def create_temp_file(extension):
if LOCATION == 'home':
return mkstemp_safe(HOME_TEMP_PATH, extension)
else:
return mkstemp_safe(LOCAL_TEMP_PATH, extension)
def run_batch_locally(scripts, language='python', paths=[], max_cpu=0.9, max_mem=0.9, submit_sleep=1, job_check_sleep=30, \
verbose=True, max_files_open=100, max_running_jobs=10, single_thread=True):
'''
Receives a list of python scripts to run
Assumes the code has an output file that will be managed by this function
Returns a list of local file names where the code has presumably stored output
'''
# Define some code constants
#### Do we need to set paths explicitly?
#### This will be deprecated in future MATLAB - hopefully the -singleCompThread command is sufficient
matlab_single_thread = '''
maxNumCompThreads(1);
'''
python_path_code = '''
import sys
sys.path.append('%s')
'''
matlab_path_code = '''
addpath(genpath('%s'))
'''
python_completion_code = '''
print 'Writing completion flag'
with open('%(flag_file)s', 'w') as f:
f.write('Goodbye, World')
print "Goodbye, World"
quit()
'''
#### TODO - Is this completely stable
matlab_completion_code = '''
fprintf('\\nWriting completion flag\\n');
ID = fopen('%(flag_file)s', 'w');
fprintf(ID, 'Goodbye, world');
fclose(ID);
fprintf('\\nGoodbye, World\\n');
quit()
'''
# Initialise lists of file locations job ids
shell_files = [None] * len(scripts)
script_files = [None] * len(scripts)
output_files = [None] * len(scripts)
stdout_files = [None] * len(scripts)
stdout_file_handles = [None] * len(scripts)
flag_files = [None] * len(scripts)
processes = [None] * len(scripts)
fear_finished = False
job_finished = [False] * len(scripts)
files_open = 0
# Loop through jobs, submitting jobs whenever CPU usage low enough, re-submitting failed jobs
if not verbose:
prog = Progress(len(scripts))
while not fear_finished:
should_sleep = True
for (i, code) in enumerate(scripts):
if (not job_finished[i]) and (processes[i] is None) and (
files_open <= max_files_open) and (len([
1 for p in processes if not p is None
]) < max_running_jobs):
# This script has not been run - check CPU and potentially run
#### FIXME - Merge if statements
if (psutil.cpu_percent() < max_cpu * 100) and (
psutil.virtual_memory().percent < max_mem * 100):
# Jobs can run
should_sleep = False
# Get the job ready
if LOCATION == 'local':
temp_dir = LOCAL_TEMP_PATH
else:
temp_dir = HOME_TEMP_PATH
if language == 'python':
script_files[i] = (mkstemp_safe(temp_dir, '.py'))
elif language == 'matlab':
script_files[i] = (mkstemp_safe(temp_dir, '.m'))
# Create necessary files in local path
shell_files[i] = (mkstemp_safe(temp_dir, '.sh'))
output_files[i] = (mkstemp_safe(temp_dir, '.out'))
stdout_files[i] = (mkstemp_safe(temp_dir, '.o'))
flag_files[i] = (mkstemp_safe(temp_dir, '.flg'))
# Customise code
#### TODO - make path and output_transfer optional
if language == 'python':
code = code + python_completion_code
for path in paths:
code = (python_path_code % path) + code
elif language == 'matlab':
code = code + matlab_completion_code
for path in paths:
code = (matlab_path_code % path) + code
code = code % {
'output_file': output_files[i],
'flag_file': flag_files[i]
}
# Write code and shell file
with open(script_files[i], 'w') as f:
f.write(code)
with open(shell_files[i], 'w') as f:
#### TODO - is os.path.join always correct - what happens if this program is being run on windows?
if language == 'python':
f.write('python ' + script_files[i] + '\n')
elif language == 'matlab':
if LOCATION == 'home':
matlab_path = HOME_MATLAB
else:
matlab_path = LOCAL_MATLAB
if single_thread:
f.write('cd ' + os.path.split(script_files[i])[0] + ';\n' + matlab_path + ' -nosplash -nojvm -nodisplay -singleCompThread -r ' + \
os.path.split(script_files[i])[-1].split('.')[0] + '\n')
else:
f.write('cd ' + os.path.split(script_files[i])[0] + ';\n' + matlab_path + ' -nosplash -nojvm -nodisplay -r ' + \
os.path.split(script_files[i])[-1].split('.')[0] + '\n')
# Start running the job
if verbose:
print 'Submitting job %d of %d' % (i + 1, len(scripts))
stdout_file_handles[i] = open(stdout_files[i], 'w')
files_open = files_open + 1
#processes[i] = subprocess.Popen(['sh', shell_files[i]], stdout = stdout_file_handles[i]);
with open(shell_files[i], 'r') as shell_file:
lines = [
line.rstrip() for line in shell_file.readlines()
]
processes[i] = subprocess.Popen(
' '.join(lines),
shell=True,
stdout=stdout_file_handles[i])
# Sleep for a bit so the process can kick in (prevents 100s of jobs being sent to processor)
time.sleep(submit_sleep)
elif (not job_finished[i]) and (not processes[i] is None):
# Ask the process how its doing
processes[i].poll()
# Check to see if the process has completed
if not processes[i].returncode is None:
if os.path.isfile(flag_files[i]):
job_finished[i] = True
if verbose:
print 'Job %d of %d has completed' % (i + 1,
len(scripts))
else:
prog.tick()
else:
if verbose:
print 'Job %d has failed - will try again later' % i + 1
processes[i] = None
# Tidy up temp files
os.remove(script_files[i])
os.remove(shell_files[i])
stdout_file_handles[i].close()
files_open = files_open - 1
os.remove(stdout_files[i])
os.remove(flag_files[i])
processes[i] = None
# Something useful happened
should_sleep = False
if all(job_finished):
fear_finished = True
if not verbose:
prog.done()
elif should_sleep:
# Count how many jobs are queued
n_queued = 0
# Count how many jobs are running
n_running = 0
if verbose:
# print '%d jobs running' % n_running
# print '%d jobs queued' % n_queued
print 'Sleeping for %d seconds' % job_check_sleep
time.sleep(job_check_sleep)
#### TODO - return job output and error files as applicable (e.g. there may be multiple error files associated with one script)
return output_files
def run_batch_on_fear(scripts,
language='python',
job_check_sleep=30,
file_copy_timeout=300,
max_jobs=500,
verbose=True,
zip_files=False):
'''
Receives a list of python scripts to run
Assumes the code has an output file - i.e. %(output_file)s - that will be managed by this function
Returns a list of local file names where the code has presumably stored output
'''
# Define some code constants
#### TODO - this path adding code should accept an optional list of paths
python_path_code = '''
import sys
sys.path.append('%s')
