Environment
GeForce GTX 1070 (8GB)
ASRock Z170M Pro4S [Intel Z170chipset]
Ubuntu 14.04 LTS desktop amd64
TensorFlow v0.11
cuDNN v5.1 for Linux
CUDA v8.0
Python 2.7.6
IPython 5.1.0 -- An enhanced Interactive Python.
gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4
GNU bash, version 4.3.8(1)-release (x86_64-pc-linux-gnu)
This article is related to ADDA (light scattering simulator based on the discrete dipole approximation).
Reading files
- chp.0 : checkpoint file
- obtained by original [iterative.c]
- aux.0 : auxiliary info
- obtained by modified [iterative.c]
- iterative.c > v0.4 > modification to save an auxiliary file and a coordinate file
code v0.5
Refactoring by adding functions and using named tuples for the return of the functions.
ref (in Japanese): http://qiita.com/7of9/items/6d37e362f7be275d2f9a
UtilReadCheckPoint.py
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import array
import sys
import collections as clc
'''
v0.5 Apr. 09, 2017
- read_chpoint_file() is called with [debugPrint=False]
- add debug_group_print()
- read_chpoint_file() returns in groups
+ IterativeGroup
+ AuxGroup
+ VectorGroup
v0.4 Apr. 09, 2017
- read_auxiliary_info() returns named tuple
- read_vectorTuple() returns named tuple
v0.3 Apr. 07, 2017
- read_iterative_info() returns named tuple
- import collections
- add read_iterative_info()
- add read_vectorTuple()
v0.2 Apr. 06, 2017
- add debug_print_vectors()
- add debug_print_scalarsList()
- add debug_print_sizes()
- add debug_print_scalars1()
v0.1 Apr. 05, 2017
- branched
===== branched from [read_chpoint.py] to [UtilReadCheckPoint.py] =====
v0.6 Dec. 23, 2016
- try to print fractional part of xvec[] in 4 digits
+ xvec[] = np.array([drel, dimg]), also for rvec[], pvec[], vectors[][]
+ add [np.set_printoptions(precision=4)]
v0.5 Dec. 23, 2016
- read scalars[], xvec[], rvec[], pvec[], vectors[][]
- refactor for PEP8 (except for E501 line too long for long comment)
- wrap_fromfile() takes [num] arg
v0.4 Dec. 21, 2016
- read from "auxiliary" file [auxfp]
+ add read_auxiliary_info()
v0.3 Dec. 19, 2016
- add wrap_fromfile()
- read [inprodR],[prev_err],[resid_scale]
v0.2 Dec. 19, 2016
- fix bug > read [local_nRows] for "size_t" type
v0.1 Dec. 18, 2016
- read_chpoint_file() > read [ind_m],[local_nRows],[niter],[counter]
'''
# codingrule:PEP8
# on Python 2.7.6
np.set_printoptions(precision=6)
def wrap_fromfile(rfp, typecode, num):
res = array.array(typecode)
res.fromfile(rfp, num)
return res
def read_auxiliary_info(auxFilename):
with open(auxFilename, "rb") as auxfp:
sc_N = wrap_fromfile(auxfp, 'i', num=1) # the number of scalars' sizes
sc_sizes = array.array('i') #
sc_sizes.fromfile(auxfp, *sc_N) # '*':unpack list
vec_N = wrap_fromfile(auxfp, 'i', num=1) # number of vercotrs' sizes
vec_sizes = array.array('i') #
vec_sizes.fromfile(auxfp, *vec_N) # '*':unpack list
AuxGroup = clc.namedtuple('AuxGroup',
['sc_N', 'sc_sizes', 'vec_N', 'vec_sizes'])
auxgrp = AuxGroup(sc_N, sc_sizes, vec_N, vec_sizes)
return auxgrp
# TODO: 0m > error handling when file is NULL
def debug_print_scalars1(ind_m, local_nRows, niter, counter,
inprodR, prev_err, resid_scale):
print('ind_m:', ind_m)
print('local_nRows:', local_nRows)
print('niter:', niter)
print('counter:', counter)
print('inprodR:', inprodR)
print('prev_err:', prev_err)
print('resid_scale:', resid_scale) # scale to get square of relative error
