def mvac_job_rdb_instance(context, job_id, volumes, rdb_vol_name, rdb_db, cwd):
import multyvac
layer = get_compmake_config('multyvac_layer')
if not layer:
layer = None
all_volumes = volumes + [rdb_vol_name]
command, _, _ = get_job_args(job_id, db=context.get_compmake_db())
misc = dict(deps=[command])
#print('Instancing (volumes: %r, layer=%r)' % (all_volumes, layer))
core = get_compmake_config('multyvac_core')
multyvac_job_id = multyvac.submit(mvac_job_rdb_worker,
job_id=job_id,
rdb_basepath=rdb_db.basepath,
misc=misc,
cwd=cwd,
_core=core,
_name=job_id,
_layer=layer,
_vol=all_volumes)
#print('Getting job %r' % multyvac_job_id)
multyvac_job = multyvac.get(multyvac_job_id)
#print('Got job')
return multyvac_job
def runbench(bench):
jid = multyvac.shell_submit(
"/bin/bash {}/run.sh {}".format(scripts_vol.mount_path, bench),
_name='bench1',
_core='f2',
_layer=args.layer,
_vol=[args.scripts_volume, args.results_volume])
return multyvac.get(jid)
def runbench(bench):
jid = multyvac.shell_submit(
"/bin/bash {}/run.sh {}".format(scripts_vol.mount_path, bench),
_name='bench1',
_core='f2',
_layer=args.layer,
_vol=[args.scripts_volume, args.results_volume])
return multyvac.get(jid)
def clean_cloud_out_dir(d):
d = os.path.realpath(d)
vol, _, _ = get_volume_for_dir(d)
import multyvac
multyvac_job_id = multyvac.submit(clean_cloud_out_dir_job,
d,
_vol=[vol.name],
_name='Cleaning directory %r' % d)
multyvac_job = multyvac.get(multyvac_job_id)
multyvac_job.get_result()
def clean_cloud_out_dir(d):
d = os.path.realpath(d)
vol, _, _ = get_volume_for_dir(d)
import multyvac
multyvac_job_id = multyvac.submit(clean_cloud_out_dir_job,
d,
_vol=[vol.name],
_name='Cleaning directory %r' % d)
multyvac_job = multyvac.get(multyvac_job_id)
multyvac_job.get_result()
def run(self, r, niters=10000):
"""Run each runner for `niters`, using the backend supplied in the
constructor for parallelism.
Parameters
----------
r : rng
niters : int
"""
validator.validate_type(r, rng, param_name='r')
validator.validate_positive(niters, param_name='niters')
if self._backend == 'multiprocessing':
pool = mp.Pool(processes=self._processes)
args = [(runner, niters, r.next(), None)
for runner in self._runners]
# map_async() + get() allows us to workaround a bug where
# control-C doesn't kill multiprocessing workers
self._runners = pool.map_async(_mp_work, args).get(10000000)
pool.close()
pool.join()
elif self._backend == 'multyvac':
# XXX(stephentu): the only parallelism strategy thus far is every
# runner gets a dedicated core (multicore=1) on a machine
jids = []
has_volume = bool(self._volume)
zipped = zip(self._runners, self._digests)
expensive_states = []
for i, (runner, digest) in enumerate(zipped):
if has_volume:
statearg = (self._volume, 'state-{}'.format(digest))
expensive_states.append(runner.expensive_state)
runner.expensive_state = None
else:
statearg = None
args = (runner, niters, r.next(), statearg)
jids.append(
multyvac.submit(
_mp_work,
args,
_ignore_module_dependencies=True,
_layer=self._layer,
_vol=self._volume,
_env=dict(self._env), # submit() mutates the env
_core=self._core,
_name='kernels-parallel-runner-{}'.format(i)))
self._runners = [multyvac.get(jid).get_result() for jid in jids]
if not expensive_states:
return
for runner, state in zip(self._runners, expensive_states):
runner.expensive_state = state
else:
assert False, 'should not be reached'
def run(self, r, niters=10000):
"""Run each runner for `niters`, using the backend supplied in the
constructor for parallelism.
