Skip to main content

performance tuning - Launching remote kernels - will it help RAM needs?


Given the exasperating RAM needs of my Mathematica program, I contemplated launching remote kernels to run my Mathematica script. This is a two part question:


Part 1


If I launch a remote kernel(s), is the need for RAM also distributed amongst all the remote computers?


Part 2


I keep getting an error message when I try to launch a remote kernel from the Mathematica GUI.



The kernel c20-0707-23 failed to connect to the front end. (Error = MLECONNECT). You should try running the kernel connection outside the front end.



I have located the Kernel Program correctly on the remote computer. When I try starting a kernel over ssh in a terminal window with:



ssh username@remote.computer /path/to/math

Or


ssh username@remote.computer /path/to/MathKernel

After I enter the password to log in to the remote computer, I see that a kernel has been launched.


However, the same doesn't occur with the front end.


Are there any easy to understand tutorials/examples on launching remote kernels, without needing the GUI as I'd like to run scripts? I tried reading, this, for instance and the only thing that it did was make me panic as it was greek. I also read this but it's not an entirely similar problem


Here's a sample script that I used to launch local kernels and execute a simple NDSolve command:


#!/usr/local/bin/MathematicaScript -script


CloseKernels[]
LaunchKernels[3]
Print["AbsoluteTiming reveals:" NDSolve[{y'[x] == y[x] Cos[x + y[x]],
     y[0] == 1}, y, {x, 0, 30}]; // AbsoluteTiming ]
CloseKernels[]

This question may help answer the other question I linked in the first line.



Answer



Sometimes, yes it is sometimes distributed. I can't say for sure when and why, but I have noticed cases where ParallelMap does not distribute all the memory, but ParallelTable does.



Basically, Mathematica is trying to make things easy. You don't always want to have to spell out each and every variable that you want available on a remote kernel, and so it does its best to figure out just what you need. There are lots of options in Mathematica 8.


If you're trying to "aggregate" memory on other nodes, then you have to be careful to create the large data on remote machines to avoid the network transfer of the contents of the master kernel to the other machines. (Please know that I have run into issues in the past, where there seemed to be a limit as to precisely how much memory could be allocated by a Remote Kernel itself. i.e. couldn't allocate a gigabyte, let alone 16 gigabytes that are found in machines today. I don't know if this is still a problem.)


Comments

Post a Comment

Popular posts from this blog

plotting - Plot 4D data with color as 4th dimension

I have a list of 4D data (x position, y position, amplitude, wavelength). I want to plot x, y, and amplitude on a 3D plot and have the color of the points correspond to the wavelength. I have seen many examples using functions to define color but my wavelength cannot be expressed by an analytic function. Is there a simple way to do this? Answer Here a another possible way to visualize 4D data: data = Flatten[Table[{x, y, x^2 + y^2, Sin[x - y]}, {x, -Pi, Pi,Pi/10}, {y,-Pi,Pi, Pi/10}], 1]; You can use the function Point along with VertexColors . Now the points are places using the first three elements and the color is determined by the fourth. In this case I used Hue, but you can use whatever you prefer. Graphics3D[ Point[data[[All, 1 ;; 3]], VertexColors -> Hue /@ data[[All, 4]]], Axes -> True, BoxRatios -> {1, 1, 1/GoldenRatio}]
Post a Comment
Read more

plotting - Filling between two spheres in SphericalPlot3D

Manipulate[ SphericalPlot3D[{1, 2 - n}, {θ, 0, Pi}, {ϕ, 0, 1.5 Pi}, Mesh -> None, PlotPoints -> 15, PlotRange -> {-2.2, 2.2}], {n, 0, 1}] I cant' seem to be able to make a filling between two spheres. I've already tried the obvious Filling -> {1 -> {2}} but Mathematica doesn't seem to like that option. Is there any easy way around this or ... Answer There is no built-in filling in SphericalPlot3D . One option is to use ParametricPlot3D to draw the surfaces between the two shells: Manipulate[ Show[SphericalPlot3D[{1, 2 - n}, {θ, 0, Pi}, {ϕ, 0, 1.5 Pi}, PlotPoints -> 15, PlotRange -> {-2.2, 2.2}], ParametricPlot3D[{ r {Sin[t] Cos[1.5 Pi], Sin[t] Sin[1.5 Pi], Cos[t]}, r {Sin[t] Cos[0 Pi], Sin[t] Sin[0 Pi], Cos[t]}}, {r, 1, 2 - n}, {t, 0, Pi}, PlotStyle -> Yellow, Mesh -> {2, 15}]], {n, 0, 1}]
Post a Comment
Read more

plotting - Mathematica: 3D plot based on combined 2D graphs

I have several sigmoidal fits to 3 different datasets, with mean fit predictions plus the 95% confidence limits (not symmetrical around the mean) and the actual data. I would now like to show these different 2D plots projected in 3D as in but then using proper perspective. In the link here they give some solutions to combine the plots using isometric perspective, but I would like to use proper 3 point perspective. Any thoughts? Also any way to show the mean points per time point for each series plus or minus the standard error on the mean would be cool too, either using points+vertical bars, or using spheres plus tubes. Below are some test data and the fit function I am using. Note that I am working on a logit(proportion) scale and that the final vertical scale is Log10(percentage). (* some test data *) data = Table[Null, {i, 4}]; data[[1]] = {{1, -5.8}, {2, -5.4}, {3, -0.8}, {4, -0.2}, {5, 4.6}, {1, -6.4}, {2, -5.6}, {3, -0.7}, {4, 0.04}, {5, 1.0}, {1, -6.8}, {2, -4.7}, {3, -1....
Post a Comment
Read more