def test_make_jobs(self):
"""writing the job files works"""
# no commands should make no jobs files
self.assertEqual(make_jobs([], "test", self.queue), [])
# one job file should be created
filenames = make_jobs([self.command], "test_qsub", self.queue)
self.assertTrue(len(filenames) == 1)
observed_text = list(open(filenames[0]))
self.assertEqual(
"".join(observed_text), QSUB_TEXT %
("72:00:00", 1, 1, self.queue, "test_qsub", "oe", self.command))
def test_make_jobs(self):
"""writing the job files works"""
# no commands should make no jobs files
self.assertEqual(make_jobs([], "test", self.queue), [])
# one job file should be created
filenames = make_jobs([self.command], "test_qsub", self.queue)
self.assertTrue(len(filenames) == 1)
observed_text = list(open(filenames[0]))
self.assertEqual(
"".join(observed_text), QSUB_TEXT % ("72:00:00", 1, 1, self.queue, "test_qsub", "oe", self.command)
)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if opts.submit_jobs and not opts.make_jobs:
option_parser.error('Must pass -m if passing -s. (Sorry about this, '+\
'it\'s for backwards-compatibility.)')
min_args = 2
if len(args) != min_args:
option_parser.error('Program requires <commands file> and <job prefix>')
if (len(args[1])>10 or len(args[1])==0):
option_parser.error('job prefix must be 1-10 characters long')
commands = list(open(args[0]))
job_prefix = args[1]
if(not exists(opts.job_dir)):
try:
makedirs(opts.job_dir)
except OSError:
exit(" Jobs directory can not be created. "
+"Check for permissions or file with the same name: %s\n"
% opts.job_dir)
if (opts.make_jobs):
filenames = make_jobs(commands, job_prefix, opts.queue, opts.job_dir)
else:
exit("Should we ever get here???")
if (opts.submit_jobs):
submit_jobs(filenames, opts.verbose)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if opts.submit_jobs and not opts.make_jobs:
option_parser.error('Must pass -m if passing -s. (Sorry about this, '
'it\'s for backwards-compatibility.)')
min_args = 2
if len(args) != min_args:
option_parser.error('Program requires <commands file> and '
'<job prefix>')
if (len(args[1]) > 10 or len(args[1]) == 0):
option_parser.error('job prefix must be 1-10 characters long')
commands = list(open(args[0]))
job_prefix = args[1]
if (not exists(opts.job_dir)):
try:
makedirs(opts.job_dir)
except OSError:
exit(" Jobs directory can not be created. "
"Check for permissions or file with the same name: %s\n" %
opts.job_dir)
if (opts.make_jobs):
filenames = make_jobs(commands, job_prefix, opts.queue, opts.job_dir,
(str(opts.max_walltime) + ":00:00"), opts.cpus,
opts.nodes)
else:
exit("Should we ever get here???")
if (opts.submit_jobs):
submit_jobs(filenames, opts.verbose)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.submit_jobs and not opts.make_jobs:
option_parser.error("Must pass -m if passing -s. (Sorry about this, " "it's for backwards-compatibility.)")
min_args = 2
if len(args) != min_args:
option_parser.error("Program requires <commands file> and " "<job prefix>")
if len(args[1]) > 10 or len(args[1]) == 0:
option_parser.error("job prefix must be 1-10 characters long")
commands = list(open(args[0]))
job_prefix = args[1]
if not exists(opts.job_dir):
try:
makedirs(opts.job_dir)
except OSError:
exit(
" Jobs directory can not be created. "
"Check for permissions or file with the same name: %s\n" % opts.job_dir
)
if opts.make_jobs:
filenames = make_jobs(
commands, job_prefix, opts.queue, opts.job_dir, (str(opts.max_walltime) + ":00:00"), opts.cpus, opts.nodes
)
else:
exit("Should we ever get here???")
if opts.submit_jobs:
submit_jobs(filenames, opts.verbose)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if opts.submit_jobs and not opts.make_jobs:
option_parser.error('Must pass -m if passing -s. (Sorry about this, '
'it\'s for backwards-compatibility.)')
min_args = 2
if len(args) != min_args:
option_parser.error('Program requires <commands file> and '
'<job prefix>')
if (len(args[1]) > 10 or len(args[1]) == 0):
option_parser.error('job prefix must be 1-10 characters long')
if(not exists(opts.job_dir)):
try:
makedirs(opts.job_dir)
except OSError:
exit(" Jobs directory can not be created. "
"Check for permissions or file with the same name: %s\n"
% opts.job_dir)
commands = list(open(args[0]))
job_prefix = args[1]
if opts.mem_per_cpu:
mem_per_cpu = " --mem_per_cpu=" + opts.mem_per_cpu
else:
mem_per_cpu = ""
if opts.queue:
queue = " -p " + opts.queue
else:
queue = ""
if (opts.make_jobs):
filenames = make_jobs(
commands,
job_prefix,
opts.queue,
opts.job_dir)
else:
exit("Should we ever get here???")
if (opts.submit_jobs):
for f in filenames:
qiime_system_call("".join([
"sbatch",
queue,
" -J ", job_prefix,
mem_per_cpu,
" -o ", normpath(opts.job_dir), sep, job_prefix, "_%j.out",
" ", f
]), shell=True)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if opts.submit_jobs and not opts.make_jobs:
option_parser.error('Must pass -m if passing -s. (Sorry about this, '
'it\'s for backwards-compatibility.)')
min_args = 2
if len(args) != min_args:
option_parser.error('Program requires <commands file> and '
'<job prefix>')
if (len(args[1]) > 10 or len(args[1]) == 0):
option_parser.error('job prefix must be 1-10 characters long')
if(not exists(opts.job_dir)):
try:
makedirs(opts.job_dir)
except OSError:
exit(" Jobs directory can not be created. "
"Check for permissions or file with the same name: %s\n"
% opts.job_dir)
commands = list(open(args[0]))
job_prefix = args[1]
if opts.mem_per_cpu:
mem_per_cpu = " --mem-per-cpu=" + opts.mem_per_cpu
else:
mem_per_cpu = ""
if opts.queue:
queue = " -p " + opts.queue
else:
queue = ""
if (opts.make_jobs):
filenames = make_jobs(
commands,
job_prefix,
opts.queue,
opts.job_dir)
else:
exit("Should we ever get here???")
if (opts.submit_jobs):
for f in filenames:
qiime_system_call("".join([
"sbatch",
queue,
" -J ", job_prefix,
mem_per_cpu,
" -o ", normpath(opts.job_dir), sep, job_prefix, "_%j.out",
" ", f
]), shell=True)
def test_submit_jobs(self):
"""submit jobs via qsub works"""
filenames = make_jobs([self.command], "test_qsub", self.queue)
submit_jobs(filenames)
for i in range(10):
if exists(self.tmp_result_file):
return
else:
#wait for job to finish
sleep(10)
self.fail("The test job apparently never finished.\n" +
"check the jobs error log and check the queue status\n.")
def test_submit_jobs(self):
"""submit jobs via qsub works"""
filenames = make_jobs([self.command], "test_qsub", self.queue)
submit_jobs(filenames)
for i in range(10):
if exists(self.tmp_result_file):
return
else:
#wait for job to finish
sleep(10)
self.fail("The test job apparently never finished.\n"
+"check the jobs error log and check the queue status\n.")
