def makejobconfig(catalog):
logging.info('Seeding 1 job')
settings = systemsettings()
# Generate new set of params/coords
pdbfile, dcdfile = deshaw.getHistoricalTrajectory_prot(0)
traj = md.load(dcdfile, top=pdbfile, frame=0)
jcID, params = generateNewJC(traj)
dcdfreq = catalog.get('dcdfreq')
runtime = catalog.get('runtime')
sim_step_size = catalog.get('sim_step_size')
# Update Additional JC Params and Decision History, as needed
config = dict(params,
name = jcID,
runtime = runtime,
dcdfreq = dcdfreq,
interval = dcdfreq * sim_step_size,
temp = 310,
timestep = 0,
gc = 1,
origin = 'deshaw',
src_index = 0,
src_bin = (0, 0),
application = settings.name)
logging.info("New Simulation Job Created: %s", jcID)
for k, v in config.items():
logging.debug(" %s: %s", k, str(v))
catalog.rpush('jcqueue', jcID)
catalog.hmset(wrapKey('jc', jcID), config)
def execute(self, thru_index):
"""Executing the Controler Algorithm. Load pre-analyzed lower dimensional
subspaces, process user query and identify the sampling space with
corresponding distribution function for each user query. Calculate
convergence rates, run sampler, and then execute fairness policy to
distribute resources among users' sampled values.
"""
logging.debug('CTL MT')
# PRE-PROCESSING ---------------------------------------------------------------------------------
logging.debug("============================ <PRE-PROCESS> =============================")
np.set_printoptions(precision=4, linewidth=150)
self.data['timestep'] += 1
logging.info('TIMESTEP: %d', self.data['timestep'])
settings = systemsettings()
bench = microbench('ctl_%s' % settings.name, self.seqNumFromID())
stat = StatCollector('ctl_%s' % settings.name, self.seqNumFromID())
# Connect to the cache
self.cacheclient = CacheClient(settings.APPL_LABEL)
# create the "binlist":
numLabels = self.data['numLabels']
numresources = self.data['numresources']
# LOAD all new subspaces (?) and values
##### BARRIER
self.wait_catalog()
# Load new RMS Labels -- load all for now
bench.start()
logging.debug('Loading RMS Labels')
start_index = max(0, self.data['ctlIndexHead'])
# labeled_pts_rms = self.catalog.lrange('label:rms', self.data['ctlIndexHead'], thru_index)
logging.debug(" Start_index=%d, thru_index=%d, ctlIndexHead=%d", start_index, thru_index, self.data['ctlIndexHead'])
feallist = [np.fromstring(i) for i in self.catalog.lrange('subspace:feal', 0, -1)]
num_pts = len(feallist)
self.data['ctlIndexHead'] = thru_index
thru_count = self.data['observe:count']
logging.debug('##NUM_RMS_THIS_ROUND: %d', num_pts)
stat.collect('numpts', len(feallist))
# Calculate variable PDF estimations for each subspace via bootstrapping:
logging.debug("======================= <SUBSPACE CONVERGENCE> =========================")
# Bootstrap current sample for RMS
logging.info("Feature Landscapes for %d points loaded. Calculating PDF.....", len(feallist))
# Static for now
blocksize = 5000
mv_convergence = op.bootstrap_block(feallist, blocksize)
global_landscape = np.mean(feallist, axis=0)
stat.collect('convergence', mv_convergence)
stat.collect('globalfeal', global_landscape)
# logging.info('MV Convergence values:\nCONV,%s', ','.join(['%5.3f'%i for i in mv_convergence]))
# logging.info('Global Feature Landscape:\nFEAL,%s', ','.join(['%5.3f'%i for i in global_landscape]))
logging.info('MV Convergence values:\nCONV,%s', str(mv_convergence[-1]))
logging.info('Global Feature Landscape:\n%s', feal.tostring(global_landscape))
# IMPLEMENT USER QUERY with REWEIGHTING:
logging.debug("======================= <QUERY PROCESSING> =========================")
##### BARRIER
self.wait_catalog()
selected_index_list = []
