/usr/bin/gpiv_series is in gpivtools-mpi 0.6.0-1.1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 | #!/usr/bin/env mpipython
# gpiv_series - Processes a set of numbered input data
# Copyright (C) 2008 Gerber van der Graaf
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
#--------------------------------------------------------------------
#
# This version is MPI enabled for parallel processing
#
import os, re
from Scientific import MPI
communicator = MPI.world.duplicate()
#
#----------- Command line arguments parser
#
from optparse import OptionParser
usage = "%prog [options] \"process\""
parser = OptionParser(usage)
parser.add_option("-a", "--arg_n",
action="store_true", dest="arg_n", default=False,
help="if the process needs the current number in its \
argument list instead of prepending/appending it to the \
filebase name, the number will be put before (-f) \
\"filename\" in the \"process\" string.")
parser.add_option("-b", "--basename", type='string', dest="basename",
help="File basename for reading", metavar="FILE")
parser.add_option("-e", "--ext", type='string', dest="ext", metavar="EXT",
help="add an extension after the file basename + number (without leading \".\")")
parser.add_option("-f", "--first", type='int', dest="first_nr", default=0,
help="first numbered file (default: 0)", metavar="N")
parser.add_option("-l", "--last", type='int', dest="last_nr", default=0,
help="last numbered file(default: 0)", metavar="N")
parser.add_option("-i", "--incr", type='int', dest="incr_nr", default=1,
help="increment file number (default: 1)", metavar="N")
parser.add_option("-p", "--print",
action="store_true", dest="pri", default=False,
help="prints process parameters/variables to stdout")
parser.add_option("--pad", type='int', dest="pad0", default=0,
help="padding number with zero's (default: 0)", metavar="N")
parser.add_option("-n", "--none",
action="store_true", dest="none", default=False,
help="suppresses real execution")
parser.add_option("-x", "--prefix", action="store_true", dest="prefix", default=False,
help="prefix numbering to file basename")
(options, args) = parser.parse_args()
if len(args) != 1:
parser.error("incorrect number of arguments")
else:
process = args[0]
#
#----------- Function definitions
#
def pri_date(msg = "Time stamp at start of series processing:"):
"""Prints time stamp.
Keyword arguments:
msg -- message to be printed before time stamp
"""
if options.pri == True:
print msg
os.system('date')
elif options.none:
print msg
os.system('date')
def count_digits(nr):
"""Counts number of digits from a number
Keyword arguments:
nr -- number to be questioned
"""
count=0
while nr/10 !=0:
nr=nr/10
count=count+1
return count
def pad0(nr):
"""Created a string for zero padding
Keyword arguments:
nr -- number of zeros to be padded
"""
pd0=""
for i in range(0, nr):
pd0 = str(pd0)+"0"
return pd0
def compose_name_nr(nr):
"""Creates proper name from basename and number.
Keyword arguments:
nr -- number of filename to be processed
"""
if options.pad0 > 0:
ndig=count_digits(nr)
null_str=pad0(options.pad0 - ndig)
nr_str=null_str+str(nr)
else:
nr_str=str(nr)
if options.prefix:
if options.arg_n:
name=str(options.basename)
else:
name=nr_str+str(options.basename)
else:
if options.arg_n:
name=str(options.basename)
else:
name=str(options.basename)+nr_str
if str(options.ext) != "None":
name=str(name)+str(".")+str(options.ext)
return(name)
def compose_cmd(name, nr):
"""Creates proper command.
Keyword arguments:
name -- complete filename
"""
command=str(process)
if options.arg_n:
# Eventually, substitutes "-f" with: "nr -f"
command_tmp=re.sub("-f", str(nr)+" -f", command)
if command_tmp != command:
command = str(command_tmp)+" "+str(name)
else:
command = str(command_tmp)+" "+str(nr)+" "+str(name)
else:
command=str(command)+" "+str(name)
return command
def proc_series_par():
"""Processes a series on identic numbered files in parallel
environment using mpipython.
"""
#
# Total number of data and number of data per node
#
Nt = (options.last_nr+1 - options.first_nr) / options.incr_nr
Nn = Nt / communicator.size
#
# Bail out if number of nodes is larger than number of data
#
if communicator.size > Nt:
print 'nprocs (',communicator.size,\
') larger then number of data (',Nt,")"
exit()
for i in range(options.first_nr, options.last_nr+1, options.incr_nr):
for j in range(0, communicator.size, 1):
if communicator.rank == j:
if i >= options.first_nr + j*Nn*options.incr_nr:
if i < options.first_nr + (j+1)*Nn*options.incr_nr:
name_nr = compose_name_nr(i)
command = compose_cmd(name_nr, i)
if options.pri == True: print "rank=",communicator.rank,command
elif options.none == True: print "rank=",communicator.rank,command
if options.none == False: os.system(command)
#
# The fraction of data left, if Nn is not an integer,
# is processed at the highest node
#
if j == communicator.size - 1:
if i >= options.first_nr + (j+1)*Nn*options.incr_nr:
name_nr = compose_name_nr(i)
command = compose_cmd(name_nr, i)
if options.pri == True: print "rank=",communicator.rank,command
elif options.none == True: print "rank=",communicator.rank,command
if options.none == False: os.system(command)
#
#----------- Calling functions
#
#if communicator.rank == 0:
# if options.pri == True: pri_date()
# elif options.none == True: pri_date()
proc_series_par()
#communicator.rank == 0:
# if options.pri == True: pri_date(msg = "Time stamp at end of series processing:")
# elif options.none == True: pri_date(msg = "Time stamp at end of series processing:")
#
#----------- That's all folks
#
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