def debug_print_sizes(sc_N, sc_sizes, vec_N, vec_sizes):
print('sc_N:', sc_N)
print('sc_sizes', sc_sizes)
print('vec_N:', vec_N)
print('vec_sizes:', vec_sizes)
def debug_print_scalarsList(sc_N_zero, scalars):
for idx in range(sc_N_zero):
print('scalars:', scalars[idx])
def debug_print_vectors(xvec, rvec, pvec, vectors):
for idx in range(3):
print('xvec:', np.array_repr(xvec[idx]).replace('\n', ''))
print('rvec:', np.array_repr(rvec[idx]).replace('\n', ''))
print('pvec:', np.array_repr(pvec[idx]).replace('\n', ''))
print('vectors:', np.array_repr(vectors[idx][0]).replace('\n', ''))
print('vectors:', np.array_repr(vectors[idx][1]).replace('\n', ''))
print('vectors:', np.array_repr(vectors[idx][2]).replace('\n', ''))
def debug_group_print(itrgrp, auxgrp, vecgrp):
debug_print_scalars1(itrgrp.ind_m, itrgrp.local_nRows,
itrgrp.niter, itrgrp.counter,
itrgrp.inprodR, itrgrp.prev_err,
itrgrp.resid_scale)
debug_print_sizes(auxgrp.sc_N, auxgrp.sc_sizes, auxgrp.vec_N,
auxgrp.vec_sizes)
debug_print_scalarsList(auxgrp.sc_N[0], vecgrp.scalars)
debug_print_vectors(vecgrp.xvec, vecgrp.rvec, vecgrp.pvec,
vecgrp.vectors)
def read_vectorTuple(chpfp, sc_N, sc_sizes, vec_N, vec_sizes, local_nRows):
# scalars[]
scalars = []
for idx in range(sc_N[0]):
if sc_sizes[idx] == 8: # double
scl = wrap_fromfile(chpfp, 'd', num=1)
scalars.append(scl)
elif sc_sizes[idx] == 16: # double complex
scl = wrap_fromfile(chpfp, 'd', num=2)
scalars.append(scl)
# xvec[] : total electric field on the dipoles
# TODO: 0m > replace 'local_nRows[0]' with function?
# TODO: 0m > replace 'vec_N[0]' with function?
# TODO: 0m > define function for read [drel,dimg]??
xvec = [[] for idx in range(local_nRows[0])]
for idx in range(local_nRows[0]):
drel = wrap_fromfile(chpfp, 'd', 1)
dimg = wrap_fromfile(chpfp, 'd', 1)
xvec[idx] = np.array([drel, dimg])
# rvec[] : current residual
rvec = [[] for idx in range(local_nRows[0])]
for idx in range(local_nRows[0]):
drel = wrap_fromfile(chpfp, 'd', 1)
dimg = wrap_fromfile(chpfp, 'd', 1)
rvec[idx] = np.array([drel, dimg])
# pvec[] : polarization of dipoles, also an auxiliary vector
# in iterative solvers
pvec = [[] for idx in range(local_nRows[0])]
for idx in range(local_nRows[0]):
drel = wrap_fromfile(chpfp, 'd', 1)
dimg = wrap_fromfile(chpfp, 'd', 1)
pvec[idx] = np.array([drel, dimg])
# vectors[] : ???
MAXNUM_VECTORS = 20
vectors = [[] for idx in range(MAXNUM_VECTORS)]
for idx_vecN in range(vec_N[0]):
alist = []
for idx_LnRows in range(local_nRows[0]):
if vec_sizes[idx_vecN] == 16:
drel = wrap_fromfile(chpfp, 'd', 1)
dimg = wrap_fromfile(chpfp, 'd', 1)
alist.append(np.array([drel, dimg]))
vectors[idx_vecN] = alist
VectorGroup = clc.namedtuple('VectorGroup',
['scalars', 'xvec', 'rvec',
'pvec', 'vectors'])
vecgrp = VectorGroup(scalars, xvec, rvec, pvec, vectors)
return vecgrp
def read_iterative_info(chpfp):
ind_m = wrap_fromfile(chpfp, 'i', num=1) # index of iterative method
# number of local rows of decomposition (only real dipoles)
# where L: unsigned long = size_t
local_nRows = wrap_fromfile(chpfp, 'L', num=1)
niter = wrap_fromfile(chpfp, 'i', num=1) # iteration count
# number of successive iterations without residual decrease
counter = wrap_fromfile(chpfp, 'i', num=1)
# used as |r_0|^2 and best squared norm of residual up to
# some iteration
inprodR = wrap_fromfile(chpfp, 'd', num=1)
