# Specific Domains

**URL:** https://discourse.julialang.org/c/domain/10.md?no_subcategories=false&page=205

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**Page:** 206

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## [Biojulia website not accessible](https://discourse.julialang.org/t/biojulia-website-not-accessible/94870)

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**Author:** [@ForestRaven](https://discourse.julialang.org/u/ForestRaven)\
**Replies:** 6\
**Last updated:** [March 23, 2023, 10:50pm UTC](https://discourse.julialang.org/t/biojulia-website-not-accessible/94870 "2023-03-23T22:50:31Z")

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Hi, I’m interested in doing bioinformatics with Julia and Google keeps redirecting me to Biojulia. However, the website does not seem to be up for at least two days. Is it still online ? Thanks,

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## [How to loop over the variables of a JuMP model?](https://discourse.julialang.org/t/how-to-loop-over-the-variables-of-a-jump-model/96463)

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**Author:** [@geo1093](https://discourse.julialang.org/u/geo1093)\
**Replies:** 4\
**Last updated:** [March 23, 2023, 7:22pm UTC](https://discourse.julialang.org/t/how-to-loop-over-the-variables-of-a-jump-model/96463 "2023-03-23T19:22:37Z")

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Hi, I hope my question is not already answered somewhere else, I couldn’t find it. Here is the beginning of a MWE (I actually have many more variables and bigger sets): using JuMP, Gurobi model = Model(Gurobi.Optimize…

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## [Which JuMP solvers support compute\_conflict!?](https://discourse.julialang.org/t/which-jump-solvers-support-compute-conflict/95733)

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**Author:** [@juliohm](https://discourse.julialang.org/u/juliohm)\
**Replies:** 9\
**Last updated:** [March 23, 2023, 7:12pm UTC](https://discourse.julialang.org/t/which-jump-solvers-support-compute-conflict/95733 "2023-03-23T19:12:45Z")

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I am trying to show the constraints of an infeasible problem in a human-readable format and found compute\_conflict! in the docs: Solutions · JuMP! The COSMO.jl solver doesn’t support the function. Is there any other pu…

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## [The solution of JuMP model cannot splice horizontally](https://discourse.julialang.org/t/the-solution-of-jump-model-cannot-splice-horizontally/96511)

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**Author:** [@kevinqiao](https://discourse.julialang.org/u/kevinqiao)\
**Replies:** 1\
**Last updated:** [March 23, 2023, 7:07pm UTC](https://discourse.julialang.org/t/the-solution-of-jump-model-cannot-splice-horizontally/96511 "2023-03-23T19:07:07Z")

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I encountered an interesting question, I defined a sub-function (it’s a model) with a variable vector of 9×1 dimension, and the variables are as follows @variable(model, varFlow\[1:9\], Bin) The problem can be solved, an…

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## [Unable to use set\_attribute](https://discourse.julialang.org/t/unable-to-use-set-attribute/96529)

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**Author:** [@lilychow233](https://discourse.julialang.org/u/lilychow233)\
**Replies:** 1\
**Last updated:** [March 23, 2023, 7:06pm UTC](https://discourse.julialang.org/t/unable-to-use-set-attribute/96529 "2023-03-23T19:06:02Z")

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Hi. My julia version is 1.8.5. I tried to run the Benders Decomposition example from However, issues occured with the Callback Method. Specifically with this line: set\_attribute(lazy\_model, MOI.LazyConstraintCallbac…

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## [CUDA Format of \_\_nvvm\_\_reflect function not recognized](https://discourse.julialang.org/t/cuda-format-of-nvvm-reflect-function-not-recognized/96370)

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**Author:** [@Mark\_Lau](https://discourse.julialang.org/u/Mark_Lau)\
**Replies:** 12\
**Last updated:** [March 23, 2023, 4:19pm UTC](https://discourse.julialang.org/t/cuda-format-of-nvvm-reflect-function-not-recognized/96370 "2023-03-23T16:19:27Z")

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I have some code that is similar to an example from the CUDA.jl Introduction. Specifically, this one: using CUDA N = 2^20 x\_d = CUDA.fill(1.0f0, N) # a vector stored on the GPU filled with 1.0 (Float32) y\_d = CUDA.fi…

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## [Search in CUDA vector](https://discourse.julialang.org/t/search-in-cuda-vector/94833)

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**Author:** [@MohHizzani](https://discourse.julialang.org/u/MohHizzani)\
**Replies:** 5\
**Last updated:** [March 23, 2023, 12:35pm UTC](https://discourse.julialang.org/t/search-in-cuda-vector/94833 "2023-03-23T12:35:46Z")

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I have a vector of binary values, need to find all indices that are one, and randomly select one to update another vector at the same index selected.

