def make_covar(self, win, slide):
covar = []
WIN_SIZE_NS = win
SLIDE_AMT_NS = slide
for i, tr in self.trlist.items():
if i % 100==0:
print(i)
cov = datareduce.calc_covar(tr.xyz, WIN_SIZE_NS, 1, slide=SLIDE_AMT_NS)
covar.extend(cov)
return covar
def doCovar(self, winsize=.1, slide=.05):
# Calculate Covariance matrices over all temporal data IAW given window param
self.covar = []
self.fealcov = []
for i, tr in self.E.trlist.items():
if i % 100 == 0:
print(i)
cov = dr.calc_covar(tr.xyz, winsize, 1, slide=slide)
if self.space in ['ds', 'dsw']:
X, C = dr.distance_space(tr), self.E.cent_ds
else:
X, C = tr.xyz, self.E.cent_c
wgt = self.E.cw if self.space in ['cw', 'dsw'] else [1,1,1,1,1]
rms = calc_rmsd(X, C, weights=wgt)
W = int(winsize * 1000)
S = int(slide * 1000)
feal = [np.mean([FL.feal.atemporal(i) for i in rms[st:st+W]], axis=0) for st in range(0, len(tr.xyz), S)]
for n in range(min(len(cov), len(feal))):
self.covar.append(cov[n])
self.fealcov.append(feal[n])
def execute(self, job):
# PRE-PREOCESS ----------------------------------------------------------
settings = systemsettings()
bench = microbench('sim_%s' % settings.name, self.seqNumFromID())
bench.start()
stat = StatCollector('sim_%s' % settings.name, self.seqNumFromID())
mylogical_seqnum = str(self.seqNumFromID())
# Prepare working directory, input/output files
conFile = os.path.join(job['workdir'], job['name'] + '.conf')
logFile = conFile.replace('conf', 'log') # log in same place as config file
dcdFile = conFile.replace('conf', 'dcd') # dcd in same place as config file
USE_SHM = True
ADAPTIVE_CENTROID = False
SIMULATE_RATIO = settings.SIMULATE_RATIO
if SIMULATE_RATIO > 1:
logging.warning(" USING SIMULATION RATIO OF %d -- THis is ONLY for debugging", SIMULATE_RATIO)
frame_size = (SIMULATE_RATIO * int(job['interval'])) / (1000)
logging.info('Frame Size is %f Using Sim Ratio of 1:%d', \
frame_size, SIMULATE_RATIO)
EXPERIMENT_NUMBER = settings.EXPERIMENT_NUMBER
logging.info('Running Experiment Configuration #%d', EXPERIMENT_NUMBER)
# TODO: FOR LINEAGE
# srcA, srcB = eval(job['src_bin'])
# stat.collect('src_bin', [str(srcA), str(srcB)])
traj = None
# EXECUTE SIMULATION ---------------------------------------------------------
if self.skip_simulation:
logging.info('1. SKIPPING SIMULATION.....')
USE_SHM = False
job['dcd'] = dcdFile
key = wrapKey('jc', job['name'])
self.data[key]['dcd'] = dcdFile
else:
logging.info('1. Run Simulation')
# Prepare & source to config file
with open(self.data['sim_conf_template'], 'r') as template:
source = template.read()
# >>>>Storing DCD into shared memory on this node
if USE_SHM:
# ramdisk = '/dev/shm/out/'
ramdisk = '/tmp/ddc/'
if not os.path.exists(ramdisk):
os.mkdir(ramdisk)
job['outputloc'] = ramdisk
dcd_ramfile = os.path.join(ramdisk, job['name'] + '.dcd')
else:
job['outputloc'] = ''
with open(conFile, 'w') as sysconfig:
sysconfig.write(source % job)
logging.info("Config written to: " + conFile)
# # Run simulation in parallel
# if 'parallel' in job:
# numnodes = job['parallel']
# total_tasks = numnodes * 24
# cmd = 'mpiexec -n %d namd2 %s > %s' % (total_tasks, conFile, logFile)
# # Run simulation single threaded
# else:
# cmd = 'namd2 %s > %s' % (conFile, logFile)
# cmd = 'mpirun -n %d namd2 %s > %s' % (PARALLELISM, conFile, logFile)
check = executecmd('module list')
logging.debug('%s', check)
cmd = 'namd2 +p%d %s > %s' % (PARALLELISM, conFile, logFile)