# previous relative error; used in ProgressReport, initialized
# in IterativeSolver
prev_err = wrap_fromfile(chpfp, 'd', num=1)
# scale to get square of relative error
resid_scale = wrap_fromfile(chpfp, 'd', num=1)
#
IterGroup = clc.namedtuple('IterativeGroup',
['ind_m', 'local_nRows', 'niter', 'counter',
'inprodR', 'prev_err', 'resid_scale'])
itrgrp = IterGroup(ind_m, local_nRows, niter, counter,
inprodR, prev_err, resid_scale)
return itrgrp
def read_chpoint_file(chpFilename, auxFilename, debugPrint=False):
if debugPrint:
print(chpFilename)
print(auxFilename)
# TODO: 0m > error handling when file is NULL
with open(chpFilename, "rb") as chpfp:
# 1. iterative information
itrgrp = read_iterative_info(chpfp)
if debugPrint:
debug_print_scalars1(itrgrp.ind_m, itrgrp.local_nRows,
itrgrp.niter, itrgrp.counter,
itrgrp.inprodR, itrgrp.prev_err,
itrgrp.resid_scale)
# 2. auxiliary information
#
# sc_N: the number of scalars' sizes
# sc_sizes:
# vec_N: the number of vercotrs' sizes
# vec_sizes:
auxgrp = read_auxiliary_info(auxFilename)
if debugPrint:
debug_print_sizes(auxgrp.sc_N, auxgrp.sc_sizes, auxgrp.vec_N,
auxgrp.vec_sizes)
# 3. vector list
vecgrp = read_vectorTuple(chpfp, auxgrp.sc_N, auxgrp.sc_sizes,
auxgrp.vec_N, auxgrp.vec_sizes,
itrgrp.local_nRows)
#
if debugPrint:
debug_print_scalarsList(auxgrp.sc_N[0], vecgrp.scalars)
if debugPrint:
debug_print_vectors(vecgrp.xvec, vecgrp.rvec, vecgrp.pvec,
vecgrp.vectors)
return itrgrp, auxgrp, vecgrp
if __name__ == '__main__':
argvs = sys.argv
argc = len(argvs)
# print(argvs)
if (argc < 3):
print("ERROR: chpoint file is not specified\r\n")
print(" [cmd] [chpoint file] [auxiliary file]\r\n")
sys.exit()
res = read_chpoint_file(chpFilename=argvs[1], auxFilename=argvs[2],
debugPrint=False)
itrgrp, auxgrp, vecgrp = res
# debug
debug_group_print(itrgrp, auxgrp, vecgrp)
run
$ python UtilReadCheckPoint.py chp.0 aux.0 #run
ind_m: array('i', [5])
local_nRows: array('L', [27984L])
niter: array('i', [210])
counter: array('i', [140])
inprodR: array('d', [4.317011265934948])
prev_err: array('d', [0.31977234550768563])
resid_scale: array('d', [0.020384616751203153])
sc_N: array('i', [8])
sc_sizes array('i', [8, 8, 8, 8, 16, 16, 16, 16])
vec_N: array('i', [3])
vec_sizes: array('i', [16, 16, 16])
scalars: array('d', [21.695179646708983])
scalars: array('d', [17.561818003907533])
scalars: array('d', [0.01622964090344006])
scalars: array('d', [0.01658574452030678])
scalars: array('d', [2.6036437445821585, 3.735208975819251])
scalars: array('d', [-0.16158984774519294, 0.33676364827430344])
scalars: array('d', [0.34430517188699605, -0.9387175013645006])
scalars: array('d', [-0.39247820060720345, -0.9196117523862111])
xvec: array([[ 0.000935], [-0.001522]])
rvec: array([[-0.002113], [ 0.002774]])
pvec: array([[ 0.007899], [ 0.002861]])
vectors: array([[-0.203491], [ 0.033598]])
vectors: array([[ 0.513358], [-0.235685]])
vectors: array([[ 0.548095], [ 0.061967]])
xvec: array([[ 0.03277], [ 0.09079]])
rvec: array([[ 0.004444], [-0.022859]])
pvec: array([[-0.020303], [-0.017681]])
vectors: array([[-0.114939], [ 0.099301]])
vectors: array([[ 0.310234], [-0.340468]])
vectors: array([[ 0.330688], [-0.145048]])
xvec: array([[-0.004644], [-0.000675]])
rvec: array([[ 0.005379], [-0.006603]])
pvec: array([[-0.019206], [-0.010089]])
vectors: array([[-0.000433], [ 0.008886]])
vectors: array([[ 0.007084], [-0.024328]])
vectors: array([[ 0.006453], [-0.022867]])