Parameters
----------
r : rng
niters : int
"""
validator.validate_type(r, rng, param_name='r')
validator.validate_positive(niters, param_name='niters')
if self._backend == 'multiprocessing':
pool = mp.Pool(processes=self._processes)
args = [(runner, niters, r.next(), None)
for runner in self._runners]
# map_async() + get() allows us to workaround a bug where
# control-C doesn't kill multiprocessing workers
self._runners = pool.map_async(_mp_work, args).get(10000000)
pool.close()
pool.join()
elif self._backend == 'multyvac':
# XXX(stephentu): the only parallelism strategy thus far is every
# runner gets a dedicated core (multicore=1) on a machine
jids = []
has_volume = bool(self._volume)
zipped = zip(self._runners, self._digests)
expensive_states = []
for i, (runner, digest) in enumerate(zipped):
if has_volume:
statearg = (self._volume, 'state-{}'.format(digest))
expensive_states.append(runner.expensive_state)
runner.expensive_state = None
else:
statearg = None
args = (runner, niters, r.next(), statearg)
jids.append(
multyvac.submit(
_mp_work,
args,
_ignore_module_dependencies=True,
_layer=self._layer,
_vol=self._volume,
_env=dict(self._env), # submit() mutates the env
_core=self._core,
_name='kernels-parallel-runner-{}'.format(i)))
self._runners = [multyvac.get(jid).get_result() for jid in jids]
if not expensive_states:
return
for runner, state in zip(self._runners, expensive_states):
runner.expensive_state = state
else:
assert False, 'should not be reached'
def delete_db_volume(db):
vol = create_db_volume(db)
entries = vol.ls('.')
if not entries:
return
entries = [os.path.join(vol.mount_path, x['path']) for x in entries]
import multyvac
multyvac_job_id = multyvac.submit(delete_entries, entries,
_vol=[vol.name],
_name='Reset Compmake DB')
multyvac_job = multyvac.get(multyvac_job_id)
multyvac_job.get_result()
def mvac_instance(db, job_id, volumes, cwd):
import multyvac
layer = get_compmake_config('multyvac_layer')
if not layer:
layer = None
command, args, kwargs = get_cmd_args_kwargs(job_id=job_id, db=db)
core = get_compmake_config('multyvac_core')
multyvac_job_id = multyvac.submit(command, *args,
_layer=layer,
_vol=volumes,
_name=job_id,
_core=core,
**kwargs)
multyvac_job = multyvac.get(multyvac_job_id)
return multyvac_job
def mvac_instance(db, job_id, volumes, cwd):
import multyvac
layer = get_compmake_config('multyvac_layer')
if not layer:
layer = None
command, args, kwargs = get_cmd_args_kwargs(job_id=job_id, db=db)
core = get_compmake_config('multyvac_core')
multyvac_job_id = multyvac.submit(command, *args,
_layer=layer,
_vol=volumes,
_name=job_id,
_core=core,
**kwargs)
multyvac_job = multyvac.get(multyvac_job_id)
return multyvac_job
def get_results(exp_wait, exp_results):
d = pickle.load(open(exp_wait, 'r'))
chains = []
# reorg on a per-seed basis
for jid in d['jids']:
job = multyvac.get(jid)
print "getting", jid
chain_data = job.get_result()
chains.append({
'scores': chain_data[0],
'state': chain_data[1],
'times': chain_data[2],
'latents': chain_data[3]
})
pickle.dump({'chains': chains, 'exp': d}, open(exp_results, 'w'))
def get_results(exp_wait, exp_results):
d = pickle.load(open(exp_wait, 'r'))
chains = []
# reorg on a per-seed basis
for jid in d['jids']:
job = multyvac.get(jid)
print "getting", jid
chain_data = job.get_result()
chains.append({'scores' : chain_data[0],
'state' : chain_data[1],
'times' : chain_data[2],
'latents' : chain_data[3]})
pickle.dump({'chains' : chains,
'exp' : d},
open(exp_results, 'w'))
import os
import multyvac
import requests
# rackspace configuration
multyvac.config.api_key = "cloudpipe18" # Rackspace Username
multyvac.config.api_secret_key = "683df297726d4bb18c6c230e5be795fe" # Rackspace API Key
multyvac.config.api_url = "https://cloudpipe.tmpnb.org/v1"
# helpers
def status(url):
return requests.get(url).status_code
def server_header(url):
return requests.get(url).headers.get('server')
# execution
jid = multyvac.submit(status, "https://developer.rackspace.com")
print(multyvac.get(jid).get_result())
# notes about execution
# multyvac.submit(some_lambda_f, _image="some_docker_image_in_which_launch_the_job")
def synchronize_db_up(context, targets):
""" Syncrhonizes the DB up """
db = context.get_compmake_db()
# first create the volume if it doesn't exist
vol = create_db_volume(db)
# now we need to put all files
keys = []
cq = CacheQueryDB(db)
jobs = set()
jobs.update(targets)
jobs.update(cq.tree(targets))
#print('%d targets, %d jobs' % (len(targets), len(jobs)))
# XXX: not all jobs
for job_id in jobs:
resources = [job2jobargskey, job2userobjectkey,
job2cachekey, job2key]
for r in resources:
key = r(job_id)
if key in db:
keys.append(key)
#print('Found %s files to upload' % len(keys))
# Shadow storage
db2 = StorageFilesystem(basepath=vol.mount_path)
already = set([os.path.basename(x['path']) for x in vol.ls('.')])