''' % REMOTE_PYTHON_PATH
#### This will be deprecated in future MATLAB - hopefully the -singleCompThread command is sufficient
#### TODO - No longer used? Remove?
matlab_single_thread = '''
maxNumCompThreads(1);
'''
matlab_path_code = '''
addpath(genpath('%s'))
''' % REMOTE_MATLAB_PATH
#### TODO - allow port forwarding / tunneling - copy to machine on network with more disk space than fear, then copy from that machine?
#### FIXME - Now does port forwarding but with fixed port numbers = bad
#### TODO - Fix port forard leak
if LOCATION == 'home':
python_transfer_code = '''
from subprocess_timeout import timeoutCommand
import subprocess
print "Setting up port forwarding"
if subprocess.Popen("netstat -an | grep %(r2rport)d | grep LISTEN", shell=True, stdout=subprocess.PIPE).communicate()[0] == '':
timeoutCommand(cmd='ssh -i %(rsa_remote)s -N -f -L %(r2rport)d:localhost:%(r2hport)d %(username)s@fear').run(timeout=%(timeout)d)
print "Moving output file"
if not timeoutCommand(cmd='scp -P %(r2rport)d -i %(rsa_home)s %(output_file)s %(home_user)s@localhost:%(local_temp_path)s; rm %(output_file)s').run(timeout=%(timeout)d)[0]:
raise RuntimeError('Copying output raised error or timed out')
''' % {
'rsa_remote': REMOTE_TO_REMOTE_KEY_FILE,
'r2rport': REMOTE_TO_REMOTE_PORT,
'r2hport': REMOTE_TO_HOME_PORT,
'username': USERNAME,
'timeout': file_copy_timeout,
'rsa_home': REMOTE_TO_HOME_KEY_FILE,
'output_file': '%(output_file)s',
'home_user': HOME_USERNAME,
'local_temp_path': HOME_TEMP_PATH
}
else:
python_transfer_code = '''
#from util import timeoutCommand
from subprocess_timeout import timeoutCommand
print "Moving output file"
if not timeoutCommand(cmd='scp -i %(rsa_key)s %(output_file)s %(username)s@%(local_host)s:%(local_temp_path)s; rm %(output_file)s').run(timeout=%(timeout)d)[0]:
raise RuntimeError('Copying output raised error or timed out')
''' % {
'rsa_key': REMOTE_TO_LOCAL_KEY_FILE,
'output_file': '%(output_file)s',
'username': USERNAME,
'local_host': LOCAL_HOST,
'local_temp_path': LOCAL_TEMP_PATH,
'timeout': file_copy_timeout
}
#### TODO - make this location independent
#### TODO - does this suffer from the instabilities that lead to the verbosity of the python command above
if LOCATION == 'home':
matlab_transfer_code = '''
[status, result] = system('netstat -an | grep %(r2rport)d | grep LISTEN')
if isempty(strfind(result, 'LISTEN'))
system('ssh -i %(rsa_remote)s -N -f -L %(r2rport)d:localhost:%(r2hport)d %(username)s@fear')
end
system('scp -o ConnectTimeout=%(timeout)d -P %(r2rport)d -i %(rsa_home)s %(output_file)s %(home_user)s@localhost:%(local_temp_path)s; rm %(output_file)s')
''' % {
'rsa_remote': REMOTE_TO_REMOTE_KEY_FILE,
'r2rport': REMOTE_TO_REMOTE_PORT,
'r2hport': REMOTE_TO_HOME_PORT,
'username': USERNAME,
'timeout': file_copy_timeout,
'rsa_home': REMOTE_TO_HOME_KEY_FILE,
'output_file': '%(output_file)s',
'home_user': HOME_USERNAME,
'local_temp_path': HOME_TEMP_PATH
}
else:
matlab_transfer_code = '''
system('scp -o ConnectTimeout=%(timeout)d -i %(rsa_key)s %(output_file)s %(username)s@%(local_host)s:%(local_temp_path)s; rm %(output_file)s')
''' % {
'rsa_key': REMOTE_TO_LOCAL_KEY_FILE,
'output_file': '%(output_file)s',
'username': USERNAME,
'timeout': file_copy_timeout,
'local_host': LOCAL_HOST,
'local_temp_path': LOCAL_TEMP_PATH
}
# python_completion_code = '''
#print 'Writing completion flag'
#with open('%(flag_file)s', 'w') as f:
# f.write('Goodbye, World')
#print "I'll bite your legs off!"
