![]() ![]() You should export plots to a file or better - save the data to a file and create plots with apropriate software like gnuplot or xmgrace (mathematica graphics looks really awful). Note about plots: there is no graphic output to the screen in this mode. If you want also input lines to appear there add in the first line of your infile: Generate a text file by choosing from menu File-> Save_As_Special.-> Package_Formatīy default only output lines go to standard output. These cells will be defined as initialization cells by clicking on Cell-> Cell Properties-> Initialization_Cell in the menu bar.ģ. Select the cell or set of cells that contain the commands you wish to be written to the infile text file.Ģ. To convert Mathematica notebook file into plain text file use Mathematica's Front End features:ġ. Please refer to man sbatch/srun and Cluster user's guide to learn about the queueing system and job submission. Various ways of using Mathematica under the queueing system are presented below. Running Mathematica in the queueing system (on cluster nodes) On the cluster - remember to login to chcuk with X forwarding: ssh -X chuck. To start Mathematica on any workstation in the CAMK network type mathematica or (if it wasn't set up) /Vol/share/Mathematica//Executables/mathematica. System administrators can kill abandoned (no immediate contact), idle (no kernel activity) sessions. If all the licenses are busy please negotiate directly with their users. To display current usage of the Mathematica licenses type monitorlm on chuck. ![]() ![]() Please do not leave Mathematica sessions open when not needed! the frontend for editing notebooks and the kernel for calculations in the text mode (useful in the batch system). Each of them can be used separatelly, e.g. The software consists of two independent components - the graphical frontend and the kernel, so actually there are 7 frontend licenses and 7 kernel licenses. ![]() There are 7 Mathematica licenses available at CAMK. The full manual is available from the program level and on the web. It's used mostly for symbolic math but can do much more. Both approaches have different pros and cons, but the results should be more or less the same.Mathematica is a platform for all forms of computations. The difference between this code and "mifcmc" is that the latter makes the plots directly from the chains but the former gets them from the data created by "getdist". Parts of the code (the Confid2D function) have been used in the "Mathematica Interface for CosmoMC" program (mifcmc) as well. NEW: There are a couple of new CosmoMC versions out (March 2013 and April 2013), which may be incompatible with these scripts, so use at your own risk.Īn example code (with mock data) that can read the data created by "getdist" (CosmoMC's program that makes contours etc) and makes nice Mathematica plots instead, can be found here. I have asked for help from Wolfram Research to see if it can somehow be fixed.Ī thread for reporting problems etc has been set up over at the CosmoCoffee forum. The lag on Linux seems to be an OS specific problem, ie the Linux version of Mathematica does not handle Dynamic content as well as it does on Windows. This way, even if you quit the kernel you will not lose all your other calculations.Ģ) Linux users might experience some lag (<0.5secs).ģ) Mathematica on Macs may give a warning in the first tab about assigning "a raw object", however the rest of the code seems to be working OK. This may be bypassed temporarily by assigning a new kernel, other than Local, to the notebook. Then choose the name of the file, the filetype (pdf, eps etc), a folder where you intend to put the figure and click OK.ĭeveloped in Windows 7 with Mathematica 8.0.1.ġ) Fixed issue where some of the Greek letters are not properly displayed in the 2D tab.ġ) You have to quit the kernel before loading a new chain. For testing purposes I have included a sample CosmoMC chain in the ".\test_chain" directory.ħ) To save a plot right click on it and choose "Save graphic as.". Version 8.0.1 recommended.Ĥ) Evaluate the cell that contains "Chains".ĥ) If you get a message about evaluating "all the initialization cells", click yes.Ħ) Click the button "Open WMAP chain." or "Open CosmoMC chain." and navigate to a folder where you keep your chains. Hint 2: Internet Explorer sucks and doesn't render this page correctly, so please use a real browser (Firefox, Chrome, Safari etc).ģ) Open "chains_interface_v1.nb" with Mathematica. Then use the left and right arrows to navigate! Hint 1: Click on the photos for a slideshow. Welcome to the Mathematica Interface for CosmoMC v1.1.ġ) Analyze your MCMC chains made with CosmoMC or downloaded from the WMAP site.Ģ) Use it as an educational tool, eg while teaching a cosmology class.ģ) Harness the power of Mathematica and apply it to your cutting edge research. ![]()
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