filename2contents = {}
#print('obtained: %r' % already)
for key in keys:
f = db.filename_for_key(key)
f2 = db2.filename_for_key(key)
local_path = f
remote_path = os.path.relpath(f2, db2.basepath)
if remote_path in already:
#print('skipping %r' % local_path)
continue
size = os.stat(local_path).st_size
use_compact = size < 6*1024
if use_compact:
with open(local_path) as f:
filename2contents[f2] = f.read()
else:
#print('%s -> %s' % (local_path, remote_path))
assert os.path.join(db2.basepath, remote_path) == f2
vol.put_file(local_path, remote_path, target_mode=None)
import multyvac
multyvac_job_id = multyvac.submit(copy_files, filename2contents,
_vol=[vol.name])
multyvac_job = multyvac.get(multyvac_job_id)
multyvac_job.get_result()
return vol, db2
import os
import multyvac
import requests
# rackspace configuration
multyvac.config.api_key = "cloudpipe18" # Rackspace Username
multyvac.config.api_secret_key = "683df297726d4bb18c6c230e5be795fe" # Rackspace API Key
multyvac.config.api_url = "https://cloudpipe.tmpnb.org/v1"
# helpers
def status(url):
return requests.get(url).status_code
def server_header(url):
return requests.get(url).headers.get('server')
# execution
jid = multyvac.submit(status, "https://developer.rackspace.com")
print(multyvac.get(jid).get_result())
# notes about execution
# multyvac.submit(some_lambda_f, _image="some_docker_image_in_which_launch_the_job")
#!/usr/bin/env python
# CLOUDPIPE_URL=http://`echo $DOCKER_HOST | cut -d ":" -f2 | tr -d "/"`:8000/v1 python2 script/sample/submitpython.py
from __future__ import print_function
import multyvac
import os
# Grab from the CLOUDPIPE_URL environment variable, otherwise assume they have
# /etc/hosts configured to point to their docker
api_url = os.environ.get('CLOUDPIPE_URL', 'http://docker:8000/v1')
multyvac.config.set_key(api_key='admin', api_secret_key='12345', api_url=api_url)
def add(a, b):
return a + b
jid = multyvac.submit(add, 3, 4)
result = multyvac.get(jid).get_result()
print("added {} and {} to get {}... in the cloud!".format(3,4,result))
"cmd": 'echo "success" > /tmp/out',
"_result_source": "file:/tmp/out",
},
"stdin": {
"cmd": 'cat',
"_stdin": "success",
},
}
longest = 0
for name in jobs.keys():
if len(name) > longest:
longest = len(name)
success = 0
failure = 0
for (name, kwargs) in jobs.items():
jid = multyvac.shell_submit(**kwargs)
print("{:<{}}: job {} ...".format(name, longest, jid), end='')
result = multyvac.get(jid).get_result().strip('\n')
print(" result [{}]".format(result))
if result == "success":
success += 1
else:
failure += 1
print("{} pass / {} fail".format(success, failure))
if failure > 0:
sys.exit(1)
#!/usr/bin/env python
from __future__ import print_function
import multyvac
multyvac.config.set_key(api_key='admin',
api_secret_key='12345',
api_url='http://docker:8000/v1')
def add(a, b):
return a + b
jid = multyvac.submit(add, 3, 4)
result = multyvac.get(jid).get_result()
print("result = {}".format(result))
#!/usr/bin/env python
# CLOUDPIPE_URL=http://`echo $DOCKER_HOST | cut -d ":" -f2 | tr -d "/"`:8000/v1 python2 script/sample/submitpython.py
from __future__ import print_function
import multyvac
import os
# Grab from the CLOUDPIPE_URL environment variable, otherwise assume they have
# /etc/hosts configured to point to their docker
api_url = os.environ.get('CLOUDPIPE_URL', 'http://docker:8000/v1')
multyvac.config.set_key(api_key='admin', api_secret_key='12345', api_url=api_url)
def add(a, b):
return a + b
jid = multyvac.submit(add, 3, 4, _layer="ubuntu:14.04")
job = multyvac.get(jid)
job.wait()
job = multyvac.get(jid)
