def __init__(self, hawc2_path, hawc2_cmd, htc_file, exe_dir, input_files, output_files, queue='workq', walltime='00:10:00'):
self.hawc2_path = hawc2_path
self.hawc2_cmd = hawc2_cmd
self.htc_file = htc_file
self.exe_dir = exe_dir
self.queue = queue
self.walltime = walltime
if not os.path.isabs(htc_file):
htc_file = pjoin(exe_dir, htc_file)
else:
htc_file = htc_file.replace("\\", "/")
if htc_file not in input_files:
input_files.append(htc_file)
self.input_files = [abspath((pjoin(exe_dir, f), abspath(f))[os.path.isabs(f)])
for f in input_files]
self.htc_file = relpath(htc_file, exe_dir)
self.output_files = [abspath((pjoin(exe_dir, f), abspath(f))[os.path.isabs(f)])
for f in output_files]
self.model_path = abspath(pjoin(exe_dir, relpath(os.path.commonprefix(
self.input_files + self.output_files).rpartition("/")[0], exe_dir)))
self.model_name = os.path.basename(abspath(self.model_path))
self.jobname = os.path.splitext(os.path.basename(htc_file))[0]
PBSFile.__init__(self, self.model_path, self.jobname, self.commands, queue, walltime=walltime)
def test_pbs_file():
if x is None:
pytest.xfail("Password missing")
pbsfile = PBSFile("/home/mmpe/tmp", "test",
'''python -c "print('hello world')"''', 'workq')
ssh = SSHClient("jess.dtu.dk", 'mmpe', x.mmpe)
pbs_job = SSHPBSJob(ssh)
pbs_job.submit(pbsfile, "./tmp")
with pbs_job.ssh:
start = time.time()
while time.time() < start + 10:
time.sleep(.1)
if pbs_job.status == DONE:
break
else:
raise Exception("job not finished within 10 s")
_, out, _ = ssh.execute('cat ./tmp/stdout/test.out')
assert "hello world" in out
def test_pbs_file_str():
pbsfile = PBSFile('/home/user/tmp', "test",
'''python -c "print('hello world')"''', 'workq')
ref = """### Jobid
#PBS -N test
### Standard Output
#PBS -o /home/user/tmp/stdout/test.out
### merge stderr into stdout
#PBS -j oe
#PBS -W umask=0003
### Maximum wallclock time format HOURS:MINUTES:SECONDS
#PBS -l walltime=00:10:00
#PBS -l nodes=1:ppn=1
### Queue name
#PBS -q workq
cd "/home/user/tmp"
mkdir -p "stdout"
if [ -z "$PBS_JOBID" ]; then echo "Run using qsub"; exit ; fi
pwd
python -c "print('hello world')"
exit
"""
assert str(pbsfile) == ref
def test_pbs_walltime(i, s):
pbsfile = PBSFile("./tmp", "test", '', 'workq', walltime=i)
assert pbsfile.walltime == s