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A small set of tools

Project description

pywup

A small set of tools.

TODO: Expand this markdown

How to install / update

pip3 install --upgrade pywup --user --no-cache-dir

If you cannot run the wup command after installation, check if the path to the folder .local/bin is in your PATH. If not, add the following to the end of your ~/.bashrc:

export PATH=/home/<YOUR_USERNAME>/.local/bin:$PATH

The library

configure

This is a python library for creating template-based configure scripts.

#!/usr/bin/env python3

from pywup.configure import *

mf = TemplateBuilder()

mf.compiler     = find_program_or_abort(["clang++", "g++"], "Compiler", "clang")
mf.python       = find_header_or_abort("m/Python.h", "Python header", "python3-dev")
mf.highgui      = find_header_or_abort("/highgui.hpp", "Opencv's highgui", "opencv-dev")
mf.imgproc      = find_header_or_abort("/imgproc.hpp", "Opencv's imgproc", "opencv-dev")
mf.valgrind_py  = find_file_or_abort("python3-devel/valgrind-python.supp", "valgrind suppression file for python3", "python3-dev")
mf.libimgcodecs = find_lib("libopencv_imgcodecs.so", "libopencv_imgcodecs")

mf.libs         = "-lopencv_core -lopencv_highgui -lopencv_imgproc -I../../wup/cpp/include"
mf.headers      = "-DPYTHON_H=$(PYTHON_H) -DHIGHGUI_H=$(HIGHGUI_H) -DIMGPROC_H=$(IMGPROC_H)"

if mf.libimgcodecs:
    mf.libs     += " -lopencv_imgcodecs"

mf.build("Makefile", """\
CC={compiler}
HIGHGUI_H={highgui}
PYTHON_H={python}
IMGPROC_H={imgproc}
VALGRIND_PYTHON={valgrind_py}

LIBS = {libs}
HEADERS= {headers}

all:
	$(CC) -fPIC -shared wup_wrapper.cpp -o libwup.so -Wall -O3 -std=c++11 $(LIBS) $(HEADERS)

run:
	$(CC) main.cpp -o main -Wall -O3 -std=c++11 $(LIBS) $(HEADERS)
	./main

debug:
	$(CC) main.cpp -o main -Wall -g -std=c++11 $(LIBS) $(HEADERS)
	gdb main

valgrind:
	$(CC) -fPIC -shared wup_wrapper.cpp -o libwup.so -Wall -O1 -g -std=c++11 $(LIBS) $(HEADERS)
	valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --verbose --suppressions=$(VALGRIND_PYTHON) python3 main3.py --model wisard --dataset mnist 2> valgrind.out
""")

wup

This is a command line utility for running experiments, plotting and executing repetitive tasks.

collect

collect runs a program multiple times and collects outputs.

Example 1 - Permutate variables and collect outputs

  • This will permutate the variables THREADS (arithmetic: 1, 3, 5, 7, ...) and JOBS (geometric: 1, 1.6, ...)
  • For each configuration, the program will run 10 times
  • For each execution, the following attributes will be collected: TRAIN_TIME, TEST_TIME and ACC
  • The output will be saved in CSV format at wespa.csv
  • The permutations values for each variable are passed to the program in the same order they are declared. Each "{}" is replaced by the variable value.
wup collect \
    --p TRAIN_TIME "Info: Time to train was ([-0-9\.e\+]+) μs" \
    --p TEST_TIME "Info: Time to test was ([-0-9\.e\+]+) μs" \
    --p ACC "Test Acc = ([0-9\.]+)" \
    --runs 10 \
    --va THREADS 1 17 2 \
    --vg JOBS 1 80000 1.6 \
    --o wespa.csv \
    --c "./wisard -createModel RamWisard -ramBits 28 -decoder classic -ramType prime \
            -train mnist ../data/emnist/byclass/emnist-byclass-train \
            -test mnist ../data/emnist/byclass/emnist-byclass-test \
            -times -numThreads {} -hashSize 18041 -jobsPerThread {} -bleaching Y -pPredict 2"

Example 2 - Collect multiple rows from the same command execution

  • The parameter --n defines a line break, allowing us to collect multiple rows for the same execution.
  • The parameter --log defines an output file to write extra details during the process.
wup collect \
    --n "[a-zA-Z0-9]+ : AvgIntersectionScore = [-0-9\.e\+]+  AvgCenterDistanceScore = [-0-9\.e\+]+" \
    --p DS_NAME "([a-zA-Z0-9]+) : AvgIntersectionScore = [-0-9\.e\+]+  AvgCenterDistanceScore = [-0-9\.e\+]+" \
    --p INTERSECTION "[a-zA-Z0-9]+ : AvgIntersectionScore = ([-0-9\.e\+]+)  AvgCenterDistanceScore = [-0-9\.e\+]+" \
    --p CENTER_DISTANCE "[a-zA-Z0-9]+ : AvgIntersectionScore = [-0-9\.e\+]+  AvgCenterDistanceScore = ([-0-9\.e\+]+)" \
    --runs 10 \
    --o "./collect.csv" \
    --log "./collect.log" \
    --c "./run_all.sh"