print("Job's stderr:\n\t{}".format(job.stderr)) # Says python is unavailable
"cmd": 'echo "success" > /tmp/out',
"_result_source": "file:/tmp/out",
},
"stdin": {
"cmd": 'cat',
"_stdin": "success",
},
}
longest = 0
for name in jobs.keys():
if len(name) > longest:
longest = len(name)
success = 0
failure = 0
for (name, kwargs) in jobs.items():
jid = multyvac.shell_submit(**kwargs)
print("{:<{}}: job {} ...".format(name, longest, jid), end='')
result = multyvac.get(jid).get_result().strip('\n')
print(" result [{}]".format(result))
if result == "success":
success += 1
else:
failure += 1
print("{} pass / {} fail".format(success, failure))
if failure > 0:
sys.exit(1)
#!/usr/bin/env python
from __future__ import print_function
import multyvac
import time
import sys
multyvac.config.set_key(api_key='admin', api_secret_key='12345', api_url='http://docker:8000/v1')
def longtime(seconds):
print("Getting started")
sys.stdout.flush()
for i in xrange(0, seconds):
time.sleep(1)
print("{} seconds".format(i))
sys.stdout.flush()
jid = multyvac.submit(longtime, 30)
time.sleep(5)
multyvac.kill(jid)
time.sleep(1)
j = multyvac.get(jid)
print("job = {}, status = {}".format(j, j.status))
#!/usr/bin/env python
# CLOUDPIPE_URL=http://`echo $DOCKER_HOST | cut -d ":" -f2 | tr -d "/"`:8000/v1 python2 script/sample/submitpython.py
from __future__ import print_function
import multyvac
import os
# Grab from the CLOUDPIPE_URL environment variable, otherwise assume they have
# /etc/hosts configured to point to their docker
api_url = os.environ.get("CLOUDPIPE_URL", "http://docker:8000/v1")
multyvac.config.set_key(api_key="admin", api_secret_key="12345", api_url=api_url)
def add(a, b):
return a + b
jid = multyvac.submit(add, 3, 4, _layer="ubuntu:14.04")
job = multyvac.get(jid)
job.wait()
job = multyvac.get(jid)
print("Job's stderr:\n\t{}".format(job.stderr)) # Says python is unavailable
def main():
gdal.AllRegister()
path = auxil.select_directory('Choose input directory')
if path:
os.chdir(path)
# input image
infile = auxil.select_infile(title='Choose image file')
if infile:
inDataset = gdal.Open(infile,GA_ReadOnly)
cols = inDataset.RasterXSize
rows = inDataset.RasterYSize
bands = inDataset.RasterCount
projection = inDataset.GetProjection()
geotransform = inDataset.GetGeoTransform()
if geotransform is not None:
gt = list(geotransform)
else:
print 'No geotransform available'
return
imsr = osr.SpatialReference()
imsr.ImportFromWkt(projection)
else:
return
pos = auxil.select_pos(bands)
if not pos:
return
N = len(pos)
rasterBands = []
for b in pos:
rasterBands.append(inDataset.GetRasterBand(b))
# training data (shapefile)
trnfile = auxil.select_infile(filt='.shp',title='Choose train shapefile')
if trnfile:
trnDriver = ogr.GetDriverByName('ESRI Shapefile')
trnDatasource = trnDriver.Open(trnfile,0)
trnLayer = trnDatasource.GetLayer()
trnsr = trnLayer.GetSpatialRef()
else:
return
# hidden neurons
L = auxil.select_integer(8,'number of hidden neurons')
if not L:
return
# outfile
outfile, fmt = auxil.select_outfilefmt()
if not outfile:
return
# coordinate transformation from training to image projection
ct= osr.CoordinateTransformation(trnsr,imsr)
# number of classes
feature = trnLayer.GetNextFeature()
while feature:
classid = feature.GetField('CLASS_ID')
feature = trnLayer.GetNextFeature()
trnLayer.ResetReading()
K = int(classid)+1
print '========================='
print ' ffncg'
print '========================='
print time.asctime()
print 'image: '+infile
print 'training: '+trnfile
# loop through the polygons
Gs = [] # train observations
ls = [] # class labels
print 'reading training data...'
