def make_sge_jobs(commands,
job_prefix,
queue,
jobs_dir="jobs/",
num_jobs=100,
max_hours_per_job=24):
"""prepare qsub text files.
command: list of commands
job_prefix: a short, descriptive name for the job.
queue: name of the queue to submit to
jobs_dir: path to directory where job submision scripts are written
max_hours_per_job: the maximum expected time for each command (this will be multiplied by number of commands per job to get a 'walltime'
ncpus: number of cpus
nodes: number of nodes
keep_output: keep standard error, standard out, both, or neither
o=std out, e=std err, oe=both, n=neither
"""
filenames = []
create_dir(jobs_dir)
#calculate the number of commands to put in each job
num_commands_per_job = int(ceil(len(commands) / float(num_jobs)))
#calculate the walltime (time before job will be killed by scheduler if still running)
total_time = max_hours_per_job * num_commands_per_job
walltime = "{0}:00:00".format(total_time)
for command_group in grouper(commands, num_commands_per_job, ''):
job_name = get_tmp_filename(tmp_dir=jobs_dir,
prefix=job_prefix + "_",
suffix=".txt")
out_fh = open(job_name, "w")
stderr_fp = job_name + "_stderr"
stdout_fp = job_name + "_stdout"
out_fh.write(
SGE_QSUB_TEXT %
(walltime, stderr_fp, stdout_fp, "\n".join(command_group)))
out_fh.close()
filenames.append(job_name)
return filenames
def make_sge_jobs(commands, job_prefix, queue, jobs_dir="jobs/",num_jobs=100,max_hours_per_job=24):
"""prepare qsub text files.
command: list of commands
job_prefix: a short, descriptive name for the job.
queue: name of the queue to submit to
jobs_dir: path to directory where job submision scripts are written
max_hours_per_job: the maximum expected time for each command (this will be multiplied by number of commands per job to get a 'walltime'
ncpus: number of cpus
nodes: number of nodes
keep_output: keep standard error, standard out, both, or neither
o=std out, e=std err, oe=both, n=neither
"""
filenames=[]
create_dir(jobs_dir)
#calculate the number of commands to put in each job
num_commands_per_job=int(ceil(len(commands)/float(num_jobs)))
#calculate the walltime (time before job will be killed by scheduler if still running)
total_time = max_hours_per_job*num_commands_per_job
walltime= "{0}:00:00".format(total_time)
for command_group in grouper(commands,num_commands_per_job,''):
job_name = get_tmp_filename(tmp_dir=jobs_dir, prefix=job_prefix+"_",
suffix = ".txt")
out_fh = open(job_name,"w")
stderr_fp = job_name+"_stderr"
stdout_fp = job_name+"_stdout"
out_fh.write(SGE_QSUB_TEXT % (walltime, stderr_fp, stdout_fp, "\n".join(command_group)))
out_fh.close()
filenames.append(job_name)
return filenames
# point paths_to_remove at job_fps
paths_to_remove = job_fps
# This is messy right now as our clusters (bmf, bmf2) require us to
# start and exit a shell for some reason which we haven't figured out.
# Running these commands as parallel shell scripts gets screwed up by
# this. For the time-being, I'm stripping this out here. Once the new
# clusters are up, I'm going to move the wrapping of commands in
# bash/exit to the cluster_jobs script. At that point this function
# will be greatly simplified.
ignored_subcommands = {}.fromkeys(["/bin/bash", "exit"])
# calculate the number of commands to put in each job
num_commands_per_job = int(ceil(len(commands) / float(num_jobs)))
for i, command_group in enumerate(grouper(commands, num_commands_per_job, "")):
job_fp = "%s/%s%d" % (jobs_dir, run_id, i)
f = open(job_fp, "w")
for command in command_group:
f.write(
"\n".join(
[subcommand for subcommand in command.split(";") if subcommand.strip() not in ignored_subcommands]
)
)
f.close()
chmod(job_fp, S_IRWXU)
job_fps.append(job_fp)
return job_fps, paths_to_remove
paths_to_remove = job_fps
# This is messy right now as our clusters (bmf, bmf2) require us to
# start and exit a shell for some reason which we haven't figured out.
# Running these commands as parallel shell scripts gets screwed up by
# this. For the time-being, I'm stripping this out here. Once the new
# clusters are up, I'm going to move the wrapping of commands in
# bash/exit to the cluster_jobs script. At that point this function
# will be greatly simplified.
ignored_subcommands = {}.fromkeys(['/bin/bash', 'exit'])
#calculate the number of commands to put in each job
num_commands_per_job = int(ceil(len(commands) / float(num_jobs)))
for i, command_group in enumerate(
grouper(commands, num_commands_per_job, '')):
job_fp = '%s/%s%d' % (jobs_dir, run_id, i)
f = open(job_fp, 'w')
for command in command_group:
f.write('\n'.join([subcommand \
for subcommand in command.split(';')
if subcommand.strip() not in ignored_subcommands]))
f.close()
chmod(job_fp, S_IRWXU)
job_fps.append(job_fp)
return job_fps, paths_to_remove
def run_commands(output_dir,
commands,
# point paths_to_remove at job_fps
paths_to_remove = job_fps
# This is messy right now as our clusters (bmf, bmf2) require us to
# start and exit a shell for some reason which we haven't figured out.
# Running these commands as parallel shell scripts gets screwed up by
# this. For the time-being, I'm stripping this out here. Once the new
# clusters are up, I'm going to move the wrapping of commands in
# bash/exit to the cluster_jobs script. At that point this function
# will be greatly simplified.
ignored_subcommands = {}.fromkeys(['/bin/bash','exit'])
#calculate the number of commands to put in each job
num_commands_per_job=int(ceil(len(commands)/float(num_jobs)))
for i,command_group in enumerate(grouper(commands,num_commands_per_job,'')):
job_fp = '%s/%s%d' % (jobs_dir, run_id, i)
f = open(job_fp,'w')
for command in command_group:
f.write('\n'.join([subcommand \
for subcommand in command.split(';')
if subcommand.strip() not in ignored_subcommands]))
f.close()
chmod(job_fp, S_IRWXU)
job_fps.append(job_fp)
return job_fps, paths_to_remove
def run_commands(output_dir,commands,run_id,submit_jobs,keep_temp,num_jobs=4):
"""
"""