#quit()
#'''
python_completion_code = '''
print "I will bite your legs off!"
quit()
'''
#### TODO - Is this completely stable
# matlab_completion_code = '''
#fprintf('\\nWriting completion flag\\n');
#ID = fopen('%(flag_file)s', 'w');
#fprintf(ID, 'Goodbye, world');
#fclose(ID);
#fprintf('\\nGoodbye, World\\n');
#quit()
#'''
matlab_completion_code = """
fprintf('\\nGoodbye, World\\n');
quit()
"""
# Open a connection to fear as a with block - ensures connection is closed
with pyfear.fear(via_gate=(LOCATION == 'home')) as fear:
# Initialise lists of file locations job ids
shell_files = [None] * len(scripts)
script_files = [None] * len(scripts)
output_files = [None] * len(scripts)
stdout_files = [None] * len(scripts)
flag_files = [None] * len(scripts)
job_ids = [None] * len(scripts)
fear_finished = False
job_finished = [False] * len(scripts)
# Modify all scripts and create local temporary files
#### TODO - Writing to the network can be slow
#### - Perhaps it would be better writing to local disk followed by a block file transfer (is this possible?)
#### - Would make sense to do this when reading output files as well - perhaps this should be provided in this module?
if LOCATION == 'local':
temp_dir = LOCAL_TEMP_PATH
else:
temp_dir = HOME_TEMP_PATH
if verbose:
print 'Writing temporary files locally'
for (i, code) in enumerate(scripts):
if language == 'python':
script_files[i] = mkstemp_safe(temp_dir, '.py')
elif language == 'matlab':
script_files[i] = mkstemp_safe(temp_dir, '.m')
shell_files[i] = mkstemp_safe(temp_dir, '.sh')
output_files[i] = mkstemp_safe(temp_dir, '.out')
flag_files[i] = mkstemp_safe(temp_dir, '.flg')
# Customise code (path, transfer of output back to local host, flag file writing)
#### TODO - make path and output_transfer optional
if language == 'python':
code = python_path_code + code + python_transfer_code + python_completion_code
elif language == 'matlab':
code = matlab_path_code + code + matlab_transfer_code + matlab_completion_code
#code = code % {'output_file': os.path.join(REMOTE_TEMP_PATH, os.path.split(output_files[i])[-1]),
# 'flag_file' : os.path.join(REMOTE_TEMP_PATH, os.path.split(flag_files[i])[-1])}
code = code % {
'output_file':
os.path.join(REMOTE_SCRATCH_PATH,
os.path.split(output_files[i])[-1])
}
# Write code and shell file
with open(script_files[i], 'w') as f:
f.write(code)
with open(shell_files[i], 'w') as f:
#### TODO - is os.path.join always correct - what happens if this program is being run on windows?
if language == 'python':
f.write('python ' +
os.path.join(REMOTE_TEMP_PATH,
os.path.split(script_files[i])[-1]) +
'\n')
elif language == 'matlab':
f.write('cd ' + REMOTE_TEMP_PATH + ';\n' + REMOTE_MATLAB + ' -nosplash -nojvm -nodisplay -singleCompThread -r ' + \
os.path.split(script_files[i])[-1].split('.')[0] + '\n')
# Zip and send files
if zip_files:
if verbose:
print 'Zipping files'
zip_file_name = mkstemp_safe(temp_dir, '.zip')
zf = zipfile.ZipFile(zip_file_name, mode='w')
for script in script_files:
zf.write(script,
arcname=(os.path.split(script)[-1]),
compress_type=zipfile.ZIP_DEFLATED)
for shell in shell_files:
zf.write(shell,
arcname=(os.path.split(shell)[-1]),
compress_type=zipfile.ZIP_DEFLATED)
zf.close()
if verbose:
print 'Sending zip file to fear'
fear.copy_to_temp(zip_file_name)
if verbose:
print 'Unzipping on fear'
fear.command(
'cd %(temp_path)s ; unzip %(zip_file)s ; rm %(zip_file)s' % {
'temp_path': REMOTE_TEMP_PATH,
'zip_file': os.path.split(zip_file_name)[-1]
})
# Loop through jobs, submitting jobs whenever fear usage low enough, re-submitting failed jobs
print 'Submitting %d jobs' % len(scripts)
while not fear_finished:
# Update knowledge of fear - trying to limit communication
fear.qstat()
jobs_alive = fear.jobs_alive(update=False)
# Sleep unless anything happens
should_sleep = True
for i in range(len(scripts)): # Make me more pythonic with zipping
#fear.qstat()
#jobs_alive = fear.jobs_alive(update=False)
# Does the job need to be run and can we run it?
if (not job_finished[i]) and (job_ids[i] is None) and (
jobs_alive <= max_jobs):
# Something has happened
should_sleep = False
# Transfer files to fear
if not zip_files:
fear.copy_to_temp(script_files[i])
fear.copy_to_temp(shell_files[i])
# Submit the job to fear
if verbose:
print 'Submitting job %d of %d' % (i + 1,
len(scripts)),
job_ids[i] = fear.qsub(
os.path.join(REMOTE_TEMP_PATH,
os.path.split(shell_files[i])[-1]),
verbose=verbose) # Hide path constant
# Increment job count
jobs_alive += 1
#### FIXME - This was an attempt at better utilisation of fear - back fired since calling qstat is slow - correct solution is to have job sending and job completion checking in different threads - but would need to be carerful with the shared lists
#for j in range(len(scripts)):
# if (not job_finished[j]) and (job_ids[j] is None) and (jobs_alive <= max_jobs):
# # Something has happened
# should_sleep = False
# # Transfer files to fear
# if not zip_files:
# fear.copy_to_temp(script_files[j])
# fear.copy_to_temp(shell_files[j])
# # Submit the job to fear
# print 'Submitting job %d of %d' % (j + 1, len(scripts))
# job_ids[j] = fear.qsub(os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[j])[-1]), verbose=verbose) # Hide path constant
