def run(self, classname, funcname, hosts='all', **kwargs):
""" Runs tasks in serial or parallel on specified hosts
"""
self.checkpoint()
self.save_kwargs(classname, funcname, kwargs)
if hosts == 'all':
# run on all available nodes
unix.run('srun '
+ '--wait=0 '
+ join(findpath('seisflows.system'), 'wrappers/run ')
+ PATH.OUTPUT + ' '
+ classname + ' '
+ funcname)
elif hosts == 'head':
# run on head node
unix.run('srun '
+ '--wait=0 '
+ join(findpath('seisflows.system'), 'wrappers/run_head ')
+ PATH.OUTPUT + ' '
+ classname + ' '
+ funcname)
else:
raise(KeyError('Hosts parameter not set/recognized.'))
def run(self, classname, funcname, hosts='all', **kwargs):
""" Runs tasks in serial or parallel on specified hosts
"""
self.checkpoint()
self.save_kwargs(classname, funcname, kwargs)
if hosts == 'all':
# run on all available nodes
unix.run('pbsdsh '
+ join(findpath('system'), 'wrapper/export_paths.sh ')
+ os.getenv('PATH') + ' '
+ os.getenv('LD_LIBRARY_PATH') + ' '
+ join(findpath('system'), 'wrapper/run_pbsdsh ')
+ PATH.OUTPUT + ' '
+ classname + ' '
+ funcname + ' '
+ dirname(findpath('seisflows')))
elif hosts == 'head':
# run on head node
unix.run('pbsdsh '
+ join(findpath('system'), 'wrapper/export_paths.sh ')
+ os.getenv('PATH') + ' '
+ os.getenv('LD_LIBRARY_PATH') + ' '
+ join(findpath('system'), 'wrapper/run_pbsdsh_head ')
+ PATH.OUTPUT + ' '
+ classname + ' '
+ funcname + ' '
+ dirname(findpath('seisflows')))
def run(self, classname, funcname, hosts='all', **kwargs):
""" Runs tasks in serial or parallel on specified hosts
"""
self.checkpoint()
self.save_kwargs(classname, funcname, kwargs)
if hosts == 'all':
unix.run(
findpath('seisflows.system') + '/' + 'wrappers/dsh2 ' +
str(PAR.NTASK) + ' ' + findpath('seisflows.system') + '/' +
'wrappers/run ' + PATH.OUTPUT + ' ' + classname + ' ' +
funcname + ' ' + PAR.ENVIRONS)
# call('srun '
# + '--wait=0 '
# + '--exclusive '
# + join(findpath('seisflows.system'), 'wrappers/run ')
# + PATH.OUTPUT + ' '
# + classname + ' '
# + funcname + ' '
# + PAR.ENVIRONS)
elif hosts == 'head':
# run on head node
unix.run(
findpath('seisflows.system') + '/' + 'wrappers/run ' +
PATH.OUTPUT + ' ' + classname + ' ' + funcname + ' ' +
PAR.ENVIRONS)
def submit(self, workflow):
"""Submits job
"""
unix.mkdir(PATH.OUTPUT)
unix.cd(PATH.OUTPUT)
# save current state
self.checkpoint()
# construct resource list
nodes = int(PAR.NTASK / PAR.NODESIZE)
cores = PAR.NTASK % PAR.NODESIZE
hours = int(PAR.WALLTIME / 60)
minutes = PAR.WALLTIME % 60
resources = 'walltime=%02d:%02d:00'%(hours, minutes)
if nodes == 0:
resources += ',mem=%dgb,nodes=1:ppn=%d'%(PAR.MEMORY, cores)
elif cores == 0:
resources += ',mem=%dgb,nodes=%d:ppn=%d'%(PAR.MEMORY, nodes, PAR.NODESIZE)
else:
resources += ',mem=%dgb,nodes=%d:ppn=%d+1:ppn=%d'%(PAR.MEMORY, nodes, PAR.NODESIZE, cores)
# construct arguments list
unix.run('qsub '
+ '-N %s '%PAR.TITLE
+ '-o %s '%(PATH.SUBMIT +'/'+ 'output.log')
+ '-l %s '%resources
+ '-j %s '%'oe'
+ findpath('system') +'/'+ 'wrappers/submit '
+ '-F %s '%PATH.OUTPUT)
def submit(self, workflow):
""" Submits workflow
"""
unix.mkdir(PATH.OUTPUT)
unix.cd(PATH.OUTPUT)
unix.mkdir(PATH.SUBMIT+'/'+'output.pbs')