# QUERY PROCESSING & SAMPLING BELOW to select indices.
EXPERIMENT_NUMBER = self.experiment_number
logging.info("RUNNING EXPER CONFIGURATION #%d", EXPERIMENT_NUMBER)
###### EXPERIMENT #5: BIASED (Umbrella) SAMPLER
if EXPERIMENT_NUMBER == 5:
if self.catalog.exists('label:deshaw'):
logging.info("Loading DEShaw historical points.... From Catalog")
rmslabel = [eval(x) for x in self.catalog.lrange('label:deshaw', 0, -1)]
else:
logging.info("Loading DEShaw historical points.... From File (and recalculating)")
rmslabel = deshaw.labelDEShaw_rmsd()
deshaw_samples = {b:[] for b in binlist}
for i, b in enumerate(rmslabel):
deshaw_samples[b].append(i)
coord_origin = []
conv_vals = np.array([v for k, v in sorted(convergence_rms.items())])
norm_pdf_conv = conv_vals / sum(conv_vals)
logging.info("Umbrella Samping PDF (Bootstrapping):")
sampled_distro_perbin = {b: 0 for b in binlist}
while numresources > 0:
# First sampling is BIASED
selected_bin = np.random.choice(len(binlist), p=norm_pdf_conv)
A, B = binlist[selected_bin]
sampled_distro_perbin[binlist[selected_bin]] += 1
if bincounts[selected_bin] is not None and bincounts[selected_bin] > 0:
# Secondary Sampling is Uniform
sample_num = np.random.randint(bincounts[selected_bin])
logging.debug('SAMPLER: selecting sample #%d from bin %s',
sample_num, str(binlist[selected_bin]))
index = self.catalog.lindex('varbin:rms:%d_%d' % binlist[selected_bin],
sample_num)
selected_index_list.append(index)
coord_origin.append(('sim', index, binlist[selected_bin], '%d-D'%A))
numresources -= 1
elif len(deshaw_samples[binlist[selected_bin]]) > 0:
index = np.random.choice(deshaw_samples[binlist[selected_bin]])
logging.debug('SAMPLER: selecting DEShaw frame #%d from bin %s',
index, str(binlist[selected_bin]))
# Negation indicates an historical index number
selected_index_list.append(-index)
coord_origin.append(('deshaw', index, binlist[selected_bin], '%d-D'%A))
numresources -= 1
else:
logging.info("NO Candidates for bin: %s", binlist[selected_bin])
###### EXPERIMENT #10: MutiVariate Nearest Neighbor (MVNN) SAMPLER
if EXPERIMENT_NUMBER == 10:
# Create the KD Tree from all feature landscapes (ignore first 5 features)
kd = KDTree(100, 15, np.array(feallist), 'median')
# Collect hypercubes
hc = kd.getleaves()
logging.info('KD Tree Stats')
logging.info(' # HCubes : %5d', len(hc))
logging.info(' Largest HC: %5d', max([v['count'] for k,v in hc.items()]))
logging.info(' Smallest HC: %5d', min([v['count'] for k,v in hc.items()]))
for key, hcube in hc.items():
hc_feal = [feallist[i] for i in hcube['elm']]
hc[key]['feal'] = np.mean(hc_feal, axis=0)
# Det scale and/or sep scales for each feature set
desired = 10 - global_landscape
logging.info('Desired Landscape:\n%s', feal.tostring(desired))
# Calc euclidean dist to each mean HC's feal
nn = {k: LA.norm(desired[5:] - v['feal'][5:]) for k,v in hc.items()}
# Grab top N Neighbors (10 for now)
neighbors = sorted(nn.items(), key=lambda x: x[1])[:10]
logging.info('BestFit Landscape:\n%s', feal.tostring(hc[neighbors[0][0]]['feal']))
## DATA SAMPLER
nn_keys = [i for i,w in neighbors]
nn_wgts = np.array([w for i,w in neighbors])
nn_wgts /= np.sum(nn_wgts) # normalize
coord_origin = []
while numresources > 0:
# First sampling is BIASED
selected_hc = np.random.choice(nn_keys, p=nn_wgts)
# Second is UNIFORM (within the HCube)
index = np.random.choice(hc[selected_hc]['elm'])
selected_index_list.append(index)
src_state = np.argmax(feallist[index][:5])
coord_origin.append(('sim', index, src_state, selected_hc))
logging.info('Sampled Landscape [hc=%s]:\n%s', selected_hc, feal.tostring(feallist[index]))
numresources -= 1
elif EXPERIMENT_NUMBER == 11:
