mirror of
https://gitlab.kitware.com/vtk/vtk-m
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Add test scripts to run tests via example application.
This commit is contained in:
Gunther H. Weber
parent
7a77b1ad89
commit
8b21a8e07d
@ -76,4 +76,13 @@ if (VTKm_ENABLE_MPI)
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if (TARGET vtkm::tbb)
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target_compile_definitions(ContourTree_Distributed PRIVATE "ENABLE_SET_NUM_THREADS")
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endif()
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add_executable(TreeCompiler TreeCompilerApp.cxx)
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target_link_libraries(TreeCompiler vtkm_filter)
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vtkm_add_target_information(TreeCompiler DROP_UNUSED_SYMBOLS)
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configure_file(split_data_2d.py split_data_2d.py COPYONLY)
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configure_file(split_data_3d.py split_data_3d.py COPYONLY)
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configure_file(hact_test.sh hact_test.sh COPYONLY)
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configure_file(testrun.sh testrun.sh COPYONLY)
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endif()
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50
examples/contour_tree_distributed/TreeCompilerApp.cxx
Normal file
50
examples/contour_tree_distributed/TreeCompilerApp.cxx
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@ -0,0 +1,50 @@
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//=======================================================================================
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//
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// Parallel Peak Pruning v. 2.0
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//
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// Started June 15, 2017
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//
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// Copyright Hamish Carr, University of Leeds
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//
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// main_tree_compiler.cpp - main routine for the external verification programme
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//
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//=======================================================================================
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//
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// COMMENTS:
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//
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// Just a harness for the TreeCompiler routines
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//
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//=======================================================================================
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#include <stdio.h>
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#include <vtkm/worklet/contourtree_distributed/TreeCompiler.h>
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// main routine
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int main(int argc, char** argv)
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{ // main()
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// the compiler for putting them together
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vtkm::worklet::contourtree_distributed::TreeCompiler compiler;
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// we just loop through the arguments, reading them in and adding them
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for (int argument = 1; argument < argc; argument++)
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{ // per argument
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// create a temporary file
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FILE* inFile = fopen(argv[argument], "r");
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// if it's bad, choke
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if (inFile == NULL)
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{ // bad filename
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printf("Bad filename %s\n", argv[argument]);
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return EXIT_FAILURE;
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} // bad filename
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// read and append
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compiler.ReadBinary(inFile);
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} // per argument
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// now compile and print
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compiler.ComputeSuperarcs();
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compiler.PrintSuperarcs(true);
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return EXIT_SUCCESS;
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} // main()
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39
examples/contour_tree_distributed/hact_test.sh
Executable file
39
examples/contour_tree_distributed/hact_test.sh
Executable file
@ -0,0 +1,39 @@
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#!/bin/sh
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GTCT_DIR=${GTCT_DIR:-${HOME}/devel/parallel-peak-pruning/ContourTree/SweepAndMergeSerial/out}
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RED=""
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GREEN=""
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NC=""
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if [ -t 1 ]; then
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# If stdout is a terminal, color Pass and FAIL green and red, respectively
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RED=$(tput setaf 1)
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GREEN=$(tput setaf 2)
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NC=$(tput sgr0)
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fi
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echo "Removing previously generated files"
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rm *.log *.dat
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echo "Copying target file "$1 "into current directory"
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filename=${1##*/}
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fileroot=${filename%.txt}
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cp $1 ${filename}
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echo "Splitting data into "$2" x "$2" parts"
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./split_data_2d.py ${filename} $2
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rm ${filename}
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echo "Running HACT"
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n_parts=$(($2*$2))
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echo mpirun -np 4 ./ContourTree_Distributed -d Any --numBlocks=${n_parts} ${fileroot}_part_%d_of_${n_parts}.txt
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mpirun -np 4 ./ContourTree_Distributed -d Any --numBlocks=${n_parts} ${fileroot}_part_%d_of_${n_parts}.txt
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rm ${fileroot}_part_*_of_${n_parts}.txt
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echo "Compiling Outputs"
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./TreeCompiler TreeCompilerOutput_*.dat | sort > outsort${fileroot}_$2x$2.txt
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echo "Diffing"