# # Increment job count
# jobs_alive += 1
# Otherwise was it running last we checked?
elif (not job_finished[i]) and (not job_ids[i] is None):
#if (not job_finished[i]) and (not job_ids[i] is None):
# Has the process terminated?
if fear.job_terminated(job_ids[i], update=False):
# Decrement job count
#jobs_alive -= 1 - would not have been counted earlier
should_sleep = False
# Has the job failed to write a flag or is the output file empty
#### FIXME - If LOCATION=='home' need to check .out file on local is non-empty
#### TODO - Can likely increase speed by checking status of files (on fear and local) in one block - not sure how to do it though
#### - In particular checking for file existence should probably be done with a SFTP client rather than SSH - might be faster?
#if (not fear.file_exists(os.path.join(REMOTE_TEMP_PATH, os.path.split(flag_files[i])[-1]))) or \
# (os.stat(output_files[i]).st_size == 0):
if (os.stat(output_files[i]).st_size == 0):
# Job has finished but missing output - resubmit later
print 'Shell script %s job_id %s failed' % (
os.path.split(shell_files[i])[-1], job_ids[i])
# Save job id for file deletion
old_job_id = job_ids[i]
job_ids[i] = None
else:
# Job has finished successfully
job_finished[i] = True
# Save job id for file deletion
old_job_id = job_ids[i]
# Move files if necessary
#if LOCATION=='home':
# # Copy the file from local storage machine (and delete it)
# fear.copy_from_localhost(localpath=output_files[i], remotepath=os.path.join(LOCAL_TEMP_PATH, os.path.split(output_files[i])[-1]))
# Tell the world
if verbose:
print '%d / %d jobs complete' % (
sum(job_finished), len(job_finished))
# Tidy up local temporary directory - actually - do this in one batch later
#os.remove(script_files[i])
#os.remove(shell_files[i])
#os.remove(flag_files[i])
# Tidy up fear
fear.rm(
os.path.join(REMOTE_TEMP_PATH,
os.path.split(script_files[i])[-1]))
fear.rm(
os.path.join(REMOTE_TEMP_PATH,
os.path.split(shell_files[i])[-1]))
#fear.rm(os.path.join(REMOTE_TEMP_PATH, os.path.split(flag_files[i])[-1]))
#### TODO - record the output and error files for future reference
fear.rm(
os.path.join(REMOTE_TEMP_PATH,
os.path.split(shell_files[i])[-1]) +
('.o%s' % old_job_id))
fear.rm(
os.path.join(REMOTE_TEMP_PATH,
os.path.split(shell_files[i])[-1]) +
('.e%s' % old_job_id))
#### TODO - is the following line faster?
#fear.command('rm ' + ' ; rm '.join([os.path.join(REMOTE_TEMP_PATH, os.path.split(script_files[i])[-1]), os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]), os.path.join(REMOTE_TEMP_PATH, os.path.split(flag_files[i])[-1]), os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]) + ('.o%s' % old_job_id), os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]) + ('.e%s' % old_job_id)]))
# Tidy up local temporary directory
#os.remove(script_files[i])
#os.remove(shell_files[i])
#os.remove(flag_files[i])
job_ids[i] = None
elif not (fear.job_queued(job_ids[i]) or fear.job_running(job_ids[i]) \
or fear.job_loading(job_ids[i])):
# Job has some status other than running, queuing or loading - something is wrong, delete it
jobs_alive -= 1
should_sleep = False
old_job_id = job_ids[i]
fear.qdel(job_ids[i])
print 'Shell script %s job_id %s stuck, deleting' % (
os.path.split(shell_files[i])[-1], job_ids[i])
#### TODO - remove this code duplication
# Tidy up fear
fear.rm(
os.path.join(REMOTE_TEMP_PATH,
os.path.split(script_files[i])[-1]))
fear.rm(
os.path.join(REMOTE_TEMP_PATH,
os.path.split(shell_files[i])[-1]))
# fear.rm(os.path.join(REMOTE_TEMP_PATH, os.path.split(flag_files[i])[-1]))
#### TODO - record the output and error files for future reference
fear.rm(
os.path.join(REMOTE_TEMP_PATH,
os.path.split(shell_files[i])[-1]) +
('.o%s' % old_job_id))
fear.rm(
os.path.join(REMOTE_TEMP_PATH,
os.path.split(shell_files[i])[-1]) +
('.e%s' % old_job_id))
#### TODO - is the following line faster?
#fear.command('rm ' + ' ; rm '.join([os.path.join(REMOTE_TEMP_PATH, os.path.split(script_files[i])[-1]), os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]), os.path.join(REMOTE_TEMP_PATH, os.path.split(flag_files[i])[-1]), os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]) + ('.o%s' % old_job_id), os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]) + ('.e%s' % old_job_id)]))
# Tidy up local temporary directory
#os.remove(script_files[i])
#os.remove(shell_files[i])
#os.remove(flag_files[i])
job_ids[i] = None
if all(job_finished):
fear_finished = True
elif should_sleep:
print '%d of %d jobs complete' % (sum(job_finished),
len(job_finished))
if verbose:
#fear.qstat()
print '%d jobs running' % fear.jobs_running(update=False)
print '%d jobs loading' % fear.jobs_loading(update=False)
print '%d jobs queued' % fear.jobs_queued(update=False)
#print 'Sleeping for %d seconds' % job_check_sleep
time.sleep(job_check_sleep)
# Tidy up temporary directory
if verbose:
print 'Removing temporary files'
for i in range(len(scripts)):
os.remove(script_files[i])
os.remove(shell_files[i])
os.remove(flag_files[i])
if zip_files:
os.remove(zip_file_name)
#### TODO - return job output and error files as applicable (e.g. there may be multiple error files associated with one script)
return output_files
def run_batch_on_fear(scripts, language='python', job_check_sleep=30, file_copy_timeout=300, max_jobs=500, verbose=True, zip_files=False):
'''
Receives a list of python scripts to run
Assumes the code has an output file - i.e. %(output_file)s - that will be managed by this function
Returns a list of local file names where the code has presumably stored output
'''
# Define some code constants
#### TODO - this path adding code should accept an optional list of paths
python_path_code = '''
import sys
sys.path.append('%s')
