def execute(log: Logger, data: Dict, wpaths: Dict) -> Dict:
"""Run Rosetta.
"""
if TBcore.get_option('slurm', 'use'):
slurm_file = wpaths['main'].joinpath('submit_hybridize.sh')
TButil.plugin_filemaker('Submission file at {}'.format(slurm_file))
with slurm_file.open('w') as fd:
fd.write(TButil.slurm_header() + '\n')
for k in ['assembly', 'design']:
cmd = [
'srun',
]
cmd.extend(data['cmd'][k])
fd.write(' '.join([str(x) for x in cmd]) + '\n')
if TBcore.get_option('system', 'verbose'):
sys.stdout.write(
'Submiting jobs to SLURM... this might take a while\n')
TButil.submit_slurm(slurm_file)
else:
for k in ['assembly', 'design']:
log.notice(
f'EXECTUE: {" ".join([str(x) for x in data["cmd"][k]])}')
run([str(x) for x in data['cmd'][k]], stdout=DEVNULL)
return data
def execute(cmd: List, wfolder: Path):
"""
"""
if not TBcore.get_option('slurm', 'use'):
run(cmd)
else:
slurm_file = wfolder.joinpath('submit_analytics.sh')
with slurm_file.open('w') as fd:
fd.write(TButil.slurm_header() + '\n')
fd.write(TButil.slurm_pyenv() + '\n')
for c in cmd:
fd.write(' '.join([str(x) for x in c]) + '\n')
TButil.submit_slurm(slurm_file)
def with_slurm( cmd: List[str],
current_case_file: Path,
current_sse: str,
unimaster: Path,
imaster: Path,
unidata: Path ):
"""
"""
# Make bashfile
bashcont = []
createbash = 'python {0} -case {1} -master {2} -present {3} -out {4}'
parts = math.ceil(len(cmd) / TBcore.get_option('slurm', 'array'))
wwd = unimaster.parent.parent
cwd = Path().cwd()
os.chdir(str(wwd))
for i, com in enumerate(cmd):
cmd[i][2] = str(Path(com[2]).relative_to(wwd))
cmd[i][-1] = str(Path(com[-1]).relative_to(wwd))
for ii, cp in enumerate(cmd):
cmd[ii][-1] = cp[-1] + '_${SLURM_ARRAY_TASK_ID}'
for j, i in enumerate(range(0, len(cmd), parts)):
sumfile = unimaster.parent.joinpath('_${SLURM_ARRAY_TASK_ID}.master').relative_to(wwd)
datfile = unimaster.parent.joinpath('_${SLURM_ARRAY_TASK_ID}.geo').relative_to(wwd)
bashcont.append('if (( ${{SLURM_ARRAY_TASK_ID}} == {} )); then'.format(j + 1))
bashcont.extend([' '.join(x) for x in cmd[i:i + parts]])
bashcont.append('cat {0} > {1}'.format(Path(cmd[-1][-1]).parent.joinpath('*_${SLURM_ARRAY_TASK_ID}'), sumfile))
bashcont.append(createbash.format(imaster, current_case_file.relative_to(wwd),
sumfile, current_sse, datfile))
bashcont.append('fi')
with unimaster.parent.joinpath('submit.sh').relative_to(wwd).open('w') as fd:
fd.write(TButil.slurm_header())
fd.write(TButil.slurm_pyenv())
fd.write('\n'.join(bashcont))
TButil.submit_slurm(unimaster.parent.joinpath('submit.sh').relative_to(wwd))
TButil.plugin_filemaker('Creating geometric coordinate file {}'.format(unidata))
allCSV = [str(x) for x in unimaster.parent.relative_to(wwd).glob('_*.geo.csv')]
pd.concat([pd.read_csv(x) for x in allCSV]).to_csv(unidata.relative_to(wwd), index=False)
TButil.plugin_filemaker('Creating MASTER search file {}'.format(unimaster))
with unimaster.relative_to(wwd).open('w') as fd:
for x in unimaster.parent.glob('_*.master'):
with x.relative_to(wwd).open() as fi:
fd.write(''.join(fi.readlines()))
os.chdir(str(cwd))
def execute_commands( self, cmd: List, wfolder: Path ):
"""
"""
if not TBcore.get_option('slurm', 'use'):
for c in list(filter(None, cmd)):
run(c)
else:
if self.metric:
slurm_file = wfolder.joinpath(f'submit_analytics_{self.analysis}_{self.metric}.sh')
else:
slurm_file = wfolder.joinpath(f'submit_analytics_{self.analysis}.sh')
with slurm_file.open('w') as fd:
fd.write(TButil.slurm_header() + '\n')
fd.write(TButil.slurm_pyenv() + '\n')
for c in cmd:
fd.write(' '.join([str(x) for x in c]) + '\n')
TButil.submit_slurm(self.log, slurm_file)
def execute(log: Logger, data: Dict, wpaths: Dict) -> Dict:
"""Run Rosetta.
"""
if TBcore.get_option('slurm', 'use'):
slurm_file = wpaths['main'].joinpath('submit_funfoldes.sh')
log.notice(f'Submission file at {slurm_file}')
with slurm_file.open('w') as fd:
fd.write(TButil.slurm_header() + '\n')
for k in ['folding', 'design']:
cmd = [
'srun',
]
cmd.extend(data['cmd'][k])
fd.write(' '.join([str(x) for x in cmd]) + '\n')
log.info('Submiting jobs to SLURM... this might take a while\n')
TButil.submit_slurm(log, slurm_file)
else:
for k in ['folding', 'design']:
log.notice(
f'EXECUTE: {" ".join([str(x) for x in data["cmd"][k]])}')
run([str(x) for x in data['cmd'][k]], stdout=DEVNULL)
return data
def execute(data: Dict, wpaths: Dict) -> Dict:
"""Run Rosetta.
"""
if TBcore.get_option('slurm', 'use'):
slurm_file = wpaths['main'].joinpath('submit_funfoldes.sh')
TButil.plugin_filemaker('Submission file at {}'.format(slurm_file))
with slurm_file.open('w') as fd:
fd.write(TButil.slurm_header() + '\n')
for k in ['folding', 'design']:
cmd = [
'srun',
]
cmd.extend(data['cmd'][k])
fd.write(' '.join([str(x) for x in cmd]) + '\n')
if TBcore.get_option('system', 'verbose'):
sys.stdout.write(
'Submiting jobs to SLURM... this might take a while\n')
TButil.submit_slurm(slurm_file)
else:
for k in ['folding', 'design']:
TButil.plugin_bash(data['cmd'][k])
run([str(x) for x in data['cmd'][k]], stdout=DEVNULL)
return data