/usr/bin/skel_extract is in libadios-bin 1.9.0-7build2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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from __future__ import absolute_import, division, print_function, unicode_literals
import argparse
import xml.dom.minidom
import sys
#import skel_settings
def parse_command_line():
parser = argparse.ArgumentParser (description='Extract data from specified skel output file')
parser.add_argument ('skel_output', metavar='Skel result', help='file to extract data from')
parser.add_argument ('-d', dest='dest', help='file to place the results in')
parser.add_argument ('-s', dest='select', help='measurement(s) to extract (default = *)')
parser.add_argument ('-r', dest='ranks', default='0', help='Use -r all to include measurements from all ranks for just one iteration.')
parser.add_argument ('-R', dest='generate_R', action="store_true", default=False, help='Extract into a form to be read by R.')
return parser.parse_args()
# By default, print all data for rank 0 as one line, repeat for each iteration
def extract (skel_output, dest, select, ranks):
doc = xml.dom.minidom.parse (skel_output)
if dest == None or dest == '':
outfile = sys.stdout
else:
outfile = open (dest, 'w')
if select == None or select == '':
select = '*'
keys = doc.getElementsByTagName('adios_timing')[0].getAttribute('keys').split(',')
tempkeys = []
for key in keys:
tempkeys.append (key.strip())
keys = tempkeys
if select == '*':
selected_fields = keys
else:
selected_fields = select.split(',')
# check the selected fields
for field in selected_fields:
if not field in keys:
print('Invalid selection, field ' + field)
return
#Print the header
header = ''
for field in selected_fields:
header = header + field
header = header +','
header = header.rstrip (',')
outfile.write (header + '\n')
for st in doc.getElementsByTagName ('adios_timing'):
#Print the data
for proc in st.getElementsByTagName('proc'):
if proc.getAttribute ('id') == '0' or ranks == 'all':
data = ''
vals = proc.getAttribute ('vals').split(',')
for field in selected_fields:
data = data + vals[keys.index(field)].strip() + ','
data = data.rstrip (',') + '\n'
outfile.write (data)
if ranks == 'all':
break
outfile.close ()
# Hilde's function for extracting to a format understood by the R script
def extract_R (skel_output, select, ranks, iteration):
doc = xml.dom.minidom.parse (skel_output)
#if dest == None or dest == '':
# outfile = sys.stdout
#else:
outfile = open (skel_output+".txt", 'w')
#runval=dest.split('.')[0].split('_')[1]
#outfile.write ("runid = " +runval +'\n')
if select == None or select == '':
select = '*'
method = doc.getElementsByTagName('adios_timing')[0].getAttribute('method')
keys = doc.getElementsByTagName('adios_timing')[0].getAttribute('keys').split(',')
tempkeys = []
for key in keys:
tempkeys.append (key.strip())
keys = tempkeys
numcores= doc.getElementsByTagName('adios_timing')[0].getAttribute('cores')
if select == '*':
selected_fields = keys
else:
selected_fields = select.split(',')
# check the selected fields
for field in selected_fields:
if not field in keys:
print 'Invalid selection, field ' + field
return
#Print the header
header = ''
for field in selected_fields:
header = header + field
header = header +' '
header = "Iteration "+"Core "+header.rstrip (' ')
outfile.write (method + '\n')
outfile.write (numcores +'\n')
outfile.write (header + '\n')
# Replacing iter with the iteration argument passed in
iter = 0
for st in doc.getElementsByTagName ('adios_timing'):
#Print the data
for proc in st.getElementsByTagName('proc'):
if proc.getAttribute ('id') == '0':
iter = iter +1
data = ''
core = proc.getAttribute ('id')
vals = proc.getAttribute ('vals').split(',')
for field in selected_fields:
data = data + vals[keys.index(field)].strip(',') + ' '
data = str(iteration)+" "+ core +" "+ data.rstrip (' ') + '\n'
outfile.write (data)
if ranks == 'all':
break
outfile.close ()
def parse_iteration (filename):
#assume filename ends with .xml
if not filename.endswith (".xml"):
print("Warning: filename does not meet expectations, should end with .xml")
filename = filename [:-4]
iteration = filename.rsplit ("_", 1)[1]
print(iteration)
return iteration
def main ():
args = parse_command_line()
if (args.generate_R):
iteration = parse_iteration (args.skel_output)
extract_R (args.skel_output, args.select, args.ranks, iteration)
else:
extract (args.skel_output, args.dest, args.select, args.ranks)
if __name__ == "__main__":
main()
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