def optimal_delphi_by_nproc(xdsinp=None,
osc_width=None,
nframes=None,
nproc=None,
min_delphi=5):
if xdsinp is not None:
kwds = dict(get_xdsinp_keyword(xdsinp))
osc_width = float(kwds["OSCILLATION_RANGE"])
data_range = map(int, kwds["DATA_RANGE"].split())
nframes = data_range[1] - data_range[0] + 1
if None in (osc_width, nframes):
print "osc_width and nframes not specified."
return None
if nproc is None:
from yamtbx import util
nproc = util.get_number_of_processors()
# TODO check nframes%nproc
# TODO check if frame chache works (limited to 2^31-1 pixels)
delphi = nproc * osc_width
delphi_org = delphi
fac = 2
while delphi < min_delphi:
delphi = delphi_org * fac
fac += 1
return delphi
def run(params):
xds_dirs = []
print "Found xds directories:"
for root, dirnames, filenames in os.walk(params.topdir, followlinks=True):
if "XDS.INP" in filenames:
print "", os.path.relpath(root, params.topdir)
xds_dirs.append(root)
print
print "Start running.."
npar = util.get_number_of_processors(
) if params.nproc is None else params.nproc
fun_local = lambda x: evaluate_run(x) #, params)
easy_mp.pool_map(fixed_func=fun_local, args=xds_dirs, processes=npar)
def run(params):
params.topdir = os.path.abspath(params.topdir)
xds_dirs = []
print "Found xds directories:"
for root, dirnames, filenames in os.walk(params.topdir, followlinks=True):
if "XDS.INP" in filenames:
if "decision.log" in filenames and params.dont_overwrite:
print "Already done - skip:", os.path.relpath(
root, params.topdir)
continue
print "", os.path.relpath(root, params.topdir)
xds_dirs.append(root)
print
print "Start running.."
import functools
from yamtbx.dataproc.auto.command_line import run_all_xds_simple
if params.multiproc:
npar = util.get_number_of_processors(
) if params.nproc is None else params.nproc
# Override nproc
if len(xds_dirs) < npar: params.nproc = npar // len(xds_dirs)
else: params.nproc = 1
print "nproc=", params.nproc
if params.parmethod == "sge": npar = len(xds_dirs)
fun = run_all_xds_simple.xds_runmanager(params)
easy_mp.parallel_map(func=fun,
iterable=map(lambda x: os.path.abspath(x),
xds_dirs),
processes=npar,
method=params.parmethod,
preserve_exception_message=True)
"""
fun_local = lambda x: xds_sequence(x, params)
easy_mp.pool_map(fixed_func=fun_local,
args=xds_dirs,
processes=npar)
"""
else:
for root in xds_dirs:
run_xds_sequence(root, params)
def run(params):
xds_dirs = []
print "Found xds directories:"
for root, dirnames, filenames in os.walk(params.topdir, followlinks=True):
if "XDS.INP" in filenames:
print "", os.path.relpath(root, params.topdir)
xds_dirs.append(root)
print
print "Start running.."
npar = util.get_number_of_processors() if params.nproc is None else params.nproc
fun_local = lambda x: evaluate_run(x)#, params)
easy_mp.pool_map(fixed_func=fun_local,
args=xds_dirs,
processes=npar)
def run(params):
xds_dirs = []
print "Found xds directories:"
for root, dirnames, filenames in os.walk(params.topdir, followlinks=True):
if "XDS.INP" in filenames:
if "decision.log" in filenames and params.dont_overwrite:
print "Already done - skip:", os.path.relpath(root, params.topdir)
continue
print "", os.path.relpath(root, params.topdir)
xds_dirs.append(root)
print
print "Start running.."
import functools
from yamtbx.dataproc.auto.command_line import run_all_xds_simple
if params.multiproc:
npar = util.get_number_of_processors() if params.nproc is None else params.nproc
# Override nproc
if len(xds_dirs) < npar: params.nproc = npar // len(xds_dirs)
else: params.nproc = 1
print "nproc=", params.nproc
if params.parmethod == "sge": npar = len(xds_dirs)
fun = run_all_xds_simple.xds_runmanager(params)
easy_mp.parallel_map(func=fun,
iterable=map(lambda x: os.path.abspath(x), xds_dirs),
processes=npar,
method=params.parmethod,
preserve_exception_message=True)
"""
fun_local = lambda x: xds_sequence(x, params)
easy_mp.pool_map(fixed_func=fun_local,
args=xds_dirs,
processes=npar)
"""
else:
for root in xds_dirs:
xds_sequence(root, params)
def optimal_delphi_by_nproc(xdsinp=None, osc_width=None, nframes=None, nproc=None, min_delphi=5):
if xdsinp is not None:
kwds = dict(get_xdsinp_keyword(xdsinp))
osc_width = float(kwds["OSCILLATION_RANGE"])
data_range = map(int, kwds["DATA_RANGE"].split())
nframes = data_range[1] - data_range[0] + 1
if None in (osc_width, nframes):
print "osc_width and nframes not specified."
return None
if nproc is None:
from yamtbx import util
nproc = util.get_number_of_processors()
# Need to check nframes%nproc
delphi = nproc * osc_width
fac = 2
while delphi < min_delphi:
delphi = delphi * fac
fac += 1
return delphi