/t/taking-fitting-seriously/13281)

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**Author:** [@oxinabox](https://discourse.julialang.org/u/oxinabox)\
**Replies:** 39\
**Last updated:** [December 8, 2018, 9:58am UTC](https://discourse.julialang.org/t/taking-fitting-seriously/13281 "2018-12-08T09:58:28Z")

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I’ve been thinking about taking our fitting APIs seriously for a while now. (But am very busy so have not advanced it too far). I got to briefly talk to some people at JuliaCon about it, so I am quickly writing up som…

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## [RigidBodyDynamics URDF inertia values](https://discourse.julialang.org/t/rigidbodydynamics-urdf-inertia-values/18384)

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**Author:** [@RogerP](https://discourse.julialang.org/u/RogerP)\
**Replies:** 3\
**Last updated:** [December 8, 2018, 3:38am UTC](https://discourse.julialang.org/t/rigidbodydynamics-urdf-inertia-values/18384 "2018-12-08T03:38:42Z")

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I am building my models directly from a relational database and the RigidBody components are loaded with those inertia values. (I can simply call up different configurations of robot arm with various numbers of links/joi…

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## [RemoteChannel with priority](https://discourse.julialang.org/t/remotechannel-with-priority/18442)

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**Author:** [@JesperMartinsson](https://discourse.julialang.org/u/JesperMartinsson)\
**Replies:** 0\
**Last updated:** [December 7, 2018, 10:49pm UTC](https://discourse.julialang.org/t/remotechannel-with-priority/18442 "2018-12-07T22:49:28Z")

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Is there a preferred way to incorporate priorities into RemoteChannels so that take! will deliver the most prioritized item first?

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## [Maximum Likelihood Example Update](https://discourse.julialang.org/t/maximum-likelihood-example-update/18436)

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**Author:** [@Donald\_Lacombe](https://discourse.julialang.org/u/Donald_Lacombe)\
**Replies:** 2\
**Last updated:** [December 7, 2018, 9:36pm UTC](https://discourse.julialang.org/t/maximum-likelihood-example-update/18436 "2018-12-07T21:36:25Z")

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Hello! I wanted to point to a new gist that I have developed to update the Normal Linear Model Maximum Likelihood example that is part of the Optim.jl examples. I am going over all of my code to make sure it is 0.7.0 c…

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## [How to test missing value in CSV package?](https://discourse.julialang.org/t/how-to-test-missing-value-in-csv-package/7535)

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**Author:** [@Fred](https://discourse.julialang.org/u/Fred)\
**Replies:** 11\
**Last updated:** [December 7, 2018, 6:01pm UTC](https://discourse.julialang.org/t/how-to-test-missing-value-in-csv-package/7535 "2018-12-07T18:01:30Z")

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Hi, I try to test if there is a missing value at a specific position of a dataframe obtained with the CSV package and I did not find the function to do that. Thank you for your help. julia\> x = CSV.read("data/data.csv"…

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## [Fibonacci Heap implementation](https://discourse.julialang.org/t/fibonacci-heap-implementation/18412)

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**Author:** [@Lefteris\_Manousakis](https://discourse.julialang.org/u/Lefteris_Manousakis)\
**Replies:** 4\
**Last updated:** [December 7, 2018, 1:07pm UTC](https://discourse.julialang.org/t/fibonacci-heap-implementation/18412 "2018-12-07T13:07:20Z")

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Hi everyone! I am implementing a Local Search algorithm using the Static Move Descriptors presented in A strategy for reducing the computational complexity of local search-based methods for the vehicle routing problem - …

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## [Buglet? Warning on groupby](https://discourse.julialang.org/t/buglet-warning-on-groupby/18390)

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**Author:** [@iwelch](https://discourse.julialang.org/u/iwelch)\
**Replies:** 1\
**Last updated:** [December 6, 2018, 5:58pm UTC](https://discourse.julialang.org/t/buglet-warning-on-groupby/18390 "2018-12-06T17:58:37Z")

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Is the Warning message a buglet? julia\> using DataFrames; df= DataFrame( n1=1:9, cat=\[ 'A','B','A', 'B','C','B', 'C','A','C' \] ); julia\> groupby(df, :cat) GroupedDataFrame{DataFrame} with 3 groups based on key: :cat Fi…

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## [Displaying plots in VegaLite opens vscode](https://discourse.julialang.org/t/displaying-plots-in-vegalite-opens-vscode/18336)

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**Author:** [@Ali\_Vahdati](https://discourse.julialang.org/u/Ali_Vahdati)\
**Replies:** 5\
**Last updated:** [December 6, 2018, 2:57pm UTC](https://discourse.julialang.org/t/displaying-plots-in-vegalite-opens-vscode/18336 "2018-12-06T14:57:50Z")

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I have no idea what configuration is wrong, but when I try to display a simple plot from VegaLite, a new instance of vscode opens. It happens when I do: using VegaLite, VegaDatasets data = dataset("cars") data |\> @vlpl…

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## [Fitting multilevel generalized linear models](https://discourse.julialang.org/t/fitting-multilevel-generalized-linear-models/18350)

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**Author:** [@jbrea](https://discourse.julialang.org/u/jbrea)\
**Replies:** 3\
**Last updated:** [December 6, 2018, 1:56pm UTC](https://discourse.julialang.org/t/fitting-multilevel-generalized-linear-models/18350 "2018-12-06T13:56:55Z")

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Is there already a julia package to fit multilevel models, e.g. for repeated measures?