# Use only right most 10 features (non-normalized ones)
inventory = np.array([f[10:] for f in feallist])
desired = 10 - global_landscape
logging.info('Desired Landscape (NOTE Only Including A-B values:\n%s', feal.tostring(desired))
selected_index_list = mvkp.knapsack(desired[10:], inventory, numresources, 2000000)
coord_origin = [('sim', index, np.argmax(feallist[index][:5]), 'D') for index in selected_index_list]
logging.info("KNAPSACK Completed:")
logging.info('Target Distribution:\n%s', str(desired[10:]))
logging.info('Target Distribution:\n%s', '\n'.join(['%s'%feallist[i] for i in selected_index_list]))
# Back Project to get new starting Coords for each sample
logging.debug("======================= <INPUT PARAM GENERATION> =================")
logging.info('All Indices sampled. Back projecting to high dim coords')
sampled_set = []
for i in selected_index_list:
traj = self.backProjection([i])
sampled_set.append(traj)
bench.mark('Sampler')
# Generate new starting positions
runtime = self.data['runtime']
jcqueue = OrderedDict()
for i, start_traj in enumerate(sampled_set):
jcID, params = generateNewJC(start_traj)
# TODO: Update/check adaptive runtime, starting state
jcConfig = dict(params,
name = jcID,
runtime = runtime, # In timesteps
dcdfreq = self.data['dcdfreq'], # Frame save rate
interval = self.data['dcdfreq'] * self.data['sim_step_size'],
temp = 310,
timestep = self.data['timestep'],
gc = 1,
origin = coord_origin[i][0],
src_index = coord_origin[i][1],
src_bin = coord_origin[i][2],
src_hcube = coord_origin[i][3],
application = settings.APPL_LABEL)
logging.info("New Simulation Job Created: %s", jcID)
for k, v in jcConfig.items():
logging.debug(" %s: %s", k, str(v))
# Add to the output queue & save config info
jcqueue[jcID] = jcConfig
logging.info("New Job Candidate Completed: %s #%d on the Queue", jcID, len(jcqueue))
bench.mark('GenInputParams')
# POST-PROCESSING -------------------------------------
logging.debug("============================ <POST-PROCESSING & OUTPUT> =============================")
self.wait_catalog()
# Clear current queue, mark previously queues jobs for GC, push new queue
qlen = self.catalog.llen('jcqueue')
logging.debug('Current queue len; %s', str(qlen))
if qlen > 0:
curqueue = self.catalog.lrange('jcqueue', 0, -1)
logging.info("Marking %d obsolete jobs for garbage collection", len(curqueue))
for jc_key in curqueue:
key = wrapKey('jc', jc_key)
config = self.catalog.hgetall(key)
config['gc'] = 0
# Add gc jobs it to the state to write back to catalog (flags it for gc)
self.addMut(key, config)
self.catalog.delete('jcqueue')
# CATALOG UPDATES
self.catalog.rpush('datacount', len(feallist))
# EXPR 7 Update:
if EXPERIMENT_NUMBER > 5 and EXPERIMENT_NUMBER < 10:
# self.catalog.storeNPArray(np.array(centroid), 'subspace:covar:centroid:%d' % cov_iteration)
self.catalog.rpush('subspace:covar:thruindex', len(covar_pts))
# Update cache hit/miss
hit = self.cache_hit
miss = self.cache_miss
logging.info('##CACHE_HIT_MISS %d %d %.3f', hit, miss, (hit)/(hit+miss))
self.catalog.rpush('cache:hit', self.cache_hit)
self.catalog.rpush('cache:miss', self.cache_miss)
self.data['jcqueue'] = list(jcqueue.keys())
logging.debug(" JCQUEUE: %s", str(self.data['jcqueue']))
# Update Each new job with latest convergence score and save to catalog(TODO: save may not be nec'y)
logging.debug("Updated Job Queue length: %d", len(self.data['jcqueue']))
for jcid, config in jcqueue.items():
# config['converge'] = self.data['converge']
self.addMut(wrapKey('jc', jcid), config)
bench.mark('PostProcessing')
print ('## TS=%d' % self.data['timestep'])
bench.show()
stat.show()
return list(jcqueue.keys())
wells = [(0, 2099, 684),
(1, 630, 602),
(2, 2364, 737),
(3, 3322, 188),
(4, 2108, 258)]
print('GEN DATA!')
