def create_batch_script(self, job_name, dispatcher_string):
command = "nice -n 10 " + dispatcher_string
days, hours, minutes, seconds = Time.sec_to_all(self.batch_parameters.max_walltime)
walltime = '%d:%d:%d' % (days*24 + hours, minutes, seconds)
num_nodes = "nodes=1:ppn=" + str(self.batch_parameters.nodes)
memory = "pmem=" + str(self.batch_parameters.memory) + "gb"
workdir = self.get_job_foldername(job_name)
output = workdir + os.sep + BatchClusterComputationEngine.output_filename
error = workdir + os.sep + BatchClusterComputationEngine.error_filename
job_string = """
#PBS -S /bin/bash
#PBS -N %s
#PBS -l %s
#PBS -l %s
#PBS -l %s
#PBS -o %s
#PBS -e %s
cd %s
%s""" % (job_name, walltime, num_nodes, memory, output, error, workdir,
command)
return job_string
def create_batch_script(self, job_name, dispatcher_string, walltime, memory, nodes):
command = "nice -n 10 " + dispatcher_string
qos = self._infer_slurm_qos(walltime,
nodes)
days, hours, minutes, seconds = Time.sec_to_all(walltime)
walltime = '%d-%d:%d:%d' % (days, hours, minutes, seconds)
num_nodes = str(nodes)
# note memory is in megabyes
memory = str(memory)
workdir = self.get_job_foldername(job_name)
output = workdir + os.sep + BatchClusterComputationEngine.output_filename
error = workdir + os.sep + BatchClusterComputationEngine.error_filename
job_strings = ["#!/bin/bash"]
job_strings += ["#SBATCH -J %s" % job_name]
job_strings += ["#SBATCH --time=%s" % walltime]
job_strings += ["#SBATCH --qos=%s" % qos]
job_strings += ["#SBATCH -n %s" % num_nodes]
job_strings += ["#SBATCH --mem=%s" % memory]
job_strings += ["#SBATCH --output=%s" % output]
job_strings += ["#SBATCH --error=%s" % error]
if self.partition is not None:
job_strings += ["#SBATCH --partition=%s" % self.partition]
job_strings += ["cd %s" % workdir]
job_strings += ["%s" % command]
return os.linesep.join(job_strings)
def create_batch_script(self, job_name, dispatcher_string, walltime,
memory, nodes):
command = "nice -n 10 " + dispatcher_string
qos = self._infer_slurm_qos(walltime, nodes)
days, hours, minutes, seconds = Time.sec_to_all(walltime)
walltime = '%d-%d:%d:%d' % (days, hours, minutes, seconds)
num_nodes = str(nodes)
# note memory is in megabyes
memory = str(memory)
workdir = self.get_job_foldername(job_name)
output = workdir + os.sep + BatchClusterComputationEngine.output_filename
error = workdir + os.sep + BatchClusterComputationEngine.error_filename
job_strings = ["#!/bin/bash"]
job_strings += ["#SBATCH -J %s" % job_name]
job_strings += ["#SBATCH --time=%s" % walltime]
job_strings += ["#SBATCH --qos=%s" % qos]
job_strings += ["#SBATCH -n %s" % num_nodes]
job_strings += ["#SBATCH --mem=%s" % memory]
job_strings += ["#SBATCH --output=%s" % output]
job_strings += ["#SBATCH --error=%s" % error]
if self.partition is not None:
job_strings += ["#SBATCH --partition=%s" % self.partition]
job_strings += ["cd %s" % workdir]
job_strings += ["%s" % command]
return os.linesep.join(job_strings)
def test_sec_to_all_11(self):
secs = 11
days, hours, minutes, seconds = Time.sec_to_all(secs)
nose.tools.assert_equal(days, 0)
nose.tools.assert_equal(hours, 0)
nose.tools.assert_equal(minutes, 0)
nose.tools.assert_equal(seconds, 11)
def create_batch_script(self, job_name, dispatcher_string, walltime, memory, nodes):
command = "nice -n 10 " + dispatcher_string
qos = self._infer_slurm_qos(walltime,
nodes)
days, hours, minutes, seconds = Time.sec_to_all(walltime)