for i in range(trnLayer.GetFeatureCount()):
feature = trnLayer.GetFeature(i)
classid = feature.GetField('CLASS_ID')
l = [0 for i in range(K)]
l[int(classid)] = 1.0
polygon = feature.GetGeometryRef()
# transform to same projection as image
polygon.Transform(ct)
# convert to a Shapely object
poly = shapely.wkt.loads(polygon.ExportToWkt())
# transform the boundary to pixel coords in numpy
bdry = np.array(poly.boundary)
bdry[:,0] = bdry[:,0]-gt[0]
bdry[:,1] = bdry[:,1]-gt[3]
GT = np.mat([[gt[1],gt[2]],[gt[4],gt[5]]])
bdry = bdry*np.linalg.inv(GT)
# polygon in pixel coords
polygon1 = asPolygon(bdry)
# raster over the bounding rectangle
minx,miny,maxx,maxy = map(int,list(polygon1.bounds))
pts = []
for i in range(minx,maxx+1):
for j in range(miny,maxy+1):
pts.append((i,j))
multipt = MultiPoint(pts)
# intersection as list
intersection = np.array(multipt.intersection(polygon1),dtype=np.int).tolist()
# cut out the bounded image cube
cube = np.zeros((maxy-miny+1,maxx-minx+1,len(rasterBands)))
k=0
for band in rasterBands:
cube[:,:,k] = band.ReadAsArray(minx,miny,maxx-minx+1,maxy-miny+1)
k += 1
# get the training vectors
for (x,y) in intersection:
Gs.append(cube[y-miny,x-minx,:])
ls.append(l)
polygon = None
polygon1 = None
feature.Destroy()
trnDatasource.Destroy()
m = len(ls)
print str(m) + ' training pixel vectors were read in'
Gs = np.array(Gs)
ls = np.array(ls)
# stretch the pixel vectors to [-1,1]
maxx = np.max(Gs,0)
minx = np.min(Gs,0)
for j in range(N):
Gs[:,j] = 2*(Gs[:,j]-minx[j])/(maxx[j]-minx[j]) - 1.0
# random permutation of training data
idx = np.random.permutation(m)
Gs = Gs[idx,:]
ls = ls[idx,:]
# setup output dataset
driver = gdal.GetDriverByName(fmt)
outDataset = driver.Create(outfile,cols,rows,1,GDT_Byte)
projection = inDataset.GetProjection()
geotransform = inDataset.GetGeoTransform()
if geotransform is not None:
outDataset.SetGeoTransform(tuple(gt))
if projection is not None:
outDataset.SetProjection(projection)
outBand = outDataset.GetRasterBand(1)
# train on 9/10 training examples
Gstrn = Gs[0:9*m//10,:]
lstrn = ls[0:9*m//10,:]
affn = Ffncg(Gstrn,lstrn,L)
print 'training on %i pixel vectors...' % np.shape(Gstrn)[0]
start = time.time()
cost = affn.train(epochs=epochs)
print 'elapsed time %s' %str(time.time()-start)
if cost is not None:
# cost = np.log10(cost)
ymax = np.max(cost)
ymin = np.min(cost)
xmax = len(cost)
plt.plot(range(xmax),cost,'k')
plt.axis([0,xmax,ymin-1,ymax])
plt.title('Cross entropy')
plt.xlabel('Epoch')
# classify the image
print 'classifying...'
tile = np.zeros((cols,N))
for row in range(rows):
for j in range(N):
tile[:,j] = rasterBands[j].ReadAsArray(0,row,cols,1)
tile[:,j] = 2*(tile[:,j]-minx[j])/(maxx[j]-minx[j]) - 1.0
cls, _ = affn.classify(tile)
outBand.WriteArray(np.reshape(cls,(1,cols)),0,row)
outBand.FlushCache()
outDataset = None
inDataset = None
print 'thematic map written to: ' + outfile
print 'please close the cross entropy plot to continue'
plt.show()
else:
print 'an error occured'
return
print 'submitting cross-validation to multyvac'
start = time.time()
jid = mv.submit(traintst,Gs,ls,L,_layer='ms_image_analysis')
print 'submission time: %s' %str(time.time()-start)
start = time.time()
job = mv.get(jid)
result = job.get_result(job)
print 'execution time: %s' %str(time.time()-start)
print 'misclassification rate: %f' %np.mean(result)
print 'standard deviation: %f' %np.std(result)
print '--------done---------------------'