''' % REMOTE_PYTHON_PATH
#### This will be deprecated in future MATLAB - hopefully the -singleCompThread command is sufficient
#### TODO - No longer used? Remove?
matlab_single_thread = '''
maxNumCompThreads(1);
'''
matlab_path_code = '''
addpath(genpath('%s'))
''' % REMOTE_MATLAB_PATH
#### TODO - allow port forwarding / tunneling - copy to machine on network with more disk space than fear, then copy from that machine?
#### FIXME - Now does port forwarding but with fixed port numbers = bad
#### TODO - Fix port forard leak
if LOCATION == 'home':
python_transfer_code = '''
from subprocess_timeout import timeoutCommand
import subprocess
print "Setting up port forwarding"
if subprocess.Popen("netstat -an | grep %(r2rport)d | grep LISTEN", shell=True, stdout=subprocess.PIPE).communicate()[0] == '':
timeoutCommand(cmd='ssh -i %(rsa_remote)s -N -f -L %(r2rport)d:localhost:%(r2hport)d %(username)s@fear').run(timeout=%(timeout)d)
print "Moving output file"
if not timeoutCommand(cmd='scp -P %(r2rport)d -i %(rsa_home)s %(output_file)s %(home_user)s@localhost:%(local_temp_path)s; rm %(output_file)s').run(timeout=%(timeout)d)[0]:
raise RuntimeError('Copying output raised error or timed out')
''' % {'rsa_remote' : REMOTE_TO_REMOTE_KEY_FILE,
'r2rport' : REMOTE_TO_REMOTE_PORT,
'r2hport' : REMOTE_TO_HOME_PORT,
'username' : USERNAME,
'timeout' : file_copy_timeout,
'rsa_home' : REMOTE_TO_HOME_KEY_FILE,
'output_file' : '%(output_file)s',
'home_user' : HOME_USERNAME,
'local_temp_path' : HOME_TEMP_PATH}
else:
python_transfer_code = '''
#from util import timeoutCommand
from subprocess_timeout import timeoutCommand
print "Moving output file"
if not timeoutCommand(cmd='scp -i %(rsa_key)s %(output_file)s %(username)s@%(local_host)s:%(local_temp_path)s; rm %(output_file)s').run(timeout=%(timeout)d)[0]:
raise RuntimeError('Copying output raised error or timed out')
''' % {'rsa_key' : REMOTE_TO_LOCAL_KEY_FILE,
'output_file' : '%(output_file)s',
'username' : USERNAME,
'local_host' : LOCAL_HOST,
'local_temp_path' : LOCAL_TEMP_PATH,
'timeout' : file_copy_timeout}
#### TODO - make this location independent
#### TODO - does this suffer from the instabilities that lead to the verbosity of the python command above
if LOCATION == 'home':
matlab_transfer_code = '''
[status, result] = system('netstat -an | grep %(r2rport)d | grep LISTEN')
if isempty(strfind(result, 'LISTEN'))
system('ssh -i %(rsa_remote)s -N -f -L %(r2rport)d:localhost:%(r2hport)d %(username)s@fear')
end
system('scp -o ConnectTimeout=%(timeout)d -P %(r2rport)d -i %(rsa_home)s %(output_file)s %(home_user)s@localhost:%(local_temp_path)s; rm %(output_file)s')
''' % {'rsa_remote' : REMOTE_TO_REMOTE_KEY_FILE,
'r2rport' : REMOTE_TO_REMOTE_PORT,
'r2hport' : REMOTE_TO_HOME_PORT,
'username' : USERNAME,
'timeout' : file_copy_timeout,
'rsa_home' : REMOTE_TO_HOME_KEY_FILE,
'output_file' : '%(output_file)s',
'home_user' : HOME_USERNAME,
'local_temp_path' : HOME_TEMP_PATH}
else:
matlab_transfer_code = '''
system('scp -o ConnectTimeout=%(timeout)d -i %(rsa_key)s %(output_file)s %(username)s@%(local_host)s:%(local_temp_path)s; rm %(output_file)s')
''' % {'rsa_key' : REMOTE_TO_LOCAL_KEY_FILE,
'output_file' : '%(output_file)s',
'username' : USERNAME,
'timeout' : file_copy_timeout,
'local_host' : LOCAL_HOST,
'local_temp_path' : LOCAL_TEMP_PATH}
# python_completion_code = '''
#print 'Writing completion flag'
#with open('%(flag_file)s', 'w') as f:
# f.write('Goodbye, World')
#print "I'll bite your legs off!"
