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Mathematica on Biowulf
Mathematica v 4.2.1 is available on Nimbus, but the later versions are suppported only on Helix and Biowulf. If you plan to use Mathematica for interactive or occasional jobs, Helix is the most appropriate platform. Mathematica jobs are only suited for the Biowulf cluster if you have many similar jobs to perform.
There are a total of 6 Mathematica licenses. The PBS Batch system on Biowulf keeps track of these licenses, and will start a Mathematica job only when a license is available. All Mathematica batch jobs must therefore specify the appropriate 'resource' (as in the example below) when the job is submitted, otherwise the batch system may start the job which will immediately exit because there is no license available. The command:
qsub -l nodes=1,math=1 my_job_scriptwill submit the job and tell PBS that a Mathematica license (math=1) is required.
Mathematica Batch Jobs
- Create a Mathematica command file:
You can insert Mathematica commands into a math command file, and submit
it to the Biowulf batch system.
Below is a sample math command file (rmsd.math). This file creates an
pdf output plot, which will appear in the same directory as the rmsd.math file.
----------------------------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["/data/username/mydir/a.pdf",plot1] Exit[] ------------------------------------------------------------------------------ - Create a Biowulf batch script. Sample batch script:
------- file myrun.batch ------------------------------------------------ #!/bin/tcsh # #PBS -N Math #PBS -m be #PBS -k oe cd /data/username/mymathdir #enter the appropriate directory here math -run "<<rmsd.math"
- Submit this job to the batch system
qsub -l nodes=1,math=1 myrun.batch
Running Mathematica interactively without the GUI
For debugging purposes, it may be most convenient to run Mathematica interactively with your Notebook file. This is done by allocating an interactive node, and typing the Mathematica command that you would normally put into your batch script. Sample session:
[user@biowulf mydir]$ qsub -I -l nodes=1,math=1
qsub: waiting for job 591449.biobos to start
qsub: job 591449.biobos ready
p227 job-busy interactive
[user@p227 ~]$ cd /data/user/mydir
[user@p227 mydir]$ math -run "<<rmsdplot.math"
Mathematica 5.0 for Linux
Copyright 1988-2003 Wolfram Research, Inc.
-- Terminal graphics initialized --
RMSD
# Backbone
3# #
# #
# #
# #
2.5# ##
# # #
# # #
2# # #
# # #
# # #
1.5# # #
# ## #
# # ## ### ## ##
# # ## # ## ## #
1# # # ### # ## # ## # #
### ## # ####### ## # ####### ### ## ### #
######### # ### ## # ##### # ## ### # ######## ###
0.5###### # ####### ## # ## # ### ## ### ### #### # ##
# ## ######### ### ###### # ## # #### #
# ## ### #
################################################################### Res. No
50 100
[user@p227 mydir]$ exit
qsub: job 591449.biobos completed
[user@biowulf mydir]
Documentation
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