Cactus Tutorial for TeraGrid 2009
Compiling Cactus on Queen Bee
- Temporary accounts for this tutorial will be hosted on Queen Bee (queenbee.loni.org), a large supercomputer on
LONI optical network. It is a 50.7 TFlops Peak Performance, 668 compute node cluster running Red Hat Enterprise Linux version 4 operating system. Each node contains dual Quad Core Xeon 64-bit processors operating at a core frequency of 2.33 GHz.
- Account usernames: train01 - train20. Login to Queen Bee using ssh:
ssh firstname.lastname@example.org # substitute 'train01' with your username
Password: # enter "*******"
- Download the GetCactus script to your home directory. Make it executable:
chmod +x GetCactus
- Download configuration files from SVN repository. The following command will create a directory misc and place all necessary installation scripts, configuration files, thornlists and parameter files to this directory.
svn co https://svn.cct.lsu.edu/repos/cactus/tutorials/introduction/examples/Cactus/misc
- Download the Cactus thornlist for this tutorial: Thorns.th. Check out the Cactus flesh and arrangements:
./GetCactus -repository=development ~/misc/Thorns.th
The script will prompt you a few questions. Simply hit <ENTER> to accept default options.
- Additional information on ways to obtain Cactus and associated arrangements are described on the Downloads section of this website.
- Make sure you have configuration options file queenbee.config in $HOME/misc directory.
- Create and compile cactus configuration WaveToy.
gmake wavetoy-config THORNLIST=~/misc/Thorns.th options=~/misc/queenbee.config
gmake -j10 wavetoy
- (optional) Check the compiled executable with --help on head node:
Running Cactus simulations:
- Have your parameter file and PBS job submission script in your $HOME/misc directory.
- Submit your job:
- Now you can monitor your job status using the qstat command. Here you can find more information about qstat and other PBS tools.
- The output data that your simulation is producing is located in $HOME/simulations/WaveToy. You can examine it while the job is running.
- (optional) Once the job has started, it announces itself on twitter.com, where it prints a temporary link to the simulation webpage. Follow the link to see various simulation parameters and control options.
- (optional) In order to examine standard output or standard error while the job is running, you will need to ssh to the job's root node and check its temporary files in /var/spool/torque/spool:
qstat -u <USER> # lists all jobs for a user <USER>
qstat -f <JOB-NUMBER> | grep exec_host; # gives you first line in the list of nodes
ssh <ROOT-NODE> -x less /var/spool/torque/spool/<JOB-NUMBER>.qb2.OU # standard output of your job
ssh <ROOT-NODE> -x less /var/spool/torque/spool/<JOB-NUMBER>.qb2.ER # standard error
- You can delete (abort) your job using qdel command.
Visualizing the output:
Using gnuplot for 1D and 2D output
is a powerful command-line interactive tool for scientific plotting. You can learn more about gnuplot here
- The WaveToy simulation produced output of 1D cuts along the X-, Y- and Z-directions for variable phi. The files with this data can be found in $HOME/simulations/WaveToy directory.
- Change to the simulation data directory and start gnuplot:
- Try various 1D and 2D plots:
gnuplot> plot "phi.x.asc" using 10:13 index 0 with linespoints # 1D cut along the X axis, t=0
gnuplot> p "phi.y.asc" u 11:13 i 0:10 w lp # 1D cut along the diagonal, t=0..30
gnuplot> sp "phi.x.asc" u 9:10:13 i 0:20 w l # 2D plot in (t,x,phi) space
- One of the powerful features of Cactus IO thorns is the ability to perform various grid function reductions for parallel runs. To compute an average, maximum and minimum values of the grid function phi, add the following lines to WaveToy.par and resubmit your job:
ActiveThorns = "CarpetIOScalar"
IOScalar::outscalar_every = 10
IOScalar::outscalar_vars = "wavetoy_simple::phi"
IOScalar::outscalar_reductions = "average minimum maximum"
Try to modify the output frequency or grid resolution to get beter plots.
- Visualise these integral quantities with gnuplot:
gnuplot> p "phi.minimum.asc" u 2:3 w l
gnuplot> p "phi.maximum.asc" u 2:3 w l
gnuplot> p "phi.average.asc" u 2:3 w l
Remote visualisation of 3D HDF5 output with VisIt
- Download and install VisIt version 1.11.x on your laptop, as described on the VisIt website.
- To enable remote visualization, you will need to add Queen Bee to the list of host profiles. This procedure for using GUI interface for a generic machine is described here.
- On Linux or Mac, you can also simply edit file ~/.visit/config by adding the following lines to host profiles section of XML (replace train01 with your username):
<Field name="profileName" type="string">serial</Field>
<Field name="host" type="string">queenbee.loni.org</Field>
<Field name="userName" type="string">train01</Field>
<Field name="profileName" type="string">serial</Field>
<Field name="active" type="bool">true</Field>
<Field name="arguments" type="stringVector">"-dir" "/home/ebentive/VisIt/1.11.2" </Field>
<Field name="hostAliases" type="string">queenbee.loni.org qb4.loni.org qb3.loni.org qb4 qb3</Field>
<Field name="tunnelSSH" type="bool">true</Field>
If the file ~/.visit/config doesn't exist, simply run VisIt once to have VisIt create it for you.
- Start VisIt on your laptop by typing
visit -debug 5 & # let's run it with debugging output in case things go wrong
- Go to "File > Open file", select "Host" = "queenbee.loni.org". Enter your password to connect to Queen Bee. Establishing connection might take a while.
- Select path /scratch/<USERNAME>/simulations/WaveToy. Select file phi.h5.
- Now you can visualize your data (e.g. the wave function phi) with VisIt using different visualization plotting types and operators. For instance, you might want to try Pseudocolor plot + a Slice operator.