walltime = '%d-%d:%d:%d' % (days, hours, minutes, seconds)
num_nodes = str(nodes)
# note memory is in megabyes
memory = str(memory)
workdir = self.get_job_foldername(job_name)
output = workdir + os.sep + BatchClusterComputationEngine.output_filename
error = workdir + os.sep + BatchClusterComputationEngine.error_filename
job_string = """#!/bin/bash
#SBATCH -J %s
#SBATCH --time=%s
#SBATCH --qos=%s
#SBATCH -n %s
#SBATCH --mem=%s
#SBATCH --output=%s
#SBATCH --error=%s
cd %s
%s""" % (job_name, walltime, qos, num_nodes, memory, output, error, workdir,
command)
return job_string
def test_sec_to_all_100001(self):
secs = 100001
days, hours, minutes, seconds = Time.sec_to_all(secs)
nose.tools.assert_equal(days, 1)
nose.tools.assert_equal(hours, 3)
nose.tools.assert_equal(minutes, 46)
nose.tools.assert_equal(seconds, 41)
def create_batch_script(self, job_name, dispatcher_string):
command = dispatcher_string
days, hours, minutes, seconds = Time.sec_to_all(
self.batch_parameters.max_walltime)
walltime = '%d:%d:%d' % (days * 24, hours, minutes, seconds)
memory = str(self.batch_parameters.memory) + "G"
workdir = self.get_job_foldername(job_name)
output = workdir + os.sep + BatchClusterComputationEngine.output_filename
error = workdir + os.sep + BatchClusterComputationEngine.error_filename
job_string = \
"""#$ -S /bin/bash
#$ -N %s
#$ -l h_rt=%s
#$ -l h_vmem=%s,tmem=%s
#$ -o %s
#$ -e %s
#$ -wd %s
source ~/.bash_profile
%s""" % (job_name, walltime, memory, memory, output, error, workdir, command)
return job_string
def test_sec_to_all_11(self):
secs = 11
days, hours, minutes, seconds = Time.sec_to_all(secs)
nose.tools.assert_equal(days, 0)
nose.tools.assert_equal(hours, 0)
nose.tools.assert_equal(minutes, 0)
nose.tools.assert_equal(seconds, 11)
def test_sec_to_all_100001(self):
secs = 100001
days, hours, minutes, seconds = Time.sec_to_all(secs)
nose.tools.assert_equal(days, 1)
nose.tools.assert_equal(hours, 3)
nose.tools.assert_equal(minutes, 46)
nose.tools.assert_equal(seconds, 41)
def create_batch_script(self, job_name, dispatcher_string):
command = "nice -n 10 " + dispatcher_string
days, hours, minutes, seconds = Time.sec_to_all(self.batch_parameters.max_walltime)
walltime = '%d:%d:%d' % (days*24 + hours, minutes, seconds)
num_nodes = "nodes=1:ppn=" + str(self.batch_parameters.nodes)
memory = "pmem=" + str(self.batch_parameters.memory) + "gb"
workdir = self.get_job_foldername(job_name)
output = workdir + os.sep + BatchClusterComputationEngine.output_filename
error = workdir + os.sep + BatchClusterComputationEngine.error_filename
job_string = """
#PBS -S /bin/bash
#PBS -N %s
#PBS -l %s
#PBS -l %s
#PBS -l %s
#PBS -o %s
#PBS -e %s
cd %s
%s""" % (job_name, walltime, num_nodes, memory, output, error, workdir,
command)
return job_string
def create_batch_script(self, job_name, dispatcher_string):
command = dispatcher_string
days, hours, minutes, seconds = Time.sec_to_all(self.batch_parameters.max_walltime)
walltime = '%d:%d:%d' % (days*24, hours, minutes, seconds)
memory = str(self.batch_parameters.memory) + "G"
workdir = self.get_job_foldername(job_name)
output = workdir + os.sep + BatchClusterComputationEngine.output_filename
error = workdir + os.sep + BatchClusterComputationEngine.error_filename
job_string = \
"""#$ -S /bin/bash
#$ -N %s
#$ -l h_rt=%s
#$ -l h_vmem=%s,tmem=%s
#$ -o %s
#$ -e %s
#$ -wd %s
source ~/.bash_profile
%s""" % (job_name, walltime, memory, memory, output, error, workdir, command)
return job_string