# MICROBENCH #1 (file to Lustre)
# logging.debug("Executing Simulation:\n %s\n", cmd)
# bench = microbench()
# bench.start()
# stdout = executecmd(cmd)
# logging.info("SIMULATION Complete! STDOUT/ERR Follows:")
# bench.mark('SimExec:%s' % job['name'])
# shm_contents = os.listdir('/dev/shm/out')
# logging.debug('Ramdisk contents (should have files) : %s', str(shm_contents))
# shutil.copy(ramdisk + job['name'] + '.dcd', job['workdir'])
# logging.info("Copy Complete to Lustre.")
# bench.mark('CopyLustre:%s' % job['name'])
# shutil.rmtree(ramdisk)
# shm_contents = os.listdir('/dev/shm')
# logging.debug('Ramdisk contents (should be empty) : %s', str(shm_contents))
# bench.show()
max_expected_obs = int(job['runtime']) // int(job['dcdfreq'])
# Retry upto 3 attempts if the sim fails
MAX_TRY = 3
for i in range(MAX_TRY, 0, -1):
min_required_obs = int(max_expected_obs * ((i-1)/(MAX_TRY)))
logging.debug("Executing Simulation:\n %s\n", cmd)
logging.debug('# Obs Expected to see: %d', max_expected_obs)
stdout = executecmd(cmd)
logging.info("SIMULATION Complete! STDOUT/ERR Follows:")
# Check file for expected data
if USE_SHM:
traj = md.load(dcd_ramfile, top=job['pdb'])
else:
traj = md.load(dcdFile, top=job['pdb'])
logging.info("Obs Threshold = %4d", min_required_obs)
logging.info("#Obs This Traj = %4d", traj.n_frames)
if traj.n_frames >= min_required_obs:
logging.info('Full (enough) Sim Completed')
break
logging.info('Detected a failed Simulation. Retrying the same sim.')
bench.mark('SimExec:%s' % job['name'])
# Internal stats
sim_length = self.data['sim_step_size'] * int(job['runtime'])
sim_realtime = bench.delta_last()
sim_run_ratio = (sim_realtime/60) / (sim_length/1000000)
logging.info('##SIM_RATIO %6.3f min-per-ns-sim', sim_run_ratio)
stat.collect('sim_ratio', sim_run_ratio)
if USE_SHM:
shm_contents = os.listdir(ramdisk)
logging.debug('Ramdisk contents (should have files) : %s', str(shm_contents))
if not os.path.exists(dcd_ramfile):
logging.warning("DCD FILE NOT FOUND!!!! Wait 10 seconds for sim to close it (???)")
time.sleep(10)
if not os.path.exists(dcd_ramfile):
logging.warning("DCD STIILL FILE NOT FOUND!!!!")
else:
logging.info("DCD File was found")
# # MICROBENCH #2 (file to Alluxio)
# allux = AlluxioClient()
# # copy to Aluxio FS
# allux.put(ramdisk + job['name'] + '.dcd', '/')
# logging.info("Copy Complete to Alluxio.")
# bench.mark('CopyAllux:%s' % job['name'])
# And copy to Lustre
# shutil.copy(ramdisk + job['name'] + '.dcd', job['workdir'])
# And copy to Lustre (usng zero-copy):
if USE_SHM:
src = open(dcd_ramfile, 'rb')
dest = open(dcdFile, 'w+b')
offset = 0
dcdfilesize = os.path.getsize(dcd_ramfile)
while True:
sent = sendfile(dest.fileno(), src.fileno(), offset, dcdfilesize)
if sent == 0:
break
offset += sent
logging.info("Copy Complete to Lustre.")
bench.mark('CopyLustre:%s' % job['name'])
# TODO: Update job's metadata
key = wrapKey('jc', job['name'])
self.data[key]['dcd'] = dcdFile
# ANALYSIS ------- ---------------------------------------------------------
# ANALYSIS ALGORITHM
# 1. With combined Sim-analysis: file is loaded locally from shared mem
logging.debug("2. Load DCD")
# Load full higher dim trajectory
# traj = datareduce.filter_heavy(dcd_ramfile, job['pdb'])
if traj is None:
if USE_SHM:
traj = md.load(dcd_ramfile, top=job['pdb'])
else:
traj = md.load(dcdFile, top=job['pdb'])
# Center Coordinates
traj.center_coordinates()
bench.mark('File_Load')
logging.debug('Trajectory Loaded: %s (%s)', job['name'], str(traj))
# DIMENSIONALITY REDUCTION --------------------------------------------------
# 4-A. Subspace Calcuation: RMS using Alpha-Filter
#------ A: RMSD-ALPHA ------------------
# S_A = rmslist
logging.info('---- RMSD Calculation against pre-defined centroids ----')