self.checkpoint()
hours = PAR.WALLTIME/60
minutes = PAR.WALLTIME%60
walltime = 'walltime=%02d:%02d:00 ' % (hours, minutes)
ncpus = PAR.NODESIZE
mpiprocs = PAR.NODESIZE
# prepare qsub arguments
unix.run( 'qsub '
+ '%s ' % PAR.PBSARGS
+ '-l select=1:ncpus=%d:mpiprocs=%d ' % (ncpus, mpiprocs)
+ '-l %s ' % walltime
+ '-N %s ' % PAR.TITLE
+ '-j %s '%'oe'
+ '-o %s ' % (PATH.SUBMIT+'/'+'output.log')
+ '-V '
+ ' -- ' + findpath('seisflows.system') +'/'+ 'wrappers/submit '
+ PATH.OUTPUT)
def submit(self, workflow):
"""Submits job
"""
unix.mkdir(PATH.OUTPUT)
unix.cd(PATH.OUTPUT)
# save current state
self.checkpoint()
# construct resource list
nodes = PAR.NTASK/PAR.NODESIZE
cores = PAR.NTASK%PAR.NODESIZE
hours = PAR.WALLTIME/60
minutes = PAR.WALLTIME%60
resources = 'walltime=%02d:%02d:00 '%(hours, minutes)
if nodes == 0:
resources += ',nodes=1:ppn=%d'%cores
elif cores == 0:
resources += ',nodes=%d:ppn=16'%nodes
else:
resources += ',nodes=%d:ppn=16+1:ppn=%d'%(nodes, cores)
# construct arguments list
unix.run('qsub '
+ '-N %s '%PAR.TITLE
+ '-o %s '%(PATH.SUBMIT +'/'+ 'output.log')
+ '-l %s '%resources
+ '-j %s '%'oe'
+ findpath('system') +'/'+ 'pbs/wrapper_qsub '
+ PATH.OUTPUT,
shell=True)
def run(self, classname, funcname, hosts='all', **kwargs):
""" Runs tasks in serial or parallel on specified hosts
"""
self.checkpoint()
self.save_kwargs(classname, funcname, kwargs)
if hosts == 'all':
# run on all available nodes
unix.run('srun '
+ '--wait=0 '
+ join(findpath('system'), 'slurm/wrapper_pbsdsh ')
+ PATH.OUTPUT + ' '
+ classname + ' '
+ funcname)
elif hosts == 'head':
# run on head node
unix.run('srun '
+ '--wait=0 '
+ join(findpath('system'), 'slurm/wrapper_pbsdsh_head ')
+ PATH.OUTPUT + ' '
+ classname + ' '
+ funcname + ' '
+ findpath('seisflows'),
shell=True)
def submit(self, workflow):
"""Submits job
"""
unix.mkdir(PATH.OUTPUT)
unix.cd(PATH.OUTPUT)
# save current state
self.checkpoint()
# construct resource list
nodes = PAR.NTASK / PAR.NODESIZE
cores = PAR.NTASK % PAR.NODESIZE
hours = PAR.WALLTIME / 60
minutes = PAR.WALLTIME % 60
resources = 'walltime=%02d:%02d:00 ' % (hours, minutes)
if nodes == 0:
resources += ',nodes=1:ppn=%d' % cores
elif cores == 0:
resources += ',nodes=%d:ppn=16' % nodes
else:
resources += ',nodes=%d:ppn=16+1:ppn=%d' % (nodes, cores)
# construct arguments list
unix.run('qsub ' + '-N %s ' % PAR.TITLE + '-o %s ' %
(PATH.SUBMIT + '/' + 'output.log') + '-l %s ' % resources +
'-j %s ' % 'oe' + findpath('system') + '/' +
'pbs/wrapper_qsub ' + PATH.OUTPUT,
shell=True)
def run(self, classname, funcname, hosts='all', **kwargs):
""" Runs tasks in serial or parallel on specified hosts
"""
self.checkpoint()
self.save_kwargs(classname, funcname, kwargs)
if hosts == 'all':
unix.cd(join(findpath('seisflows.system'), 'wrappers'))
unix.run('mpiexec -n {} '.format(PAR.NTASK)
+ PAR.MPIARGS + ' '
+ 'run_mpi' + ' '
+ PATH.OUTPUT + ' '
+ classname + ' '
+ funcname)
elif hosts == 'head':
unix.cd(join(findpath('seisflows.system'), 'wrappers'))
unix.run('mpiexec -n 1 '
+ PAR.MPIARGS + ' '
+ 'run_mpi_head' + ' '
+ PATH.OUTPUT + ' '
+ classname + ' '
+ funcname)
else:
raise(KeyError('Hosts parameter not set/recognized.'))