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diff outsort${fileroot}_$2x$2.txt ${GTCT_DIR}/outsort${fileroot}.txt
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if test $? -eq 0; then echo "${GREEN}Pass${NC}"; rm outsort${fileroot}_$2x$2.txt; else echo "${RED}FAIL${NC}"; fi;
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# echo "Generating Dot files"
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# ./makedot.sh
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58
examples/contour_tree_distributed/split_data_2d.py
Executable file
58
examples/contour_tree_distributed/split_data_2d.py
Executable file
@ -0,0 +1,58 @@
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#!/usr/bin/env python3
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import numpy as np
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import math
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import os
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import sys
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# Read a 2D text file from disk into a NumPy array
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def read_file(fn):
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data = np.fromfile(fn, dtype=np.int, sep=" ")
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data = data[2:].reshape(tuple(data[0:2]))
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return data
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# Save a block from a 2D NumPy array to disk
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def save_piece(fn, array, offset, n_blocks, size):
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with open(fn, 'w') as f:
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f.write('#GLOBAL_EXTENTS ' + ' '.join(map(str, array.shape)) + '\n')
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f.write('#OFFSET ' + ' '.join(map(str, offset))+'\n')
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f.write('#BLOCKS_PER_DIM ' + ' '.join(map(str, n_blocks))+'\n')
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f.write(' '.join(map(str, size)) + '\n')
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np.savetxt(f, array[offset[0]:offset[0]+size[0],offset[1]:offset[1]+size[1]], fmt='%.16g')
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# Compute split points for splitting into n blocks
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def split_points(shape, nblocks):
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dx = float(shape-1) / nblocks
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return [ math.floor(i*dx) for i in range(nblocks)] + [ shape - 1 ]
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if len(sys.argv) < 2:
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print("Error: Usage split_data_2d.py <filename> [<n_blocks_per_axis>|<n_blocks_x> <n_blocks_y>]", file=sys.stderr)
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sys.exit(1)
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# Parse parameters
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in_filename = sys.argv[1]
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n_blocks = (2, 2)
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if len(sys.argv) > 2:
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if len(sys.argv) >= 4:
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n_blocks = (int(sys.argv[2]), int(sys.argv[3]))
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else:
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n_blocks = (int(sys.argv[2]), int(sys.argv[2]))
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name, ext = os.path.splitext(in_filename)
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out_filename_pattern = name + '_part_%d_of_' + str(n_blocks[0]*n_blocks[1]) + ext
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# Read data
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data = read_file(in_filename)
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# Compute split points
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split_points_x = split_points(data.shape[0], n_blocks[0])
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split_points_y = split_points(data.shape[1], n_blocks[1])
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# Save blocks
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block_no = 0
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for x_start, x_stop in zip(split_points_x, split_points_x[1:]):
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for y_start, y_stop in zip(split_points_y, split_points_y[1:]):
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n_x = x_stop - x_start + 1
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n_y = y_stop - y_start + 1
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save_piece(out_filename_pattern % block_no, data, (x_start, y_start), n_blocks, (n_x, n_y))
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# print("Wrote block %d, origin %d %d, size %d %d" % (block_no, x_start, y_start, n_x, n_y))
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block_no += 1
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100
examples/contour_tree_distributed/split_data_3d.py
Executable file
100
examples/contour_tree_distributed/split_data_3d.py
Executable file
@ -0,0 +1,100 @@
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#!/usr/bin/env python3
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import numpy as np
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import math
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import os
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import sys
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# For readBOV
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from functools import reduce
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import operator
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# Read a 3D text file from disk into a NumPy array
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# ... Plain text
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def read_file(fn):
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data = np.fromfile(fn, dtype=np.int, sep=" ")
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data = data[3:].reshape((data[2],data[0],data[1]))
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return data
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# ... VisItBOV
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def readBOV(filename):
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with open(filename, 'r') as f:
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header = dict([(lambda x: (x[0].strip().lower(), x[1].strip()))(l.strip().split(':')) for l in f.readlines()])
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if 'data_endian' in header:
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if header['data_endian'].lower() != sys.byteorder:
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print('Unsopported endianess ' + eader['data_endian'].lower())
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return None
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shape = tuple([int(x) for x in header['data_size'].split(' ')])
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count = reduce(operator.mul, shape, 1)
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dtype_map = { 'float': 'float32', 'double': 'float64', 'char': 'uint8' }
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dtype = np.dtype(dtype_map[header['data_format'].lower()])
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dataname = os.path.realpath(os.path.join(os.path.dirname(filename), header['data_file']))
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if 'variable' not in header:
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header['variable'] = 'val'
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return (header['variable'], header['centering'].lower(), np.fromfile(dataname, dtype, count).reshape(tuple(reversed(shape))))
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return None
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# Save a block from a 3D NumPy array to disk
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# Python order is slice, row, col
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# TXT file order is row, col, slice
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# offset and size are in file order
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def save_piece(fn, array, offset, n_blocks, size):
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with open(fn, 'w') as f:
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perm = [1, 2, 0]
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f.write('#GLOBAL_EXTENTS ' + ' '.join(map(str, [array.shape[i] for i in perm])) + '\n')
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f.write('#OFFSET ' + ' '.join(map(str, offset))+'\n')
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f.write('#BLOCKS_PER_DIM ' + ' '.join(map(str, n_blocks))+'\n')
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f.write(' '.join(map(str, size)) + '\n')
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if fn[-5:]=='.bdem':
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array[offset[2]:offset[2]+size[2],offset[0]:offset[0]+size[0],offset[1]:offset[1]+size[1]].astype(np.double).tofile(f)
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else:
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for s in range(offset[2], offset[2]+size[2]):
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np.savetxt(f, array[s, offset[0]:offset[0]+size[0],offset[1]:offset[1]+size[1]], fmt='%.16g')
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f.write('\n')
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# Compute split points for splitting into n blocks
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def split_points(shape, nblocks):
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dx = float(shape-1) / nblocks
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return [ math.floor(i*dx) for i in range(nblocks)] + [ shape - 1 ]
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if len(sys.argv) < 2:
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print("Error: Usage split_data_3d.py <filename> <outfilepattern> [<n_blocks_per_axis>|<n_blocks_x> <n_blocks_y> <n_blocks_z>]", file=sys.stderr)
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sys.exit(1)
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# Parse parameters
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in_filename = sys.argv[1]
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name, ext = os.path.splitext(in_filename)
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#out_filename_pattern = name + '_split_%d.txt'
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out_filename_pattern = sys.argv[2]
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n_blocks = (2, 2, 2)
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if len(sys.argv) > 3:
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if len(sys.argv) >= 6:
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n_blocks = (int(sys.argv[3]), int(sys.argv[4]), int(sys.argv[5]))
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else:
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n_blocks = (int(sys.argv[3]), int(sys.argv[3]), int(sys.argv[3]))
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# Read data
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if ext == '.bov':
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data = readBOV(in_filename)[2]
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else:
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data = read_file(in_filename)
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# Python order is slice, row, col
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# Compute split points
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split_points_s = split_points(data.shape[0], n_blocks[0])
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split_points_r = split_points(data.shape[1], n_blocks[1])
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split_points_c = split_points(data.shape[2], n_blocks[2])
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# Create the file that records the slice values
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slice_filename = name + '_slices.txt'
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# Save blocks
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block_no = 0
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for s_start, s_stop in zip(split_points_s, split_points_s[1:]):
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for r_start, r_stop in zip(split_points_r, split_points_r[1:]):
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for c_start, c_stop in zip(split_points_c, split_points_c[1:]):
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n_s = s_stop - s_start + 1
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n_r = r_stop - r_start + 1
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n_c = c_stop - c_start + 1
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save_piece(out_filename_pattern % block_no, data, (r_start, c_start, s_start), (n_r, n_c, n_s))
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block_no += 1
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99
examples/contour_tree_distributed/testrun.sh
Executable file
99
examples/contour_tree_distributed/testrun.sh
Executable file
@ -0,0 +1,99 @@
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#!/bin/sh
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mkdir -p out
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DATA_DIR=${DATA_DIR:-${HOME}/devel/parallel-peak-pruning/Data/2D}
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if [ ! -d $DATA_DIR ]; then
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echo "Error: Directory $DATA_DIR does not exist!"
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exit 1;
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fi;
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echo
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echo "Starting Timing Runs"
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echo
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echo "8x9 Test Set"
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./hact_test.sh $DATA_DIR/8x9test.txt 2
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#./hact_test.sh $DATA_DIR/8x9test.txt 4
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# ./hact_test.sh $DATA_DIR/8x9test.txt 8
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echo
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echo "Vancouver Test Set"
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./hact_test.sh $DATA_DIR/vanc.txt 2
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#./hact_test.sh $DATA_DIR/vanc.txt 4
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# ./hact_test.sh $DATA_DIR/vanc.txt 8
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# ./hact_test.sh $DATA_DIR/vanc.txt 16
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echo
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echo "Vancouver SWSW Test Set"
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./hact_test.sh $DATA_DIR/vancouverSWSW.txt 2
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./hact_test.sh $DATA_DIR/vancouverSWSW.txt 4