# RMSD is calculated on the Ca ('alpha') atoms in distance space
# whereby all pairwise distances are calculated for each frame.
# Pairwise distances are plotted in euclidean space
# Distance to each of the 5 pre-calculated centroids is calculated
# 1. Filter to Alpha atoms
alpha = traj.atom_slice(deshaw.FILTER['alpha'])
# 2. (IF USED) Convert to distance space: pairwise dist for all atom combinations
# alpha_dist = dr.distance_space(alpha)
# 3. Calc RMS for each conform to all centroids
# Heuristic centroid weight (TODO: make this trained)\
# 4. For adaptive Centriods
# Centroids Will be pulled & updated.
logging.info('CENTROID Retrieval & Updating')
self.wait_catalog()
# If they were mutable....
# logging.info('Acquiring a Lock on the Centroids')
# centroids = self.catalog.loadNPArray('centroid')
# thetas = self.catalog.loadNPArray('thetas')
# lock = self.catalog.lock_acquire('centroid')
# if lock is None:
# logging.info('Could not lock the Centroids. Will use current cached (possibly stale) data.')
# bench.mark('ConcurrLockCentroid'%(A,B))
# Implemented as a Transactional Data Structure....
if ADAPTIVE_CENTROID:
centroids = []
for state in range(numLabels):
cent_raw = self.catalog.lrange('centroid:xyz:%d'%state, 0, -1)
cent_xyz = [pickle.loads(i) for i in cent_raw]
cent_npts = [int(i) for i in self.catalog.lrange('centroid:npts:%d'%state, 0, -1)]
c_sum = np.zeros(shape=cent_xyz[0].shape)
c_tot = 0
for x, n in zip(cent_xyz, cent_npts):
c = x * n
c_sum += c
c_tot += n
centroids.append(c_sum / c_tot)
else:
centroids = self.catalog.loadNPArray('centroid')
# if EXPERIMENT_NUMBER < 10:
# 5. Calculate the RMSD for each filtered point to 5 pre-determined centroids
# cw = [.92, .94, .96, .99, .99]
cw = [.94, .95, .97, .99, .99]
numLabels = len(self.data['centroid'])
numConf = len(traj.xyz)
stat.collect('numpts',numConf)
# 4. Account for noise : Simple spatial mean filter over a small window
# Where size of window captures extent of noise
# (e.g. 10000fs window => motions under 10ps are considered "noisy")
noise = self.data['obs_noise']
stepsize = 500 if 'interval' not in job else int(job['interval'])
nwidth = noise//(2*stepsize)
noisefilt = lambda x, i: np.mean(x[max(0,i-nwidth):min(i+nwidth, len(x))], axis=0)
rms_filtered = np.array([noisefilt(alpha.xyz, i) for i in range(numConf)])
# Notes: Delta_S == rmslist
rmslist_sv = calc_rmsd(rms_filtered, centroids, weights=cw)
# rmslist = adaptive_rmsd(rms_filtered, centroids, theta)
# else:
rmslist = calc_rmsd(alpha, centroids)
numConf = traj.n_frames
numLabels = len(centroids)
# rmslist = calc_rmsd(alpha.xyz, self.data['centroid'], weights=cw)
logging.debug(' RMS: %d points projected to %d centroid-distances', \
numConf, numLabels)
# 6. Apply Heuristics Labeling -- Single Variate
rmslabel = []
binlist = [(a, b) for a in range(numLabels) for b in range(numLabels)]
label_count = {ab: 0 for ab in binlist}
groupbystate = [[] for i in range(numLabels)]
groupbybin = {ab: [] for ab in binlist}
for i, rms in enumerate(rmslist_sv):
# Sort RMSD by proximity & set state A as nearest state's centroid
A, B = np.argsort(rms)[:2]