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## [MTK & Linearization](https://discourse.julialang.org/t/mtk-linearization/95803)

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**Author:** [@BLI](https://discourse.julialang.org/u/BLI)\
**Replies:** 26\
**Last updated:** [March 23, 2023, 11:29am UTC](https://discourse.julialang.org/t/mtk-linearization/95803 "2023-03-23T11:29:34Z")

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MTK documentation case I’m looking at the linearization example in the MTK documentation: using ModelingToolkit @variables t x(t)=0 y(t)=0 u(t)=0 r(t)=0 @parameters kp = 1 D = Differential(t) eqs = \[u ~ kp \* (r - y) # …

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## [MTK and Jacobian](https://discourse.julialang.org/t/mtk-and-jacobian/96075)

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**Author:** [@BLI](https://discourse.julialang.org/u/BLI)\
**Replies:** 5\
**Last updated:** [March 23, 2023, 11:22am UTC](https://discourse.julialang.org/t/mtk-and-jacobian/96075 "2023-03-23T11:22:14Z")

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I have an unbalanced/partial model consisting of 2 differential equations, 11 algebraic equations, and 17 unknowns/states. I want to compute the Jacobian of the model. I have 3 questions regarding the calculate\_jacobian …

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## [Extracting data vectors in constraint from sum notation in JuMP](https://discourse.julialang.org/t/extracting-data-vectors-in-constraint-from-sum-notation-in-jump/96448)

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**Author:** [@Shuvomoy\_Das\_Gupta](https://discourse.julialang.org/u/Shuvomoy_Das_Gupta)\
**Replies:** 4\
**Last updated:** [March 22, 2023, 10:25pm UTC](https://discourse.julialang.org/t/extracting-data-vectors-in-constraint-from-sum-notation-in-jump/96448 "2023-03-22T22:25:27Z")

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Dear All, I am working on an optimization problem where I have a variable y\_{i,j} where i,j \\in \[1:n\] = \\{1,2,\\ldots,n\\}. I have a constraint of the form \\sum\_{j \\in \[1:n\]} y\_{j,i} - \\sum\_{j \\in \[1:n\]} y\_{i,j} \\geq b\_…

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## [DynamicalSystems: dynamic rule evaluates to nonzero but trajectory stays at initial condition](https://discourse.julialang.org/t/dynamicalsystems-dynamic-rule-evaluates-to-nonzero-but-trajectory-stays-at-initial-condition/96481)

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**Author:** [@cjoshliu](https://discourse.julialang.org/u/cjoshliu)\
**Replies:** 3\
**Last updated:** [March 22, 2023, 10:25pm UTC](https://discourse.julialang.org/t/dynamicalsystems-dynamic-rule-evaluates-to-nonzero-but-trajectory-stays-at-initial-condition/96481 "2023-03-22T22:25:02Z")

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Hi, I’m new to Julia and trying to find fixed points of an s-species generalized Lotka-Volterra model using DynamicalSystems. My model is d\_t\\vec{u}=\\vec{\\lambda}+\\vec{r}\\cdot\\vec{u}\\cdot (1-\\hat{\\alpha}\\vec{u}) where \\…

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## [ITERATION\_LIMIT with small changes in constraints](https://discourse.julialang.org/t/iteration-limit-with-small-changes-in-constraints/96403)

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**Author:** [@juliohm](https://discourse.julialang.org/u/juliohm)\
**Replies:** 3\
**Last updated:** [March 22, 2023, 7:07pm UTC](https://discourse.julialang.org/t/iteration-limit-with-small-changes-in-constraints/96403 "2023-03-22T19:07:40Z")

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I have a linear problem with linear equality and inequality constraints (and interval constraints). It works perfectly with various lower and upper bounds, but specific values trigger this ITERATION\_LIMIT and there is no…