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# ./hact_test.sh $DATA_DIR/vancouverSWSW.txt 8
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# ./hact_test.sh $DATA_DIR/vancouverSWSW.txt 16
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echo
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echo "Vancouver SWNW Test Set"
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./hact_test.sh $DATA_DIR/vancouverSWNW.txt 2
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./hact_test.sh $DATA_DIR/vancouverSWNW.txt 4
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# ./hact_test.sh $DATA_DIR/vancouverSWNW.txt 8
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# ./hact_test.sh $DATA_DIR/vancouverSWNW.txt 16
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echo
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echo "Vancouver SWSE Test Set"
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./hact_test.sh $DATA_DIR/vancouverSWSE.txt 2
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./hact_test.sh $DATA_DIR/vancouverSWSE.txt 4
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# ./hact_test.sh $DATA_DIR/vancouverSWSE.txt 8
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# ./hact_test.sh $DATA_DIR/vancouverSWSE.txt 16
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echo
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echo "Vancouver SWNE Test Set"
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./hact_test.sh $DATA_DIR/vancouverSWNE.txt 2
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./hact_test.sh $DATA_DIR/vancouverSWNE.txt 4
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# ./hact_test.sh $DATA_DIR/vancouverSWNE.txt 8
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# ./hact_test.sh $DATA_DIR/vancouverSWNE.txt 16
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echo
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echo "Vancouver NE Test Set"
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./hact_test.sh $DATA_DIR/vancouverNE.txt 2
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./hact_test.sh $DATA_DIR/vancouverNE.txt 4
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# ./hact_test.sh $DATA_DIR/vancouverNE.txt 8
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# ./hact_test.sh $DATA_DIR/vancouverNE.txt 16
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echo
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echo "Vancouver NW Test Set"
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./hact_test.sh $DATA_DIR/vancouverNW.txt 2
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./hact_test.sh $DATA_DIR/vancouverNW.txt 4
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# ./hact_test.sh $DATA_DIR/vancouverNW.txt 8
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# ./hact_test.sh $DATA_DIR/vancouverNW.txt 16
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echo
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echo "Vancouver SE Test Set"
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./hact_test.sh $DATA_DIR/vancouverSE.txt 2
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./hact_test.sh $DATA_DIR/vancouverSE.txt 4
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# ./hact_test.sh $DATA_DIR/vancouverSE.txt 8
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# ./hact_test.sh $DATA_DIR/vancouverSE.txt 16
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echo
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echo "Vancouver SW Test Set"
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./hact_test.sh $DATA_DIR/vancouverSW.txt 2
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./hact_test.sh $DATA_DIR/vancouverSW.txt 4
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# ./hact_test.sh $DATA_DIR/vancouverSW.txt 8
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# ./hact_test.sh $DATA_DIR/vancouverSW.txt 16
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echo
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echo "Icefields Test Set"
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./hact_test.sh $DATA_DIR/icefield.txt 2
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./hact_test.sh $DATA_DIR/icefield.txt 4
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# ./hact_test.sh $DATA_DIR/icefield.txt 8
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# ./hact_test.sh $DATA_DIR/icefield.txt 16
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# ./hact_test.sh $DATA_DIR/icefield.txt 32
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# ./hact_test.sh $DATA_DIR/icefield.txt 64
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echo
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echo "GTOPO30 Full Tiny Test Set"
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./hact_test.sh $DATA_DIR/gtopo_full_tiny.txt 2
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./hact_test.sh $DATA_DIR/gtopo_full_tiny.txt 4
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# ./hact_test.sh $DATA_DIR/gtopo_full_tiny.txt 8
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# ./hact_test.sh $DATA_DIR/gtopo_full_tiny.txt 16
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# ./hact_test.sh $DATA_DIR/gtopo_full_tiny.txt 32
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# ./hact_test.sh $DATA_DIR/gtopo_full_tiny.txt 64
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echo
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echo "GTOPO30 UK Tile Test Set"
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./hact_test.sh $DATA_DIR/gtopo30w020n40.txt 2
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./hact_test.sh $DATA_DIR/gtopo30w020n40.txt 4
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# ./hact_test.sh $DATA_DIR/gtopo30w020n40.txt 8
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# ./hact_test.sh $DATA_DIR/gtopo30w020n40.txt 16
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# ./hact_test.sh $DATA_DIR/gtopo30w020n40.txt 32
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# ./hact_test.sh $DATA_DIR/gtopo30w020n40.txt 64
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# ./hact_test.sh $DATA_DIR/gtopo30w020n40.txt 128
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# ./hact_test.sh $DATA_DIR/gtopo30w020n40.txt 256
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# ./hact_test.sh $DATA_DIR/gtopo30w020n40.txt 512
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echo "Done"
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@ -193,7 +193,7 @@ public:
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static void PrintSuperarcArray(const std::vector<Edge>& superarc_array);
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// routine to print the superarcs
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void PrintSuperarcs() const;
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void PrintSuperarcs(bool) const;
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// routine to write out binary file
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void WriteBinary(FILE* outFile) const;
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@ -380,8 +380,14 @@ inline void TreeCompiler::PrintSuperarcArray(const std::vector<Edge>& superarc_a
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} // TreeCompiler::PrintSuperarcArray()
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inline void TreeCompiler::PrintSuperarcs() const
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inline void TreeCompiler::PrintSuperarcs(bool printHeader = false) const
|
||||
{
|
||||
if (printHeader)
|
||||
{
|
||||
std::cout << "============" << std::endl;
|
||||
std::cout << "Contour Tree" << std::endl;
|
||||
}
|
||||
|
||||
PrintSuperarcArray(this->superarcs);
|
||||
}
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user