#quit()
#'''
python_completion_code = '''
print "I will bite your legs off!"
quit()
'''
#### TODO - Is this completely stable
# matlab_completion_code = '''
#fprintf('\\nWriting completion flag\\n');
#ID = fopen('%(flag_file)s', 'w');
#fprintf(ID, 'Goodbye, world');
#fclose(ID);
#fprintf('\\nGoodbye, World\\n');
#quit()
#'''
matlab_completion_code = """
fprintf('\\nGoodbye, World\\n');
quit()
"""
# Open a connection to fear as a with block - ensures connection is closed
with pyfear.fear(via_gate=(LOCATION=='home')) as fear:
# Initialise lists of file locations job ids
shell_files = [None] * len(scripts)
script_files = [None] * len(scripts)
output_files = [None] * len(scripts)
stdout_files = [None] * len(scripts)
flag_files = [None] * len(scripts)
job_ids = [None] * len(scripts)
fear_finished = False
job_finished = [False] * len(scripts)
# Modify all scripts and create local temporary files
#### TODO - Writing to the network can be slow
#### - Perhaps it would be better writing to local disk followed by a block file transfer (is this possible?)
#### - Would make sense to do this when reading output files as well - perhaps this should be provided in this module?
if LOCATION == 'local':
temp_dir = LOCAL_TEMP_PATH
else:
temp_dir = HOME_TEMP_PATH
if verbose:
print 'Writing temporary files locally'
for (i, code) in enumerate(scripts):
if language == 'python':
script_files[i] = mkstemp_safe(temp_dir, '.py')
elif language == 'matlab':
script_files[i] = mkstemp_safe(temp_dir, '.m')
shell_files[i] = mkstemp_safe(temp_dir, '.sh')
output_files[i] = mkstemp_safe(temp_dir, '.out')
flag_files[i] = mkstemp_safe(temp_dir, '.flg')
# Customise code (path, transfer of output back to local host, flag file writing)
#### TODO - make path and output_transfer optional
if language == 'python':
code = python_path_code + code + python_transfer_code + python_completion_code
elif language == 'matlab':
code = matlab_path_code + code + matlab_transfer_code + matlab_completion_code
#code = code % {'output_file': os.path.join(REMOTE_TEMP_PATH, os.path.split(output_files[i])[-1]),
# 'flag_file' : os.path.join(REMOTE_TEMP_PATH, os.path.split(flag_files[i])[-1])}
code = code % {'output_file': os.path.join(REMOTE_SCRATCH_PATH, os.path.split(output_files[i])[-1])}
# Write code and shell file
with open(script_files[i], 'w') as f:
f.write(code)
with open(shell_files[i], 'w') as f:
#### TODO - is os.path.join always correct - what happens if this program is being run on windows?
if language == 'python':
f.write('python ' + os.path.join(REMOTE_TEMP_PATH, os.path.split(script_files[i])[-1]) + '\n')
elif language == 'matlab':
f.write('cd ' + REMOTE_TEMP_PATH + ';\n' + REMOTE_MATLAB + ' -nosplash -nojvm -nodisplay -singleCompThread -r ' + \
os.path.split(script_files[i])[-1].split('.')[0] + '\n')
# Zip and send files
if zip_files:
if verbose:
print 'Zipping files'
zip_file_name = mkstemp_safe(temp_dir, '.zip')
zf = zipfile.ZipFile(zip_file_name, mode='w')
for script in script_files:
zf.write(script, arcname=(os.path.split(script)[-1]), compress_type=zipfile.ZIP_DEFLATED)
for shell in shell_files:
zf.write(shell, arcname=(os.path.split(shell)[-1]), compress_type=zipfile.ZIP_DEFLATED)
zf.close()
if verbose:
print 'Sending zip file to fear'
fear.copy_to_temp(zip_file_name)
if verbose:
print 'Unzipping on fear'
fear.command('cd %(temp_path)s ; unzip %(zip_file)s ; rm %(zip_file)s' % {'temp_path' : REMOTE_TEMP_PATH, 'zip_file' : os.path.split(zip_file_name)[-1]})
# Loop through jobs, submitting jobs whenever fear usage low enough, re-submitting failed jobs
print 'Submitting %d jobs' % len(scripts)
while not fear_finished:
# Update knowledge of fear - trying to limit communication
fear.qstat()
jobs_alive = fear.jobs_alive(update=False)
# Sleep unless anything happens
should_sleep = True
for i in range(len(scripts)): # Make me more pythonic with zipping
#fear.qstat()
#jobs_alive = fear.jobs_alive(update=False)
# Does the job need to be run and can we run it?
if (not job_finished[i]) and (job_ids[i] is None) and (jobs_alive <= max_jobs):
# Something has happened
should_sleep = False
# Transfer files to fear
if not zip_files:
fear.copy_to_temp(script_files[i])
fear.copy_to_temp(shell_files[i])
# Submit the job to fear
if verbose:
print 'Submitting job %d of %d' % (i + 1, len(scripts)),
job_ids[i] = fear.qsub(os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]), verbose=verbose) # Hide path constant
# Increment job count
jobs_alive += 1
#### FIXME - This was an attempt at better utilisation of fear - back fired since calling qstat is slow - correct solution is to have job sending and job completion checking in different threads - but would need to be carerful with the shared lists
#for j in range(len(scripts)):
# if (not job_finished[j]) and (job_ids[j] is None) and (jobs_alive <= max_jobs):
# # Something has happened
# should_sleep = False
# # Transfer files to fear
# if not zip_files:
# fear.copy_to_temp(script_files[j])
# fear.copy_to_temp(shell_files[j])
# # Submit the job to fear
# print 'Submitting job %d of %d' % (j + 1, len(scripts))
# job_ids[j] = fear.qsub(os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[j])[-1]), verbose=verbose) # Hide path constant
# # Increment job count
# jobs_alive += 1
# Otherwise was it running last we checked?
elif (not job_finished[i]) and (not job_ids[i] is None):
#if (not job_finished[i]) and (not job_ids[i] is None):
# Has the process terminated?
if fear.job_terminated(job_ids[i], update=False):
# Decrement job count
#jobs_alive -= 1 - would not have been counted earlier
should_sleep = False
# Has the job failed to write a flag or is the output file empty
#### FIXME - If LOCATION=='home' need to check .out file on local is non-empty
#### TODO - Can likely increase speed by checking status of files (on fear and local) in one block - not sure how to do it though
#### - In particular checking for file existence should probably be done with a SFTP client rather than SSH - might be faster?