# REDO WELLs
for well in wells:
state, win, frame = well
logging.error(' NEED TO REDO Well start point gen')
pdbfile, archiveFile = getHistoricalTrajectory(win)
jcID, params = generateNewJC(archiveFile, ppdbfile, frame, jcid='test_%d'%state)
jcConfig = dict(params,
name = jcID,
runtime = 20000,
interval = 500,
temp = 310,
state = state,
weight = 0.0,
timestep = 0,
gc = 1,
application = DEFAULT.APPL_LABEL)
print("Data Generated! ")
print("Job = ", jcID)
for k, v in jcConfig.items():
def seedJob_Uniform(catalog, num=1, exact=None):
"""
Seeds jobs into the JCQueue -- pulled from DEShaw
Selects equal `num` of randomly start frames from each bin
to seed as job candidates
"""
logging.info('Seeding %d jobs per transtion bin', num)
settings = systemsettings()
numLabels = int(catalog.get('numLabels'))
binlist = [(A, B) for A in range(numLabels) for B in range(numLabels)]
dcdfreq = int(catalog.get('dcdfreq'))
runtime = int(catalog.get('runtime'))
sim_step_size = int(catalog.get('sim_step_size'))
if catalog.exists('label:deshaw'):
rmslabel = [eval(x) for x in catalog.lrange('label:deshaw', 0, -1)]
elif os.path.exists(DESHAW_LABEL_FILE):
logging.info('Loading DEShaw Points From File....')
with open(DESHAW_LABEL_FILE) as lfile:
rmslabel = [eval(label) for label in lfile.read().strip().split('\n')]
logging.info('Loaded DEShaw %d Labels from file, %s', len(rmslabel), DESHAW_LABEL_FILE)
pipe = catalog.pipeline()
for rms in rmslabel:
pipe.rpush('label:deshaw', rms)
pipe.execute()
logging.info('DEShaw Labels stored in the catalog.')
else:
rmslabel = labelDEShaw_rmsd(store_to_disk=True)
pipe = catalog.pipeline()
for rms in rmslabel:
pipe.rpush('label:deshaw', rms)
pipe.execute()
logging.info('DEShaw Labels stored in the catalog.')
logging.info('Grouping all prelabeled Data:')
groupby = {b:[] for b in binlist}
for i, b in enumerate(rmslabel):
groupby[b].append(i)
for k in sorted(groupby.keys()):
v = groupby[k]
logging.info('%s %7d %4.1f', str(k), len(v), (100*len(v)/len(rmslabel)))
if exact is None:
source_list = sorted(groupby.keys())
else:
bin_list = list(groupby.keys())
if exact <= 25:
idx_list = np.random.choice(len(bin_list), exact, replace=False)
else:
idx_list = np.random.choice(len(bin_list), exact, replace=True)
source_list = [bin_list[i] for i in idx_list]
for binlabel in source_list:
clist = groupby[binlabel]
A, B = binlabel
# No candidates
if len(clist) == 0:
logging.info('NO Candidates for %s', str(binlabel))
if binlabel == (1, 3):
logging.info('Swapping (1,2) for (1,3)')
clist = groupby[(1,2)]
B = 2
elif binlabel == (3, 1):
logging.info('Swapping (3,0) for (3,1)')
clist = groupby[(3,0)]
B = 0
else:
logging.info('Not sampling this bin')
continue
for k in range(num):
logging.debug('\nSeeding Job #%d for bin (%d,%d) ', k, A, B)
index = np.random.choice(clist)
src, frame = deshaw.refFromIndex(index)
logging.debug(" Selected: BPTI %s, frame: %s", src, frame)
pdbfile, dcdfile = deshaw.getHistoricalTrajectory_prot(int(src))
traj = md.load(dcdfile, top=pdbfile, frame=int(frame))
# Generate new set of params/coords
jcID, params = generateNewJC(traj)
# Update Additional JC Params and Decision History, as needed
config = dict(params,
name = jcID,
runtime = runtime,
dcdfreq = dcdfreq,
interval = dcdfreq * sim_step_size,
temp = 310,
timestep = 0,
gc = 1,
origin = 'deshaw',
src_index = index,
src_bin = (A, B),
src_hcube = 'D',
application = settings.APPL_LABEL)
logging.info("New Simulation Job Created: %s", jcID)
for k, v in config.items():
logging.debug(" %s: %s", k, str(v))
catalog.rpush('jcqueue', jcID)
catalog.hmset(wrapKey('jc', jcID), config)