# Calc Absolute proximity between nearest 2 states' centroids
# THETA Calc derived from static run. it is based from the average std dev of all rms's from a static run
# of BPTI without solvent. It could be dynamically calculated, but is hard coded here
# The theta is divided by four based on the analysis of DEShaw:
# est based on ~3% of DEShaw data in transition (hence )
# avg_stddev = 0.34119404492089034
# theta = settings.RMSD_THETA
## FOR ADAPTIVE Cantroids. Theta is now updated dyamically
# NOTE: Original formulate was relative. Retained here for reference:
# Rel vs Abs: Calc relative proximity for top 2 nearest centroids
# relproximity = rms[A] / (rms[A] + rms[rs[1]])
# B = rs[1] if relproximity > (.5 - theta) else A
# proximity = abs(rms[prox[1]] - rms[A]) / (rms[prox[1]] + rms[A]) #relative
#proximity = abs(rms[prox[1]] - rms[A]) #abs
# Update for Adaptive Centroid.
delta = np.abs(rms[B] - rms[A])
# (TODO: Factor in more than top 2, better noise)
# Label secondary sub-state
# sub_state = B prox[1] if proximity < theta else A
# For ADAPTIVE Centroids
if delta < 0.33:
sub_state = B
else:
sub_state = A
rmslabel.append((A, sub_state))
# Add this index to the set of indices for this respective label
# TODO: Should we evict if binsize is too big???
# logging.debug('Label for observation #%3d: %s', i, str((A, B)))
label_count[(A, sub_state)] += 1
# Group high-dim point by state
# TODO: Consider grouping by stateonly or well/transitions (5 vs 10 bins)
groupbystate[A].append(i)
groupbybin[(A, sub_state)].append(i)
# stat.collect('observe', label_count)
bench.mark('RMS')
logging.info('Labeled the following:')
for A in range(numLabels):
if len(groupbystate[A]) > 0:
logging.info('label,state,%d,num,%d', A, len(groupbystate[A]))
for ab in binlist:
if len(groupbybin[ab]) > 0:
A, B = ab
logging.info('label,bin,%d,%d,num,%d', A, B, len(groupbybin[ab]))
# FEATURE LANDSCAPE -- Multi-Variate
# Calc Feature landscape for each frame's RMSD
feal_list = [feal.atemporal(rms) for rms in rmslist]
logging.info('Calculated Feature Landscape. Aggregate for this traj')
# For logging purposes
agg_feal = np.mean(feal_list, axis=0)
logging.info('CountsMax [C]: %s', str(agg_feal[:5]))
logging.info('StateDist [S]: %s', str(agg_feal[5:10]))
logging.info('RelDist [A-B]: %s', str(agg_feal[10:]))
# ADAPTIVE CENTROID & THETA CALCULATION
# if lock is None:
# logging.info('Never acqiured a lock. Skipping adaptive update (TODO: Mark pts as stale)')
# else:
# logging.info('Updating Adaptive Centroid')
if ADAPTIVE_CENTROID:
pipe = self.catalog.pipeline()
for state in range(numLabels):
n_pts = len(groupbybin[(state, state)])
if n_pts == 0:
logging.info('Skipping State %d Centroid -- Well not visited on this trajectory')
continue
cent_xyz = [alpha.xyz[i] for i in groupbybin[(state, state)]]
cent_npts = len(groupbybin[(state, state)])
c_sum = np.zeros(shape=alpha.xyz[0].shape)
for pt in cent_xyz:
c_sum += pt
centroid_local = c_sum / n_pts
centroid_delta = LA.norm(centroids[state] - cent)
pipe.rpush('centroid:xyz:%d' % state, pickle.dumps(centroid_local))
pipe.rpush('centroid:npts:%d' % state, n_pts)
pipe.rpush('centroid:delta:%d' % state, centroid_delta)
pipe.execute()
# 4-B. Subspace Calcuation: COVARIANCE Matrix, 200ns windows, Full Protein
#------ B: Covariance Matrix -----------------
if EXPERIMENT_NUMBER > 5:
# 1. Project Pt to PC's for each conform (top 3 PC's)
logging.info('---- Covariance Calculation on 200ns windows (Full Protein, cartesian Space) ----')