#if (not fear.file_exists(os.path.join(REMOTE_TEMP_PATH, os.path.split(flag_files[i])[-1]))) or \
# (os.stat(output_files[i]).st_size == 0):
if (os.stat(output_files[i]).st_size == 0):
# Job has finished but missing output - resubmit later
print 'Shell script %s job_id %s failed' % (os.path.split(shell_files[i])[-1], job_ids[i])
# Save job id for file deletion
old_job_id = job_ids[i]
job_ids[i] = None
else:
# Job has finished successfully
job_finished[i] = True
# Save job id for file deletion
old_job_id = job_ids[i]
# Move files if necessary
#if LOCATION=='home':
# # Copy the file from local storage machine (and delete it)
# fear.copy_from_localhost(localpath=output_files[i], remotepath=os.path.join(LOCAL_TEMP_PATH, os.path.split(output_files[i])[-1]))
# Tell the world
if verbose:
print '%d / %d jobs complete' % (sum(job_finished), len(job_finished))
# Tidy up local temporary directory - actually - do this in one batch later
#os.remove(script_files[i])
#os.remove(shell_files[i])
#os.remove(flag_files[i])
# Tidy up fear
fear.rm(os.path.join(REMOTE_TEMP_PATH, os.path.split(script_files[i])[-1]))
fear.rm(os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]))
#fear.rm(os.path.join(REMOTE_TEMP_PATH, os.path.split(flag_files[i])[-1]))
#### TODO - record the output and error files for future reference
fear.rm(os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]) + ('.o%s' % old_job_id))
fear.rm(os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]) + ('.e%s' % old_job_id))
#### TODO - is the following line faster?
#fear.command('rm ' + ' ; rm '.join([os.path.join(REMOTE_TEMP_PATH, os.path.split(script_files[i])[-1]), os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]), os.path.join(REMOTE_TEMP_PATH, os.path.split(flag_files[i])[-1]), os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]) + ('.o%s' % old_job_id), os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]) + ('.e%s' % old_job_id)]))
# Tidy up local temporary directory
#os.remove(script_files[i])
#os.remove(shell_files[i])
#os.remove(flag_files[i])
job_ids[i] = None
elif not (fear.job_queued(job_ids[i]) or fear.job_running(job_ids[i]) \
or fear.job_loading(job_ids[i])):
# Job has some status other than running, queuing or loading - something is wrong, delete it
jobs_alive -= 1
should_sleep = False
old_job_id = job_ids[i]
fear.qdel(job_ids[i])
print 'Shell script %s job_id %s stuck, deleting' % (os.path.split(shell_files[i])[-1], job_ids[i])
#### TODO - remove this code duplication
# Tidy up fear
fear.rm(os.path.join(REMOTE_TEMP_PATH, os.path.split(script_files[i])[-1]))
fear.rm(os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]))
# fear.rm(os.path.join(REMOTE_TEMP_PATH, os.path.split(flag_files[i])[-1]))
#### TODO - record the output and error files for future reference
fear.rm(os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]) + ('.o%s' % old_job_id))
fear.rm(os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]) + ('.e%s' % old_job_id))
#### TODO - is the following line faster?
#fear.command('rm ' + ' ; rm '.join([os.path.join(REMOTE_TEMP_PATH, os.path.split(script_files[i])[-1]), os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]), os.path.join(REMOTE_TEMP_PATH, os.path.split(flag_files[i])[-1]), os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]) + ('.o%s' % old_job_id), os.path.join(REMOTE_TEMP_PATH, os.path.split(shell_files[i])[-1]) + ('.e%s' % old_job_id)]))
# Tidy up local temporary directory
#os.remove(script_files[i])
#os.remove(shell_files[i])
#os.remove(flag_files[i])
job_ids[i] = None
if all(job_finished):
fear_finished = True
elif should_sleep:
print '%d of %d jobs complete' % (sum(job_finished), len(job_finished))
if verbose:
#fear.qstat()
print '%d jobs running' % fear.jobs_running(update=False)
print '%d jobs loading' % fear.jobs_loading(update=False)
print '%d jobs queued' % fear.jobs_queued(update=False)
#print 'Sleeping for %d seconds' % job_check_sleep
time.sleep(job_check_sleep)
# Tidy up temporary directory
if verbose:
print 'Removing temporary files'
for i in range(len(scripts)):
os.remove(script_files[i])
os.remove(shell_files[i])
os.remove(flag_files[i])
if zip_files:
os.remove(zip_file_name)
#### TODO - return job output and error files as applicable (e.g. there may be multiple error files associated with one script)
return output_files
def create_temp_file(extension):
if LOCATION=='home':
return mkstemp_safe(HOME_TEMP_PATH, extension)
else:
return mkstemp_safe(LOCAL_TEMP_PATH, extension)
def run_batch_locally(scripts, language='python', paths=[], max_cpu=0.9, max_mem=0.9, submit_sleep=1, job_check_sleep=30, \
verbose=True, max_files_open=100, max_running_jobs=10, single_thread=True):
'''
Receives a list of python scripts to run
Assumes the code has an output file that will be managed by this function
Returns a list of local file names where the code has presumably stored output
'''
