def wrap_redrock(info, mp=1, prefix='lenssource'):
"""Simple wrapper on redrock given a simulation table."""
from redrock.external.desi import rrdesi
os.environ['OMP_NUM_THREADS'] = '1'
nchunk = len(set(info['CHUNK']))
zbestfiles = []
for ichunk in set(info['CHUNK']):
specfile = '{}-spectra-chunk{:03d}.fits'.format(prefix, ichunk)
zbestfile = specfile.replace('-spectra-', '-zbest-')
rrfile = zbestfile.replace('.fits', '.h5')
if os.path.isfile(rrfile):
os.remove(rrfile)
zbestfiles.append(zbestfile)
print('Writing redshifts for chunk {}/{} to {}'.format(ichunk, nchunk-1, zbestfile))
rrdesi(options=['--zbest', zbestfile, '--mp', str(mp), '--output', rrfile, specfile])
# Gather up all the results and write out a summary table.
zbest = Table(np.hstack([fitsio.read(zbestfile) for zbestfile in zbestfiles]))
zbest = zbest[np.argsort(zbest['TARGETID'])]
infofile = '{}-zbest.fits'.format(prefix)
print('Writing {} redshifts to {}'.format(len(zbest), infofile))
zbest.write(infofile, overwrite=True)
return zbest
def run(self, grph, task, opts, comm=None):
"""
Run Redrock on a spectral group.
Args:
grph (dict): pruned graph with this task and dependencies.
task (str): the name of this task.
opts (dict): options to use for this task.
comm (mpi4py.MPI.Comm): optional MPI communicator.
"""
nproc = 1
rank = 0
if comm is not None:
nproc = comm.size
rank = comm.rank
log = get_logger()
node = grph[task]
spectra = "spectra-{}-{}".format(node["nside"], node["pixel"])
specfile = graph_path(spectra)
outfile = graph_path(task)
outdir = os.path.dirname(outfile)
details = io.findfile('redrock',
nside=node["nside"],
groupname=node["pixel"],
outdir=outdir)
options = {}
options["output"] = details
options["zbest"] = outfile
options.update(opts)
optarray = option_list(options)
optarray.append(specfile)
# write out the equivalent commandline
if rank == 0:
com = ["RUN", "rrdesi_mpi"]
com.extend(optarray)
log.info(" ".join(com))
failcount = 0
try:
rrdesi(options=optarray, comm=comm)
except:
failcount += 1
sys.stdout.flush()
if comm is not None:
failcount = comm.allreduce(failcount)
if failcount > 0:
# all processes throw
raise RuntimeError("some redshifts failed for task "
"{}".format(task))
return
def run(self, grph, task, opts, comm=None):
"""
Run Redrock on a spectral group.
Args:
grph (dict): pruned graph with this task and dependencies.
task (str): the name of this task.
opts (dict): options to use for this task.
comm (mpi4py.MPI.Comm): optional MPI communicator.
"""
nproc = 1
rank = 0
if comm is not None:
nproc = comm.size
rank = comm.rank
log = get_logger()
node = grph[task]
spectra = "spectra-{}-{}".format(node["nside"], node["pixel"])
specfile = graph_path(spectra)
outfile = graph_path(task)
outdir = os.path.dirname(outfile)
details = io.findfile('redrock',
nside=node["nside"], groupname=node["pixel"], outdir=outdir)
options = {}
options["output"] = details
options["zbest"] = outfile
options.update(opts)
optarray = option_list(options)
optarray.append(specfile)
# write out the equivalent commandline
if rank == 0:
com = ["RUN", "rrdesi_mpi"]
com.extend(optarray)
log.info(" ".join(com))
failcount = 0
try:
rrdesi(options=optarray, comm=comm)
except:
failcount += 1
sys.stdout.flush()
if comm is not None:
failcount = comm.allreduce(failcount)
if failcount > 0:
# all processes throw
raise RuntimeError("some redshifts failed for task "
"{}".format(task))
return
def bgs_redshifts(sim, simdir, overwrite=False):
"""Fit for the redshifts.