# Calculate Covariance over 200 ps Windows sliding every 100ps
# These could be user influenced...
WIN_SIZE_NS = .2
SLIDE_AMT_NS = .1
logging.debug("Calculating Covariance over trajectory. frame_size = %.1f, WINSIZE = %dps, Slide = %dps",
frame_size, WIN_SIZE_NS*1000, SLIDE_AMT_NS*1000)
covar = dr.calc_covar(alpha.xyz, WIN_SIZE_NS, frame_size, slide=SLIDE_AMT_NS)
bench.mark('CalcCovar')
stat.collect('numcovar', len(covar))
logging.debug("Calcualted %d covariance matrices. Storing variances", len(covar))
# BARRIER: WRITE TO CATALOG HERE -- Ensure Catalog is available
# try:
self.wait_catalog()
# except OverlayNotAvailable as e:
# logging.warning("Catalog Overlay Service is not available. Scheduling ASYNC Analysis")
# Update Catalog with 1 Long Atomic Transaction
global_index = []
with self.catalog.pipeline() as pipe:
while True:
try:
logging.debug('Update Filelist')
pipe.watch(wrapKey('jc', job['name']))
file_idx = pipe.rpush('xid:filelist', job['dcd']) - 1
# HD Points
logging.debug('Update HD Points')
for x in range(traj.n_frames):
# Note: Pipelined insertions "should" return contiguous set of index points
index = pipe.rpush('xid:reference', (file_idx, x)) - 1
global_index.append(index - 1)
pipe.multi()
logging.debug('Update RMS Subspace')
for x in range(traj.n_frames):
A, B = rmslabel[x]
index = global_index[x]
# Labeled Observation (from RMSD)
pipe.rpush('label:rms', rmslabel[x])
pipe.rpush('varbin:rms:%d_%d' % (A, B), index)
# pipe.rpush('lineage:rms:%d_%d:%d_%d' % (srcA, srcB, A, B), index)
# pipe.rpush('lineage:pca:%s:%d_%d' % (job['src_hcube'], A, B), index)
pipe.rpush('subspace:rms', bytes(rmslist_sv[x]))
pipe.rpush('subspace:feal', bytes(feal_list[x]))
logging.debug('Update OBS Counts')
for b in binlist:
pipe.rpush('observe:rms:%d_%d' % b, label_count[b])
pipe.incr('observe:count')
pipe.hset('anl_sequence', job['name'], mylogical_seqnum)
if EXPERIMENT_NUMBER > 5:
logging.debug('Update Covar Subspace')
for i, si in enumerate(covar):
logging.debug('Update COVAR Pt #%d', i)
local_index = int(i * frame_size * SLIDE_AMT_NS)
pipe.rpush('subspace:covar:pts', bytes(si))
pipe.rpush('subspace:covar:xid', global_index[local_index])
pipe.rpush('subspace:covar:fidx', (file_idx, local_index))
logging.debug('Executing')
pipe.execute()
break
except redis.WatchError as e:
logging.debug('WATCH ERROR')
continue
self.data[key]['xid:start'] = global_index[0]
self.data[key]['xid:end'] = global_index[-1]
bench.mark('Indx_Update')
# (Should we Checkpoint here?)
# 4-C. Subspace Calcuation: PCA BY Strata (PER STATE) using Alpha Filter
#------ C: GLOBAL PCA by state -----------------
# Update PCA Vectors for each state with new data
if EXPERIMENT_NUMBER > 5 and EXPERIMENT_NUMBER < 10:
logging.info('---- PCA per BIN over Alpha Filter in cartesian Space ----')