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## [How can I perform GLM regression on column names with spaces?](https://discourse.julialang.org/t/how-can-i-perform-glm-regression-on-column-names-with-spaces/96442)

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**Author:** [@bertulli](https://discourse.julialang.org/u/bertulli)\
**Replies:** 6\
**Last updated:** [March 22, 2023, 5:06pm UTC](https://discourse.julialang.org/t/how-can-i-perform-glm-regression-on-column-names-with-spaces/96442 "2023-03-22T17:06:37Z")

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Hi all, very noob question but I can’t find an answer. I’m trying to do a linear regression on some data I have: julia\> df\_under\_test\[:, \[instruction\_sym, measure\_power\_sym, binary\_weight\_sym\]\] 1165×3 DataFrame Row │…

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## [How to solve Path Integral Problems with Probabilistic Programming Techniques?](https://discourse.julialang.org/t/how-to-solve-path-integral-problems-with-probabilistic-programming-techniques/96430)

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**Author:** [@GDufenshuoo](https://discourse.julialang.org/u/GDufenshuoo)\
**Replies:** 8\
**Last updated:** [March 22, 2023, 2:45pm UTC](https://discourse.julialang.org/t/how-to-solve-path-integral-problems-with-probabilistic-programming-techniques/96430 "2023-03-22T14:45:34Z")

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Hello everyone, I’m not very familiar with probabilistic programming, so I may not be approaching this problem in the most optimal way. Essentially, I’m trying to solve a problem of the following form: Z \\sim \\int\\int..…

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## [TimeSeries.jl and upsampling](https://discourse.julialang.org/t/timeseries-jl-and-upsampling/88896)

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**Author:** [@olivier](https://discourse.julialang.org/u/olivier)\
**Replies:** 3\
**Last updated:** [March 22, 2023, 3:14pm UTC](https://discourse.julialang.org/t/timeseries-jl-and-upsampling/88896 "2023-03-22T15:14:35Z")

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Hi, I need to be able to resample time series both ways : downsampling and upsimpling. I was able to downsample my time series using both TimeSeries.jl and TimeSeriesResampler.jl But the later doesn’t support upsampli…

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## [Score function error for simple custom Gaussian node in RxInfer](https://discourse.julialang.org/t/score-function-error-for-simple-custom-gaussian-node-in-rxinfer/96368)

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**Author:** [@John\_Boik](https://discourse.julialang.org/u/John_Boik)\
**Replies:** 1\
**Last updated:** [March 22, 2023, 12:46pm UTC](https://discourse.julialang.org/t/score-function-error-for-simple-custom-gaussian-node-in-rxinfer/96368 "2023-03-22T12:46:05Z")

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I’m testing a simple Gaussian custom node in RxInfer just to make sure I have the syntax correct, but I’m having trouble with the score function for Bethe free energy. My inference() function runs fine and returns BFE if…

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## [How to solve a Markov decision process with randomness](https://discourse.julialang.org/t/how-to-solve-a-markov-decision-process-with-randomness/96426)

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**Author:** [@Jian\_ZUO](https://discourse.julialang.org/u/Jian_ZUO)\
**Replies:** 0\
**Last updated:** [March 22, 2023, 12:24am UTC](https://discourse.julialang.org/t/how-to-solve-a-markov-decision-process-with-randomness/96426 "2023-03-22T00:24:21Z")

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Hi, I have a Markov decision process as follows: states: S1, S2; the increment of S1 follows a Gamma law, i.e. S1(t+d)-S1(t) ~ gamma(alpha, beta), S1 has a fixed range of zero to a failure threshold FT (thus the transi…

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## [Minibatching neural ODEs with different initial conditions](https://discourse.julialang.org/t/minibatching-neural-odes-with-different-initial-conditions/96361)

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**Author:** [@kaido975](https://discourse.julialang.org/u/kaido975)\
**Replies:** 7\
**Last updated:** [March 21, 2023, 8:18pm UTC](https://discourse.julialang.org/t/minibatching-neural-odes-with-different-initial-conditions/96361 "2023-03-21T20:18:39Z")