# Define some code constants
#### Do we need to set paths explicitly?
#### This will be deprecated in future MATLAB - hopefully the -singleCompThread command is sufficient
matlab_single_thread = '''
maxNumCompThreads(1);
'''
python_path_code = '''
import sys
sys.path.append('%s')
'''
matlab_path_code = '''
addpath(genpath('%s'))
'''
python_completion_code = '''
print 'Writing completion flag'
with open('%(flag_file)s', 'w') as f:
f.write('Goodbye, World')
print "Goodbye, World"
quit()
'''
#### TODO - Is this completely stable
matlab_completion_code = '''
fprintf('\\nWriting completion flag\\n');
ID = fopen('%(flag_file)s', 'w');
fprintf(ID, 'Goodbye, world');
fclose(ID);
fprintf('\\nGoodbye, World\\n');
quit()
'''
# Initialise lists of file locations job ids
shell_files = [None] * len(scripts)
script_files = [None] * len(scripts)
output_files = [None] * len(scripts)
stdout_files = [None] * len(scripts)
stdout_file_handles = [None] * len(scripts)
flag_files = [None] * len(scripts)
processes = [None] * len(scripts)
fear_finished = False
job_finished = [False] * len(scripts)
files_open = 0
# Loop through jobs, submitting jobs whenever CPU usage low enough, re-submitting failed jobs
if not verbose:
prog = Progress(len(scripts))
while not fear_finished:
should_sleep = True
for (i, code) in enumerate(scripts):
if (not job_finished[i]) and (processes[i] is None) and (files_open <= max_files_open) and (len([1 for p in processes if not p is None]) < max_running_jobs):
# This script has not been run - check CPU and potentially run
#### FIXME - Merge if statements
if (psutil.cpu_percent() < max_cpu * 100) and (psutil.virtual_memory().percent < max_mem * 100):
# Jobs can run
should_sleep = False
# Get the job ready
if LOCATION == 'local':
temp_dir = LOCAL_TEMP_PATH
else:
temp_dir = HOME_TEMP_PATH
if language == 'python':
script_files[i] = (mkstemp_safe(temp_dir, '.py'))
elif language == 'matlab':
script_files[i] = (mkstemp_safe(temp_dir, '.m'))
# Create necessary files in local path
shell_files[i] = (mkstemp_safe(temp_dir, '.sh'))
output_files[i] = (mkstemp_safe(temp_dir, '.out'))
stdout_files[i] = (mkstemp_safe(temp_dir, '.o'))
flag_files[i] = (mkstemp_safe(temp_dir, '.flg'))
# Customise code
#### TODO - make path and output_transfer optional
if language == 'python':
code = code + python_completion_code
for path in paths:
code = (python_path_code % path) + code
elif language == 'matlab':
code = code + matlab_completion_code
for path in paths:
code = (matlab_path_code % path) + code
code = code % {'output_file': output_files[i],
'flag_file' : flag_files[i]}
# Write code and shell file
with open(script_files[i], 'w') as f:
f.write(code)
with open(shell_files[i], 'w') as f:
#### TODO - is os.path.join always correct - what happens if this program is being run on windows?
if language == 'python':
f.write('python ' + script_files[i] + '\n')
elif language == 'matlab':
if LOCATION == 'home':
matlab_path = HOME_MATLAB
else:
matlab_path = LOCAL_MATLAB
if single_thread:
f.write('cd ' + os.path.split(script_files[i])[0] + ';\n' + matlab_path + ' -nosplash -nojvm -nodisplay -singleCompThread -r ' + \
os.path.split(script_files[i])[-1].split('.')[0] + '\n')
else:
f.write('cd ' + os.path.split(script_files[i])[0] + ';\n' + matlab_path + ' -nosplash -nojvm -nodisplay -r ' + \
os.path.split(script_files[i])[-1].split('.')[0] + '\n')
# Start running the job
if verbose:
print 'Submitting job %d of %d' % (i + 1, len(scripts))
stdout_file_handles[i] = open(stdout_files[i], 'w')
files_open = files_open + 1
#processes[i] = subprocess.Popen(['sh', shell_files[i]], stdout = stdout_file_handles[i]);
with open(shell_files[i], 'r') as shell_file:
lines = [line.rstrip() for line in shell_file.readlines()]
processes[i] = subprocess.Popen(' '.join(lines), shell=True, stdout = stdout_file_handles[i]);
# Sleep for a bit so the process can kick in (prevents 100s of jobs being sent to processor)
time.sleep(submit_sleep)
elif (not job_finished[i]) and (not processes[i] is None):
# Ask the process how its doing
processes[i].poll()
# Check to see if the process has completed
if not processes[i].returncode is None:
if os.path.isfile(flag_files[i]):
job_finished[i] = True
if verbose:
print 'Job %d of %d has completed' % (i + 1, len(scripts))
else:
prog.tick()
else:
if verbose:
print 'Job %d has failed - will try again later' % i + 1
processes[i] = None
# Tidy up temp files
os.remove(script_files[i])
os.remove(shell_files[i])
stdout_file_handles[i].close()
files_open = files_open - 1
os.remove(stdout_files[i])
os.remove(flag_files[i])
processes[i] = None
# Something useful happened
should_sleep = False
if all(job_finished):
fear_finished = True
if not verbose:
prog.done()
elif should_sleep:
# Count how many jobs are queued
n_queued = 0
# Count how many jobs are running
n_running = 0
if verbose:
# print '%d jobs running' % n_running
# print '%d jobs queued' % n_queued
print 'Sleeping for %d seconds' % job_check_sleep
time.sleep(job_check_sleep)
#### TODO - return job output and error files as applicable (e.g. there may be multiple error files associated with one script)
return output_files