# TODO: This will eventually get moved into a User process macrothread
# which will set in between analysis and controller.
# For now, we're recalculating using a lock
# Check if vectors need to be recalculated
# Connect to reservoir samples
# TODO: Catalog or Cache?
reservoir = ReservoirSample('rms', self.catalog)
# STALENESS_FACTOR = .25 # Recent updates account for 25% of the sample (Just a guess)
num_inserted = {ab: 0 for ab in binlist}
num_params = np.prod(alpha.xyz.shape[1:])
for A, B in binlist:
num_observations = len(groupbybin[(A,B)])
if num_observations == 0:
logging.info('No data received for bin (%d,%d). Not processing this bin here.', A, B)
continue
res_label = '%d_%d' % (A,B)
updateVectors = False
kpca_key = 'subspace:pca:kernel:%d_%d' % (A, B)
kpca = PCAnalyzer.load(self.catalog, kpca_key)
newkpca = False
if kpca is None:
# kpca = PCAKernel(None, 'sigmoid')
kpca = PCAKernel(6, 'rbf')
newkpca = True
logging.info('PCA: Checking if current vectors for state %d are out of date', A)
rsize = reservoir.getsize(res_label)
tsize = kpca.trainsize
# KPCA is out of date is the sample size is 20% larger than previously used set
# Heuristics --- this could be a different "staleness" factor or we can check it some other way
if newkpca or rsize > (tsize * 1.5):
# Should we only use a sample here??? (not now -- perhaps with larger rervoirs or if KPCA is slow
traindata = reservoir.get(res_label)
if newkpca:
logging.info('New PCA Kernel. Trained on data set of size %d. Current \
reservoir is %d pts.', tsize, rsize)
logging.info('Projecting %d points on Kernel PCA for bin (%d,%d)',
num_observations, A, B)
traindata = np.zeros(shape=((num_observations,)+alpha.xyz.shape[1:]),
dtype=np.float32)
for i, index in enumerate(groupbybin[(A,B)]):
np.copyto(traindata[i], alpha.xyz[index])
else:
logging.info('PCA Kernel is old (Updating it). Trained on data set of \
size %d. Current reservoir is %d pts.', tsize, rsize)
if len(traindata) <= num_params:
logging.info("Not enough data to calculate PC's (Need at least %d \
observations). Skipping PCA for Bin (%d,%d)", num_params, A, B)
hd_pts = np.zeros(shape=((num_observations,)+alpha.xyz.shape[1:]), dtype=np.float32)
for i, index in enumerate(groupbybin[(A,B)]):
np.copyto(hd_pts[i], alpha.xyz[index])
num_inserted[(A,B)] = reservoir.insert(res_label, hd_pts)
logging.debug('Updating reservoir Sample for Bin (%d, %d)')
continue
logging.info(' Performing Kernel PCA (Gaussian) for bin (%d,%d) using traindata of size %d', \
A, B, len(traindata))
kpca.solve(traindata)
# NOTE: Pick PCA Algorithm HERE
# pca = calc_kpca(np.array(traindata), kerneltype='sigmoid')
# pca = calc_pca(np.array(traindata))
bench.mark('CalcKPCA_%d_%d'%(A,B))
# new_vect = pca.alphas_.T
lock = self.catalog.lock_acquire(kpca_key)
if lock is None:
logging.info('Could not lock the PC Kernel for Bin (%d,%d). Not updating', A, B)
else:
kpca.store(self.catalog, kpca_key)
lock = self.catalog.lock_release(kpca_key, lock)
bench.mark('ConcurrPCAWrite_%d_%d'%(A,B))
# Project Reservoir Sample to the Kernel and overwrite current set of points
# This should only happen up until the reservior is filled
# If we are approx above to train, be sure to project all reservor points
if not newkpca:
logging.info('Clearing and Re-Projecting the entire reservoir of %d points for Bin (%d,%d).', \
rsize, A, B)
rsamp_lowdim = kpca.project(traindata)
pipe = self.catalog.pipeline()
pipe.delete('subspace:pca:%d_%d'%(A,B))
for si in rsamp_lowdim:
pipe.rpush('subspace:pca:%d_%d'%(A,B), bytes(si))
pipe.execute()
else:
logging.info('PCA Kernel is good -- no need to change them')
bench.mark('start_ProjPCA')
logging.info('Projecting %d points on Kernel PCA for Bin (%d,%d)', num_observations, A, B)
hd_pts = np.zeros(shape=((num_observations,)+alpha.xyz.shape[1:]), dtype=np.float32)
for i, index in enumerate(groupbybin[(A,B)]):
np.copyto(hd_pts[i], alpha.xyz[index])
pc_proj = kpca.project(hd_pts)
bench.mark('ProjPCA_%d_%d'%(A,B))
# 2. Append subspace in catalog
pipe = self.catalog.pipeline()
for si in pc_proj:
pipe.rpush('subspace:pca:%d_%d' % (A,B), bytes(si))
pipe.execute()
logging.debug('Updating reservoir Sample')
num_inserted[(A,B)] = reservoir.insert(res_label, hd_pts)
bench.mark('PCA')
pipe = self.catalog.pipeline()
for ab, num in num_inserted.items():
if num > 0:
pipe.rpush('subspace:pca:updates:%d_%d' % (A, B), num)
pipe.execute()
# ---- POST PROCESSING
if USE_SHM:
shutil.rmtree(ramdisk)
# shm_contents = os.listdir('/dev/shm')
shm_contents = os.listdir('/tmp')
logging.debug('Ramdisk contents (should be empty of DDC) : %s', str(shm_contents))
# For benchmarching:
# print('##', job['name'], dcdfilesize/(1024*1024*1024), traj.n_frames)
bench.show()
stat.show()
# Return # of observations (frames) processed
return [numConf]