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I am trying to train a neural ODE on different time trajectories, starting with different initial conditions. I am able to observe a reduction in loss with ADAM (with good outputs), but BFGS does not work at all. Why is …

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## [Surprisingly inaccurate sparse Cholesky factorization](https://discourse.julialang.org/t/surprisingly-inaccurate-sparse-cholesky-factorization/96410)

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**Author:** [@jarapo](https://discourse.julialang.org/u/jarapo)\
**Replies:** 2\
**Last updated:** [March 21, 2023, 6:01pm UTC](https://discourse.julialang.org/t/surprisingly-inaccurate-sparse-cholesky-factorization/96410 "2023-03-21T18:01:41Z")

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I am surprised by how inaccurate cholesky() can be for sparse matrices; so much so it me wonder if I am not using it correctly. Define a finite different matrix A: L=2; dvec=-2\*ones(2^L);restvec=ones(2^L-1); A =sparse(…

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## [DiffEqJump/Catalyst, Turing possible?](https://discourse.julialang.org/t/diffeqjump-catalyst-turing-possible/83479)

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**Author:** [@jae0](https://discourse.julialang.org/u/jae0)\
**Replies:** 4\
**Last updated:** [March 21, 2023, 5:52pm UTC](https://discourse.julialang.org/t/diffeqjump-catalyst-turing-possible/83479 "2023-03-21T17:52:09Z")

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Hi, I am wondering if it is possible to do parameter inference using Turing for a DiffEqJump model? I understand that this type of problem might be better handled using an optimizer, but I am curious if it can be done …

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## [How to use hovertemplate with Plotly Python via Pycall](https://discourse.julialang.org/t/how-to-use-hovertemplate-with-plotly-python-via-pycall/96337)

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**Author:** [@this\_josh](https://discourse.julialang.org/u/this_josh)\
**Replies:** 6\
**Last updated:** [March 21, 2023, 4:54pm UTC](https://discourse.julialang.org/t/how-to-use-hovertemplate-with-plotly-python-via-pycall/96337 "2023-03-21T16:54:18Z")

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I’d like to create this plotly example in Julia by using PyCall to access python plotly. Below is the code from the example converted to julia: using PyCall go = pyimport("plotly.graph\_objects") subplots = pyimport("plo…

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## [Error with a new syntax of Flux](https://discourse.julialang.org/t/error-with-a-new-syntax-of-flux/96331)

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**Author:** [@iHany](https://discourse.julialang.org/u/iHany)\
**Replies:** 2\
**Last updated:** [March 21, 2023, 12:28am UTC](https://discourse.julialang.org/t/error-with-a-new-syntax-of-flux/96331 "2023-03-21T00:28:57Z")

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Hi, I’m trying to make my neural network compatible with a new syntax of Flux. Note that the network I used, PLSE, receives two arguments as PLSE(x, u). Code using Test using ParametrisedConvexApproximators using Lin…

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## [How can I combine different density plots in a 3D plot?](https://discourse.julialang.org/t/how-can-i-combine-different-density-plots-in-a-3d-plot/96194)

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**Author:** [@bertulli](https://discourse.julialang.org/u/bertulli)\
**Replies:** 8\
**Last updated:** [March 20, 2023, 10:36pm UTC](https://discourse.julialang.org/t/how-can-i-combine-different-density-plots-in-a-3d-plot/96194 "2023-03-20T22:36:15Z")

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Hi all! I’m analyzing some data that follows a more-or-less-linear dependency. Here’s a picture: I’d like to show the dispersion around the mean for each of the vertical bins you see. What I need is (I think) the den…

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## [Extract binary file from HTTP request body](https://discourse.julialang.org/t/extract-binary-file-from-http-request-body/96322)

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**Author:** [@sschmidhuber](https://discourse.julialang.org/u/sschmidhuber)\
**Replies:** 2\
**Last updated:** [March 20, 2023, 10:14pm UTC](https://discourse.julialang.org/t/extract-binary-file-from-http-request-body/96322 "2023-03-20T22:14:20Z")

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Hello, I’m struggling currently with extracting a binary file from a POST request body. On the client side I submit a form with a binary file and the enctype=“multipart/form-data”, that seems to work well. On the serv…

