Difference between revisions of "CompSciWeek4"
(→Class 1: Formal Proofs) |
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* managing queued jobs |
* managing queued jobs |
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* advanced scripting tips and tricks |
* advanced scripting tips and tricks |
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+ | |||
+ | == Profiling and Plotting Code == |
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+ | |||
+ | '''lib/ltime.py''' |
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+ | <source lang="python"> |
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+ | # Functions to time |
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+ | from random import random |
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+ | |||
+ | def lappend(n): |
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+ | l = [1]*n |
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+ | l.append(random()) |
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+ | |||
+ | def lmod(n): |
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+ | l = [1]*n |
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+ | l[0] = random() |
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+ | |||
+ | def make_list(n): |
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+ | l = [1]*n |
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+ | |||
+ | def rand(n): |
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+ | random() |
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+ | </source> |
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+ | |||
+ | Make sure that PYTHONPATH includes your '''lib''' directory (where ltime.py lives), e.g. |
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+ | |||
+ | PYTHONPATH=/usr/lib/python2.7/site-packages:$HOME/scicomp/lib |
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+ | |||
+ | '''time.sh''' |
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+ | <source lang="bash"> |
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+ | #!/bin/bash |
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+ | |||
+ | if [ $# -ne 1 ]; then |
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+ | echo "Usage: $0 <function name from ltime.py>" |
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+ | exit 1 |
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+ | fi |
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+ | |||
+ | cmd=$1 |
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+ | |||
+ | k=1 |
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+ | for((n=1;n<8;n++)); do |
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+ | echo -n "$k " |
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+ | python -m timeit -s"import ltime as m;" "m.$cmd($k)" | sed 's/.*[^0-9]\([0-9]*\.\)/\1/; s/ usec.*//;' |
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+ | k=$(($k*2)) |
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+ | done |
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+ | </source> |
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+ | |||
+ | '''analyze.py''' |
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+ | <source lang="python"> |
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+ | from numpy import * |
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+ | import sys, pylab |
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+ | |||
+ | assert len(sys.argv) == 2, "Usage: %s <function name>"%sys.argv[0] |
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+ | |||
+ | name = sys.argv[1] |
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+ | x = fromfile(name+".dat", sep=' ') |
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+ | x = reshape(x, (-1,2)) |
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+ | pylab.plot(x[:,0], x[:,1]) |
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+ | pylab.savefig(name+".png") |
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+ | </source> |
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+ | |||
+ | Both the shell and python scripts above have been modified from the version in class to show how to read command-line arguments. In the shell, the number of arguments is in the variable '''$#''', and the '''if''' statement checks for the right usage. '''$0''' is the program name and ''is not'' counted in '''$#'''. In python, the arguments are in the list, sys.argv, sys.argv[0] is the program name, and ''is'' counted in len(sys.argv). The '''assert''' statement checks for the right usage, and immediately terminates with an error (raises an AssertionError exception) if the assertion fails. |
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= Homework 3 - due Monday, Sept. 22 = |
= Homework 3 - due Monday, Sept. 22 = |
Revision as of 11:14, 18 September 2014
Contents
Reading Assignment
- Algorithms, Chapter 2-3
Class 1: Formal Proofs
- Complexity Notation
- Rules - state assumptions, use logical operations on assumptions
- Modus Ponens - (a, a =>b) => b
- Modus Tollens - (a => b, ~b) => ~a
- Disjunctive Syllogism - ((a v b), ~a) => b
- Contradiction - (a, ~a) => Yikes!
ex. from 1+1 = 1, prove that I am the Pope. A: The Pope and I make 2, but 1+1 = 1, so I and the Pope are one and the same.
- Anything that proves a false statement is false.
- If a then False => ~a
- Induction
Class 2: Using HPC Resources
- accessing binaries and libraries, using modules
- using scratch space
- submitting a job script
- managing queued jobs
- advanced scripting tips and tricks
Profiling and Plotting Code
lib/ltime.py <source lang="python">
- Functions to time
from random import random
def lappend(n): l = [1]*n l.append(random())
def lmod(n): l = [1]*n l[0] = random()
def make_list(n): l = [1]*n
def rand(n): random() </source>
Make sure that PYTHONPATH includes your lib directory (where ltime.py lives), e.g.
PYTHONPATH=/usr/lib/python2.7/site-packages:$HOME/scicomp/lib
time.sh <source lang="bash">
- !/bin/bash
if [ $# -ne 1 ]; then
echo "Usage: $0 <function name from ltime.py>" exit 1
fi
cmd=$1
k=1 for((n=1;n<8;n++)); do
echo -n "$k " python -m timeit -s"import ltime as m;" "m.$cmd($k)" | sed 's/.*[^0-9]\([0-9]*\.\)/\1/; s/ usec.*//;' k=$(($k*2))
done </source>
analyze.py <source lang="python"> from numpy import * import sys, pylab
assert len(sys.argv) == 2, "Usage: %s <function name>"%sys.argv[0]
name = sys.argv[1] x = fromfile(name+".dat", sep=' ') x = reshape(x, (-1,2)) pylab.plot(x[:,0], x[:,1]) pylab.savefig(name+".png") </source>
Both the shell and python scripts above have been modified from the version in class to show how to read command-line arguments. In the shell, the number of arguments is in the variable $#, and the if statement checks for the right usage. $0 is the program name and is not counted in $#. In python, the arguments are in the list, sys.argv, sys.argv[0] is the program name, and is counted in len(sys.argv). The assert statement checks for the right usage, and immediately terminates with an error (raises an AssertionError exception) if the assertion fails.
Homework 3 - due Monday, Sept. 22
- Coding Problems
- Write a code to build a graph representation of what's inside the /usr/share/X11 directory on circe. Use (os.walk and/or os.listdir, os.path.join).
- How many directories are there total?
- What is the maximum depth, counting files and dirs so the depth of a dir with no files/subdirs = 0, and with any files/subdirs = 1?
- How many references are there to each directory -- node in-degree? (ignore symlinks)
- What is the maximum number of references from a directory (i.e. maximum out-
- Write a code to build a graph representation of what's inside the /usr/share/X11 directory on circe. Use (os.walk and/or os.listdir, os.path.join).
degree)?
- Problems from Algorithms in Python:
- 2-4
- 2-7 (write and turn in a test code for each case mentioned)
- 2-10
- 2-12