def process(self, item):
job = item.jobObj
## It is very likely that the job's downloading task has been created
## and assigned in a previous monitoring loop ignore such kind of cases
if job.status in ['completing', 'completed', 'failed']:
return True
job.updateStatus('completing')
try:
logger.info("poststaging output sandbox files")
logger.info(" * %s", saga.url(job.backend.saga_job_out).url)
stdout = saga.filesystem.file(saga.url(job.backend.saga_job_out))
stdout.copy("file://localhost/" +
job.getOutputWorkspace().getPath() + "stdout")
logger.info(" * %s", saga.url(job.backend.saga_job_err).url)
stderr = saga.filesystem.file(saga.url(job.backend.saga_job_err))
stderr.copy("file://localhost/" +
job.getOutputWorkspace().getPath() + "stderr")
if len(job.outputsandbox) > 0:
output_sandbox = saga.url(job.backend.filesystem_url + "/" +
job.backend.workdir_uuid +
"/_output_sandbox.tgz")
logger.info(" * %s", output_sandbox.url)
osb = saga.filesystem.file(output_sandbox)
osb.copy("file://localhost/" +
job.getOutputWorkspace().getPath())
## Unpack the output sandbox and delete the archive
osbpath = job.getOutputWorkspace().getPath(
) + "_output_sandbox.tgz"
if os.path.exists(osbpath):
if os.system("tar -C %s -xzf %s" %
(job.getOutputWorkspace().getPath(),
job.getOutputWorkspace().getPath() +
"/_output_sandbox.tgz")) != 0:
job.updateStatus('failed')
raise Exception('cannot upack output sandbox')
os.remove(osbpath)
job.updateStatus('completed')
except saga.exception as e:
logger.error('exception caught while poststaging: %s',
e.get_full_message())
job.updateStatus('failed')
return True
def process(self, item):
job = item.jobObj
## It is very likely that the job's downloading task has been created
## and assigned in a previous monitoring loop ignore such kind of cases
if job.status in ['completing', 'completed', 'failed']:
return True
job.updateStatus('completing')
try:
logger.info("poststaging output sandbox files")
logger.info(" * %s", saga.url(job.backend.saga_job_out).url)
stdout = saga.filesystem.file(saga.url(job.backend.saga_job_out));
stdout.copy("file://localhost/"+job.getOutputWorkspace().getPath()+"stdout");
logger.info(" * %s", saga.url(job.backend.saga_job_err).url)
stderr = saga.filesystem.file(saga.url(job.backend.saga_job_err));
stderr.copy("file://localhost/"+job.getOutputWorkspace().getPath()+"stderr");
if len(job.outputsandbox) > 0 :
output_sandbox = saga.url(job.backend.filesystem_url+"/"+job.backend.workdir_uuid+"/_output_sandbox.tgz")
logger.info(" * %s", output_sandbox.url)
osb = saga.filesystem.file(output_sandbox)
osb.copy("file://localhost/"+job.getOutputWorkspace().getPath())
## Unpack the output sandbox and delete the archive
osbpath = job.getOutputWorkspace().getPath()+"_output_sandbox.tgz"
if os.path.exists(osbpath):
if os.system("tar -C %s -xzf %s"%(job.getOutputWorkspace().getPath(),job.getOutputWorkspace().getPath()+"/_output_sandbox.tgz")) != 0:
job.updateStatus('failed')
raise Exception('cannot upack output sandbox')
os.remove(osbpath)
job.updateStatus('completed')
except saga.exception as e:
logger.error('exception caught while poststaging: %s', e.get_full_message())
job.updateStatus('failed')
return True
def prestagesandbox(self, jobconfig):
job = self.getJobObject()
mon = job.getMonitoringService()
inw = job.getInputWorkspace()
sandbox_files = jobconfig.getSandboxFiles()
logger.info("pre-staging files for saga job with id: %s", job.id)
## Compression is ENABLED. All input sandbox files are archived
## into an uncompressed tarball which is then transfered to the
## execution host. This speeds up things a lot in many scenarios.
##
if self.enable_compression:
logger.info(" * adding %s user defined files to input sandbox", len(sandbox_files))
import Ganga.Core.Sandbox as Sandbox
compressed_input_sandbox = job.createPackedInputSandbox(
jobconfig.getSandboxFiles()
+ Sandbox.getGangaModulesAsSandboxFiles(Sandbox.getDefaultModules())
+ Sandbox.getGangaModulesAsSandboxFiles(mon.getSandboxModules())
)
try:
for f in compressed_input_sandbox:
archive_url = saga.url("file://localhost/" + f)
logger.info(
" * copying %s -> %s ", archive_url.url, self.filesystem_url + "/" + self.workdir_uuid + "/"
)
sf = saga.filesystem.file(archive_url.url)
sf.copy(self.filesystem_url + "/" + self.workdir_uuid + "/", saga.filesystem.Overwrite)
except saga.exception as e:
logger.error("exception caught while transfering file: %s", e.get_all_exceptions())
job.updateStatus("failed")