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## [Training is 500x slower than inference for a custom loss function](https://discourse.julialang.org/t/training-is-500x-slower-than-inference-for-a-custom-loss-function/96283)

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**Author:** [@neuromancer](https://discourse.julialang.org/u/neuromancer)\
**Replies:** 5\
**Last updated:** [March 20, 2023, 9:41pm UTC](https://discourse.julialang.org/t/training-is-500x-slower-than-inference-for-a-custom-loss-function/96283 "2023-03-20T21:41:10Z")

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I am trying to use gradient descent to optimize a matrix (a single layer neural network) using a custom loss function. The loss function is a sum of a Gaussian-kernel-embedded maximum mean discrepancy plus the L1 norm of…

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## [Flux: trainmode!() and testmode!() needed?](https://discourse.julialang.org/t/flux-trainmode-and-testmode-needed/94155)

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**Author:** [@wsshin](https://discourse.julialang.org/u/wsshin)\
**Replies:** 3\
**Last updated:** [March 20, 2023, 9:16pm UTC](https://discourse.julialang.org/t/flux-trainmode-and-testmode-needed/94155 "2023-03-20T21:16:52Z")

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I started using Flux recently, and I am wondering when Flux.trainmode!() and Flux.testmode!() need to be called. Am I correct that these functions do not need to be called explicitly during normal training and testing, …

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## [LoadError: Could not find any suitable device for this configuration](https://discourse.julialang.org/t/loaderror-could-not-find-any-suitable-device-for-this-configuration/96253)

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**Author:** [@stmorg](https://discourse.julialang.org/u/stmorg)\
**Replies:** 2\
**Last updated:** [March 20, 2023, 4:58pm UTC](https://discourse.julialang.org/t/loaderror-could-not-find-any-suitable-device-for-this-configuration/96253 "2023-03-20T16:58:02Z")

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Hello, Currently setting up julia on my new machine and having some trouble with getting CUDA to work. I am getting errors during test. Below is the output with JULIA\_DEBUG=all Pkg.test("CUDA") ┌ Debug: Loading cache f…

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## [Is it possible to store the JuMP output to an \*.xlsx?](https://discourse.julialang.org/t/is-it-possible-to-store-the-jump-output-to-an-xlsx/95887)

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**Author:** [@Optimization](https://discourse.julialang.org/u/Optimization)\
**Replies:** 15\
**Last updated:** [March 20, 2023, 3:30pm UTC](https://discourse.julialang.org/t/is-it-possible-to-store-the-jump-output-to-an-xlsx/95887 "2023-03-20T15:30:19Z")

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Hi, I have a model that uses CPLEX to find optimal solution. When I call JuMP.value.(x) ir cannot show all elements in the terminal. So, I’ve tried write\_to\_file(model, "model.xlsx") to store it in excel file to see wh…

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## [AssertionError when deleting and updating constraint in JuMP using Mosek solver](https://discourse.julialang.org/t/assertionerror-when-deleting-and-updating-constraint-in-jump-using-mosek-solver/96238)

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**Author:** [@bobo](https://discourse.julialang.org/u/bobo)\
**Replies:** 2\
**Last updated:** [March 20, 2023, 12:53pm UTC](https://discourse.julialang.org/t/assertionerror-when-deleting-and-updating-constraint-in-jump-using-mosek-solver/96238 "2023-03-20T12:53:45Z")

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Dear team, I would like to sequentially solve a problem by updating a constraint, the way I do it is to delete and restate the constraint inside a loop. Once the problem is solved and I try to delete the constraint I ge…

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## [Dierckx to perform a derivative over a 2d spline](https://discourse.julialang.org/t/dierckx-to-perform-a-derivative-over-a-2d-spline/96101)

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**Author:** [@roi.holtzman](https://discourse.julialang.org/u/roi.holtzman)\
**Replies:** 8\
**Last updated:** [March 20, 2023, 11:24am UTC](https://discourse.julialang.org/t/dierckx-to-perform-a-derivative-over-a-2d-spline/96101 "2023-03-20T11:24:08Z")

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I cannot use Dierckx.jl to perform a derivative over a 2d spline even though from the documentation it seems like it should work. The help of the function derivative gives: Dierckx.derivative is a Function. # 10 metho…

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