https://github.com/geodynamics/citcoms
Tip revision: 0085e638d888859d800e309088cf4163fabc5d52 authored by Thorsten Becker on 28 February 2009, 21:23:21 UTC
Added ic_method_for_flavors=2, which works like the ggrd based tracer flavor init method
Added ic_method_for_flavors=2, which works like the ggrd based tracer flavor init method
Tip revision: 0085e63
batchcombine.py
#!/usr/bin/env python
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#<LicenseText>
#
# CitcomS.py by Eh Tan, Eun-seo Choi, and Pururav Thoutireddy.
# Copyright (C) 2002-2005, California Institute of Technology.
#
# 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 of the License, 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
#
#</LicenseText>
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
'''
Paste and combine Citcom data
Usage: batchcombine.py <machinefile | node-list> datadir datafile timestep nodex nodey nodez ncap nprocx nprocy nprocz [fields [ncompositions]]
'''
def machinefile2nodes(machinefile, totalnodes):
nodelist = machinefile2nodelist(machinefile, totalnodes)
nodes = nodelist2nodes(nodelist)
return nodes
def machinefile2nodelist(machinefile, totalnodes):
'''Read the machinefile to get a list of machine names. If machinefile
is not readable, treat it as a string containing the machine names.
Return the list of machine names. The length of the list is totalnodes.
'''
try:
nodelist = file(machinefile).readlines()
except IOError:
nodelist = machinefile.split()
# check the length of nodelist
n = len(nodelist)
if not n == totalnodes:
print 'WARNING: length of machinefile does not match number of processors, try to duplicate machinefile...'
if (totalnodes > n) and ((totalnodes % n) == 0):
# try to match number of processors by duplicating nodelist
nodelist *= (totalnodes / n)
else:
raise ValueError, 'incorrect machinefile size'
return nodelist
def nodelist2nodes(nodelist):
# generate a string of machine names
nodes = ' '.join([x.strip() for x in nodelist])
return nodes
def batchpaste(datadir, datafile, fields, timestep, nodes):
from socket import gethostname
hostname = gethostname()
import os
cwd = os.getcwd()
for rank, node in enumerate(nodes):
if node == 'localhost' or node == hostname:
# local paste
import pasteCitcomData
pasteCitcomData.run(datadir, datafile, fields, rank, timestep, cwd)
else:
# remote paste
# replace 'rsh' with 'ssh' if necessary
remote_shell = 'rsh'
cmd = '%(remote_shell)s %(node)s pasteCitcomData.py %(datadir)s %(datafile)s %(fields)s %(rank)d %(timestep)d %(cwd)s' % vars()
os.system(cmd)
return
def batchcombine(nodes, datadir, datafile, timestep, nodex, nodey, nodez,
ncap, nprocx, nprocy, nprocz, fields,
ncompositions):
# paste
batchpaste(datadir, datafile, fields, timestep, nodes)
# combine
import combine
combined_files = combine.combine(datafile, fields, timestep,
nodex, nodey, nodez,
ncap, nprocx, nprocy, nprocz)
# delete pasted files
import glob
filenames = glob.glob('%(datafile)s.*.%(timestep)d.pasted' % vars())
import os
for filename in filenames:
os.remove(filename)
# create .general file
import dxgeneral
dxgeneral.write(fields, ncompositions, combined_files)
return
if __name__ == '__main__':
import sys
if not (12 <= len(sys.argv) <= 14):
print __doc__
sys.exit(1)
machinefile = sys.argv[1]
datadir = sys.argv[2]
datafile = sys.argv[3]
timestep = int(sys.argv[4])
nodex = int(sys.argv[5])
nodey = int(sys.argv[6])
nodez = int(sys.argv[7])
ncap = int(sys.argv[8])
nprocx = int(sys.argv[9])
nprocy = int(sys.argv[10])
nprocz = int(sys.argv[11])
fields = 'coord,velo,visc'
ncompositions = 0
if len(sys.argv) >= 13:
fields = sys.argv[12]
if len(sys.argv) == 14:
ncompositions = int(sys.argv[13])
totalnodes = nprocx * nprocy * nprocz * ncap
nodelist = machinefile2nodelist(machinefile, totalnodes)
batchcombine(nodelist, datadir, datafile, timestep, nodex, nodey, nodez,
ncap, nprocx, nprocy, nprocz, fields, ncompositions)
# version
# $Id$
# End of file