Description
Mathematica is a fully integrated environment for technical and scientific computing. Mathematica combines numerical and symbolic computation, visualization, and programming in a single, flexible interactive system. The Mathematica system is very broad, and provides a systematic interface to all sorts of computations, from traditional numeric and symbolic computation, to visualization, to data format conversion, and the creation of user interfaces.
Version
There are multiple versions of Mathematica available. An easy way of selecting the version is to use modules.To see the modules available, type
[user@helix ~]$ module avail mathTo select a module, type[user@helix ~]$ module load math/[ver]where [ver] is the version of choice. The default version is 9.0.0.
License status
Total and free licenses, the resource name, and the per-user license limit can be seen by typing 'licenses' at the Biowulf prompt or by checking the current license status webpage at any time.
How to Use
Running the Mathematica GUI Interactively
To run the Mathematica graphics interface, an X-Windows connection is required. Open an X-Windows connection to helix.nih.gov, and check that it is working by typing 'xclock' at the prompt.
[user@helix ~]$ module load math
[user@helix ~]$ mathematica &You should see the Mathematica Welcome Screen as below:
The main Mathematica Notebook window will appear when you open a file by clicking Open or a file listed on the Welcome screen.
To run a demo, in the main Mathematica window, click Open. Enter the filename /usr/local/math-9000/Documentation/English/Demos/Animations.nb. You should see a window appear with several graphic images. Double-click on one of them to animate:
Run Mathematica interactively without the GUI
It is also possible to run Mathematica interactively on the command-line, without the GUI. This would be useful if you do not wish to use Xwindows, and is obviously most useful for calculations rather than interactive graphics. Sample session (user input in bold):
[user@helix ~]$ math
Mathematica 9.0 for Linux x86 (64-bit)
Copyright 1988-2012 Wolfram Research, Inc.
In[1]:= data=ReadList["rmsdplot.list",{Number,Number,Number}];
In[2]:= [..enter other Mathematica commands..]
In[22]:= Exit[]
[user@helix ~]$
Run Mathematica using a math command file
You can insert Mathematica commands into a math command file, and run that file interactively at the prompt. This is convenient if you perform the same Mathematica tasks frequently. Sample session with a Math command file bfactorplot.math.
[user@helix ~]$ math
Mathematica 9.0 for Linux x86 (64-bit)
Copyright 1988-2012 Wolfram Research, Inc.
In[1]:= <<bfactorplot.math
In[2]:= Exit[]
[user@helix ~]$
Alternatively, you can type directly at the command prompt:
[user@helix ~] math -run "<<rmsd.math"Below is an example of the command file "rmsd.math", which produces EPS graphic output.
----------------------------file rmsd.math---------------------------------- (* file geomanal/rmsdplot.math -- make a plot rmsd vs residue *) (*===>*) data=ReadList["rmsdplot.list",{Number,Number,Number}]; SetOptions[Plot,DisplayFunction->Identity] column0 = Transpose[data][[1]]; column1 = Transpose[data][[2]]; column2 = Transpose[data][[3]]; len=Length[column0]; b1=Join[column0,column1]; b2=Partition[b1,len]; b3=Transpose[b2]; xmax=Max[column0]; xmin=Min[column0]; y1max=Max[column1]; y1min=Min[column1]; y2max=Max[column2]; y2min=Min[column2]; plot1= ListPlot[b3, AxesLabel->{"Res. No.","RMSD"}, Ticks->{Range[0,xmax+5,50],Range[0.0, y1max+0.2 ,0.5]}, PlotLabel->"Backbone",Axes->{0,0},PlotJoined->True, PlotRange->{{0,xmax+2 }, {0., y1max +0.1 }}, AxesStyle->{PostScript ["/Times-Roman findfont 13 scalefont setfont"]} ]; s1=Join[column0,column2]; s2=Partition[s1,len]; s3=Transpose[s2]; Export["a.eps",plot1] Exit[] ------------------------------------------------------------------------------Tip: The output graphics file "a.eps" can be converted to a PDF with the command epstopdf a.eps producing the PDF file "a.pdf".