Example 3 - Multiple commands and parallelization

  • Specify multiple --c to call multiple commands. When multiple commands are presented they will receive the same variables.
  • Their output will also be concatenated, you probably want to use --n to separate them in distinct lines.
  • The program will parse all their outputs as if they were continuous, one after the other.
  • Use --jobs to define the number of parallel processes.
  • Parallelization is be applied across parameter permutation and commands. If you have 16 permutations and 2 commands we have 32 parallel tasks.
  • You may also use --jobs without multiple commands.
  • You may also use --c with just one --jobs.
  • Use parallelism to tune parameters and single process to measure times. When you are measuring execution time, multiple processes may slightly slow each other as they compete for resources.
wup collect \
    --n "[a-zA-Z0-9]+ : AvgIntersectionScore = [-0-9\.e\+]+  AvgCenterDistanceScore = [-0-9\.e\+]+" \
    --p DS_NAME "([a-zA-Z0-9]+) : AvgIntersectionScore = [-0-9\.e\+]+  AvgCenterDistanceScore = [-0-9\.e\+]+" \
    --p INTERSECTION "[a-zA-Z0-9]+ : AvgIntersectionScore = ([-0-9\.e\+]+)  AvgCenterDistanceScore = [-0-9\.e\+]+" \
    --p CENTER_DISTANCE "[a-zA-Z0-9]+ : AvgIntersectionScore = [-0-9\.e\+]+  AvgCenterDistanceScore = ([-0-9\.e\+]+)" \
    --jobs 4 \
    --runs 10 \
    --o "./collect.csv" \
    --log "./collect.log" \
    --c "./run.sh 'Basketball'" \
    --c "./run.sh 'Biker'" \
    --c "./run.sh 'Bird1'" \
    --c "./run.sh 'Bird2'"

heatmap

heatmap receives a csv file and generates a heatmap.

wup heatmap \
    --data ./wespa.csv \
    --y "THREADS" \
    --x "JOBS" \
    --z "TEST_TIME" \
    --tz "data[0,z] / data[i,z]" \
    --tx "\"%d\" % int(float(data[i,x]))" \
    --ty "\"%d\" % int(float(data[i,y]))" \
    --tzz "\"%.2f\" % data[i,j]" \
    --title "Speedup (threads / blockSize)" \
    --size 10 4 \
    --o heatmap_wespa.png

bars

Generates a bar graphic using one or more csv files.

wup bars \
    --load ./note.csv \
    --line THREADS TEST_TIME "note test" \
    --line THREADS TRAIN_TIME "note train" \
 \
    --load ./out.csv \
    --line THREADS TEST_TIME "wespa test" \
    --line THREADS TRAIN_TIME "wespa train"\
 \
    --title "Predict speedups (threads / speedup)" \
    --ty "y[0,0] / y[i,j]" \
    --ts "y[0,0]*s[i,j] / (y[i,j]**2)" \
    --tyy "\"%.2f\" % ty[i,j] if ty[i,j] else ''" \
    --tx "int(float(x[i]))" \
    --xlabel "Threads" \
    --ylabel "Speedup" \
    --barwidth 0.9 \
    --size 10 4 \
    --verbose \
    --o bars_parallelPredictSpeedup.png

backup

Example ~/Dropbox/backups/system/wup.bak file

file;~/.local/bin/macro_play;./local_bin/
file;~/.local/bin/macro_rec_start;./local_bin/
file;~/.local/bin/macro_rec_stop;./local_bin/
folder;~/.config/compton;./compton
file;~/.vimrc;./vimrc
folder;~/.config/i3;./i3

Invoke backup / restore

# This will copy files from system (left) to backup folder (right), overwriting any change or previous file in the backup folder.
wup backup create ~/Dropbox/backups/system/wup.bak

# This will copy files from the backup folder (right) to the system (left), overwriting any change or previous file in the system.
wup backup restore ~/Dropbox/backups/system/wup.bak

# This will sync all files and backup folders, copying the most recent one to the right direction. 
wup backup sync ~/Dropbox/backups/system/wup.bak

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