Thursday, April 8, 2010

Changing 3D Correlation Function

One of my "things to think about" from yesterday's blog post was to make changes to the 3D correlation function so that it was truly an auto-correlation (only having one set of randoms which should speed up the calculation by a bit).

I made changes to my 3D correlation function to do this (at least I think I have) and I am running a test to see if I get the same solution as when I have two separate random catalogs (what I was doing) and also to see how much this speeds things up.

This set of runs in in the working directory: ../pythonjess/run201048_1527 and the log file where the code to run this is ../logs/

The new version runs in 7 seconds, whereas before it took 20 seconds! So that is a good improvement.

Here is a plot to show they look the same

Buzz Comments from Erin about qsub and splitting up the jobs:

Erin Sheldon - Have you used the PBS system on riemann? You can submit jobs and they get sent to different machines on the system. You could split your random runs into 25 different jobs, run them in parallel on 25 different machines, and then just add up the counts later.

That's a factor of n_machines speedup, better than you could every hope to get by just writing faster code.

Below is a sample script, let's call it test.pbs. You can submit with "qsub test.pbs". Of course change all the log file paths to make sense for you.

#PBS -l nodes=1:ppn=1
#PBS -l walltime=24:00:00
#PBS -q batch
#PBS -N this_job_name
#PBS -j oe
#PBS -o /path/to/where/the/pbs/script/is/test.pbs.pbslog
#PBS -m a
#PBS -r n
#PBS -W umask=0022

# put setups here

setup numpy -r ~esheldon/exports/numpy-trunk
setup scipy -r ~esheldon/exports/scipy-trunk
setup esutil -r ~esheldon/exports/esutil-trunk
setup python -r ~esheldon/exports/python/2.6.4

# this log is different than above, you can
# watch it in real time

# send commands to python
python &> "$logfile" <6:49 am
DeleteUndo deleteReport spamNot spam

Erin Sheldon - oh, and to see the status of your jobs
qstat -n -1 -u your_user_name

or equivalently:
6:55 am

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