return False
## Compression is DISABLED. All input sandbox files are transfered
## one-by-one to the execution host. This can be very slow, especially
## if SAGA is using the Globus GridFTP adaptor.
else:
logger.info("prestaging %s input sandbox files", len(sandbox_files))
for f in sandbox_files:
try:
source = saga.url(f.name)
if len(source.scheme) == 0:
source.scheme = "file"
if len(source.host) == 0:
source.host = "localhost"
if f.subdir != ".": # create subdirectory & copy
target = saga.url(self.filesystem_url + "/" + self.workdir_uuid + "/" + f.subdir + "/")
sd = saga.filesystem.directory(target, saga.filesystem.Create)
sf = saga.filesystem.file(source)
logger.info(" * copying %s -> %s ", source, target)
sf.copy(target, saga.filesystem.Overwrite) # copy the file
else: # copy to remote work dir
logger.info(
" * copying %s -> %s ", source, self.filesystem_url + "/" + self.workdir_uuid + "/"
)
sf = saga.filesystem.file(source)
sf.copy(self.filesystem_url + "/" + self.workdir_uuid + "/", saga.filesystem.Overwrite)
except saga.exception as e:
logger.error("exception caught while transfering file: %s", e.get_all_exceptions())
job.updateStatus("failed")
return False
##
## copy the job script
##
try:
jobscript_path = saga.url("file://localhost/" + inw.getPath() + "/__jobscript__")
if os.path.exists(jobscript_path.path):
logger.info(
" * copying %s -> %s ", jobscript_path.url, self.filesystem_url + "/" + self.workdir_uuid + "/"
)
sf = saga.filesystem.file(jobscript_path.url)
sf.copy(self.filesystem_url + "/" + self.workdir_uuid + "/", saga.filesystem.Overwrite)
except saga.exception as e:
logger.error("exception caught while transfering file: %s", e.get_all_exceptions())
job.updateStatus("failed")
return False
return True
def prestagesandbox(self, jobconfig):
job = self.getJobObject()
mon = job.getMonitoringService()
inw = job.getInputWorkspace()
sandbox_files = jobconfig.getSandboxFiles()
logger.info("pre-staging files for saga job with id: %s", job.id)
## Compression is ENABLED. All input sandbox files are archived
## into an uncompressed tarball which is then transfered to the
## execution host. This speeds up things a lot in many scenarios.
##
if self.enable_compression:
logger.info(" * adding %s user defined files to input sandbox",
len(sandbox_files))
import Ganga.Core.Sandbox as Sandbox
from Ganga.GPIDev.Lib.File import File
from Ganga.Core.Sandbox.WNSandbox import PYTHON_DIR
import inspect
fileutils = File(inspect.getsourcefile(Ganga.Utility.files),
subdir=PYTHON_DIR)
compressed_input_sandbox = job.createPackedInputSandbox(
jobconfig.getSandboxFiles() + [fileutils])
try:
for f in compressed_input_sandbox:
archive_url = saga.url("file://localhost/" + f)
logger.info(
" * copying %s -> %s ", archive_url.url,
self.filesystem_url + "/" + self.workdir_uuid + "/")
sf = saga.filesystem.file(archive_url.url)
sf.copy(
self.filesystem_url + "/" + self.workdir_uuid + "/",
saga.filesystem.Overwrite)
except saga.exception as e:
logger.error('exception caught while transfering file: %s',
e.get_all_exceptions())
job.updateStatus("failed")
return False
## Compression is DISABLED. All input sandbox files are transfered
## one-by-one to the execution host. This can be very slow, especially
## if SAGA is using the Globus GridFTP adaptor.
else:
logger.info("prestaging %s input sandbox files",
len(sandbox_files))
for f in sandbox_files:
try:
source = saga.url(f.name)
if (len(source.scheme) == 0):
source.scheme = "file"
if (len(source.host) == 0):
source.host = "localhost"
if (f.subdir != '.'): # create subdirectory & copy
target = saga.url(self.filesystem_url + "/" +
self.workdir_uuid + "/" + f.subdir +
"/")
sd = saga.filesystem.directory(target,
saga.filesystem.Create)
sf = saga.filesystem.file(source)
logger.info(" * copying %s -> %s ", source, target)
sf.copy(target,
saga.filesystem.Overwrite) # copy the file
else: # copy to remote work dir
logger.info(
" * copying %s -> %s ", source,
self.filesystem_url + "/" + self.workdir_uuid +
"/")
sf = saga.filesystem.file(source)
sf.copy(
self.filesystem_url + "/" + self.workdir_uuid +
"/", saga.filesystem.Overwrite)
except saga.exception as e:
logger.error('exception caught while transfering file: %s',
e.get_all_exceptions())
job.updateStatus("failed")
return False
##
## copy the job script
##
try:
jobscript_path = saga.url("file://localhost/" + inw.getPath() +
"/__jobscript__")
if os.path.exists(jobscript_path.path):
logger.info(
" * copying %s -> %s ", jobscript_path.url,
self.filesystem_url + "/" + self.workdir_uuid + "/")
sf = saga.filesystem.file(jobscript_path.url)
sf.copy(self.filesystem_url + "/" + self.workdir_uuid + "/",
saga.filesystem.Overwrite)
except saga.exception as e:
logger.error('exception caught while transfering file: %s',
e.get_all_exceptions())
job.updateStatus("failed")
return False
return True