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## [How does one use empirical distributions?](https://discourse.julialang.org/t/how-does-one-use-empirical-distributions/18360)

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**Author:** [@iwelch](https://discourse.julialang.org/u/iwelch)\
**Replies:** 1\
**Last updated:** [December 6, 2018, 4:41am UTC](https://discourse.julialang.org/t/how-does-one-use-empirical-distributions/18360 "2018-12-06T04:41:04Z")

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dear stats experts—the following used to work. julia\> using Random, Distributions; Random.seed!(0); julia\> x= max.(randn(10000), (rand(10000) .- 0.5)); julia\> empcdfun= EmpiricalUnivariateDistribution( x ); julia\> c…

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## [Another error with defining Flux.jl gradients](https://discourse.julialang.org/t/another-error-with-defining-flux-jl-gradients/17803)

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**Author:** [@xiaodai](https://discourse.julialang.org/u/xiaodai)\
**Replies:** 5\
**Last updated:** [December 5, 2018, 4:09pm UTC](https://discourse.julialang.org/t/another-error-with-defining-flux-jl-gradients/17803 "2018-12-05T16:09:50Z")

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Here is the MWE x = rand(12, 1000) y = rand(1000) W = param(\[1 for i=1:12\]) a = param(\[0.5\]) b = param(\[0.5\]) model(x) = begin x1 = \[maximum(x\[:,j\] .\* W) for j in 1:size(x, 2)\] (a .+ (x1 .- StatsBase.mean(x1)).…

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## [Animation on Julia 1.0.x](https://discourse.julialang.org/t/animation-on-julia-1-0-x/18270)

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**Author:** [@HerAdri](https://discourse.julialang.org/u/HerAdri)\
**Replies:** 18\
**Last updated:** [December 5, 2018, 3:24pm UTC](https://discourse.julialang.org/t/animation-on-julia-1-0-x/18270 "2018-12-05T15:24:48Z")

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I try to reproduce the following two examples in Julia 1.0.2,: using Plots anim = Animation() p = plot(\[sin,cos\], 0, π, size=(300,300)) scatter!(\[0\], \[sin,cos\]) for i in 0:0.1:π p\[3\] = \[i\], \[sin(i)\] p\[4\] = \[i\], …

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## [Problems about dealing with missing values, maybe connected to DataFrames.jl](https://discourse.julialang.org/t/problems-about-dealing-with-missing-values-maybe-connected-to-dataframes-jl/18282)

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**Author:** [@Jaime](https://discourse.julialang.org/u/Jaime)\
**Replies:** 4\
**Last updated:** [December 4, 2018, 5:32pm UTC](https://discourse.julialang.org/t/problems-about-dealing-with-missing-values-maybe-connected-to-dataframes-jl/18282 "2018-12-04T17:32:54Z")

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julia\> a=DataFrame(\[1 2 3; 4 missing 6\]) 2×3 DataFrame │ Row │ x1 │ x2 │ x3 │ │ │ Int64⍰ │ Int64⍰ │ Int64⍰ │ ├─────┼────────┼─────────┼────────┤ │ 1 │ 1 │ 2 │ 3 │ │ 2 │ 4 │ miss…

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## [\\ left division operator in editors (emacs)](https://discourse.julialang.org/t/left-division-operator-in-editors-emacs/18225)

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**Author:** [@jlapeyre](https://discourse.julialang.org/u/jlapeyre)\
**Replies:** 5\
**Last updated:** [December 4, 2018, 12:00pm UTC](https://discourse.julialang.org/t/left-division-operator-in-editors-emacs/18225 "2018-12-04T12:00:00Z")

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This operator \\ puts my emacs julia-mode in a bad state. After this symbol, it no longer understands expressions. If I want to use it, or add methods, I do eval(Meta.parse("import Base: \\\\")) const left\_division = eval…

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## [CUDAnative is awesome!](https://discourse.julialang.org/t/cudanative-is-awesome/17861)

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**Author:** [@LaurentPlagne](https://discourse.julialang.org/u/LaurentPlagne)\
**Replies:** 12\
**Last updated:** [December 3, 2018, 10:47pm UTC](https://discourse.julialang.org/t/cudanative-is-awesome/17861 "2018-12-03T22:47:11Z")

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Hi, I have just finished to rewrite my FEM solver with CUDAnative.jl and I want to address a big thank you to Tim and all the contributors for this package ! The performance is on par with the native C++/CUDA implement…

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## [Plotting with JuMP variables](https://discourse.julialang.org/t/plotting-with-jump-variables/18255)

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**Author:** [@muriloasouza](https://discourse.julialang.org/u/muriloasouza)\
**Replies:** 2\
**Last updated:** [December 3, 2018, 5:58pm UTC](https://discourse.julialang.org/t/plotting-with-jump-variables/18255 "2018-12-03T17:58:45Z")

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Hello, Not sure if i should post this here or in the visualization domain… but how can i plot a bar graph that has JuMP variables and regular Julia variables? For example, i’m trying to plot a bargraph, like this: Usi…

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## [Best practice for executing many instances parallel](https://discourse.julialang.org/t/best-practice-for-executing-many-instances-parallel/18107)

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**Author:** [@mike\_k](https://discourse.julialang.org/u/mike_k)\
**Replies:** 8\
**Last updated:** [December 3, 2018, 1:31pm UTC](https://discourse.julialang.org/t/best-practice-for-executing-many-instances-parallel/18107 "2018-12-03T13:31:05Z")

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Dear community, as indicated in the title, I would like to run many (thousands) of computational experiments on a hpc-cluster using julia code. Notice that I’m new to julia, so hopefully there are better options than th…

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