"""
from redrock.external.desi import rrdesi
for ii in range(sim['nsim']):
zbestfile = os.path.join(
simdir, sim['suffix'],
'bgs-{}-{:03}-zbest.fits'.format(sim['suffix'], ii))
spectrafile = os.path.join(
simdir, sim['suffix'],
'bgs-{}-{:03}.fits'.format(sim['suffix'], ii))
if overwrite or not os.path.isfile(zbestfile):
rrdesi(options=[
'--zbest', zbestfile, '--mp',
str(nproc), spectrafile
])
else:
print('File {} exists...skipping.'.format(zbestfile))
"""
Run redrock by hand for DC17a (2% sprint)
"""
from __future__ import absolute_import, division, print_function
import sys, os, glob
import numpy as np
from redrock.external import desi
#- run from /scratch2/scratchdirs/sjbailey/desi/dc17a/spectro/redux/dc17a
bricks = list()
for brickfile in glob.glob('bricks/*/brick-b-*.fits'):
#- extract brickname from /path/to/{brickname}/brick-b-{brickname}.fits
bricks.append(brickfile[-13:-5])
todo = list()
for brickname in sorted(bricks):
rrout = 'redrock/rr-{}.h5'.format(brickname)
zbout = 'redrock/zbest-{}.fits'.format(brickname)
if os.path.exists(rrout) and os.path.exists(zbout):
print('---- skipping completed brick {}'.format(brickname))
else:
print('---- '+brickname)
cmd = 'rrdesi -o {} --zbest {}'.format(rrout, zbout)
for brickfile in glob.glob('bricks/{}/brick-*.fits'.format(brickname)):
cmd = cmd + ' ' + brickfile
#print(cmd)
desi.rrdesi(cmd.split()[1:])
def _run(self, name, opts, comm, db):
"""See BaseTask.run.
"""
optlist = self._option_list(name, opts)
rrdesi(options=optlist, comm=comm)
return
def _run(self, name, opts, comm, db):
"""See BaseTask.run.
"""
optlist = self._option_list(name, opts)
rrdesi(options=optlist, comm=comm)
return
from desispec.pipeline import load_prod
import optparse
parser = optparse.OptionParser(usage="%prog [options]")
parser.add_option("--hang", action="store_true", help="make it hang")
opts, args = parser.parse_args()
grph = None
if comm.rank == 0:
grph = load_prod(nightstr='20190829', spectrographs=None)
# graph_db_check(grph)
if opts.hang:
#- This command doesn't hang, but it causes later commands to hang
grph = comm.bcast(grph, root=0)
#--- DEBUG ---
cmd1 = "rrdesi --zbest /scratch2/scratchdirs/sjbailey/desi/dc17a/spectro/redux/dc17a-test/bricks/0001m067/zbest-0001m067.fits --output /scratch2/scratchdirs/sjbailey/desi/dc17a/spectro/redux/dc17a-test/bricks/0001m067/rr-0001m067.h5 /scratch2/scratchdirs/sjbailey/desi/dc17a/spectro/redux/dc17a-test/bricks/0001m067/brick-b-0001m067.fits /scratch2/scratchdirs/sjbailey/desi/dc17a/spectro/redux/dc17a-test/bricks/0001m067/brick-r-0001m067.fits /scratch2/scratchdirs/sjbailey/desi/dc17a/spectro/redux/dc17a-test/bricks/0001m067/brick-z-0001m067.fits --ncpu 24 --ntargets 4"
cmd2 = "rrdesi --output /scratch2/scratchdirs/sjbailey/desi/dc17a/spectro/redux/dc17a-test/bricks/2766p445/rr-2766p445.h5 --zbest /scratch2/scratchdirs/sjbailey/desi/dc17a/spectro/redux/dc17a-test/bricks/2766p445/zbest-2766p445.fits /scratch2/scratchdirs/sjbailey/desi/dc17a/spectro/redux/dc17a-test/bricks/2766p445/brick-b-2766p445.fits /scratch2/scratchdirs/sjbailey/desi/dc17a/spectro/redux/dc17a-test/bricks/2766p445/brick-r-2766p445.fits /scratch2/scratchdirs/sjbailey/desi/dc17a/spectro/redux/dc17a-test/bricks/2766p445/brick-z-2766p445.fits --ncpu 24 --ntargets 4"
cmds = [cmd1, cmd2]
from redrock.external.desi import rrdesi
rrdesi(cmds[comm.rank].split()[1:])
print('Rank {} done'.format(comm.rank))
sys.stdout.flush()
comm.barrier()
#--- DEBUG ---
# grph = comm.bcast(grph, root=0)