def submit(self, workflow):
""" Submits workflow
"""
unix.mkdir(PATH.OUTPUT)
unix.cd(PATH.OUTPUT)
unix.mkdir(PATH.SUBMIT + '/' + 'output.slurm')
self.checkpoint()
# prepare sbatch arguments
unix.run('sbatch ' + '--job-name=%s ' % PAR.SUBTITLE + '--output %s ' %
(PATH.SUBMIT + '/' + 'output.log') +
'--ntasks-per-node=%d ' % PAR.NODESIZE + '--nodes=%d ' % 1 +
'--time=%d ' % PAR.WALLTIME + findpath('system') + '/' +
'slurm/wrapper_sbatch ' + PATH.OUTPUT)
def submit(self, workflow):
""" Submits workflow
"""
unix.mkdir(PATH.OUTPUT)
unix.cd(PATH.OUTPUT)
self.checkpoint()
# submit workflow
unix.run('sbatch ' + '--job-name=%s ' % PAR.SUBTITLE + '--output=%s ' %
(PATH.SUBMIT + '/' + 'output.log') +
'--cpus-per-task=%d ' % PAR.NPROC +
'--ntasks=%d ' % PAR.NTASK + '--time=%d ' % PAR.WALLTIME +
findpath('system') + '/' + 'slurm/wrapper_sbatch ' +
PATH.OUTPUT)
def submit(self, workflow):
""" Submits workflow
"""
unix.mkdir(PATH.OUTPUT)
unix.cd(PATH.OUTPUT)
self.checkpoint()
# submit workflow
unix.run('sbatch '
+ '--job-name=%s '%PAR.SUBTITLE
+ '--output=%s '%(PATH.SUBMIT +'/'+ 'output.log')
+ '--cpus-per-task=%d '%PAR.NPROC
+ '--ntasks=%d '%PAR.NTASK
+ '--time=%d '%PAR.WALLTIME
+ findpath('system') +'/'+ 'wrappers/submit '
+ PATH.OUTPUT)
def run(self, classname, funcname, hosts='all', **kwargs):
""" Runs tasks in serial or parallel on specified hosts
"""
self.checkpoint()
self.save_kwargs(classname, funcname, kwargs)
if hosts == 'all':
# run on all available nodes
unix.run('srun ' + '--wait=0 ' +
join(findpath('system'), 'slurm/wrapper_srun ') +
PATH.OUTPUT + ' ' + classname + ' ' + funcname)
elif hosts == 'head':
# run on head node
unix.run('srun ' + '--wait=0 ' +
join(findpath('system'), 'slurm/wrapper_srun_head ') +
PATH.OUTPUT + ' ' + classname + ' ' + funcname)
def submit(self, workflow):
""" Submits workflow
"""
unix.mkdir(PATH.OUTPUT)
unix.cd(PATH.OUTPUT)
unix.mkdir(PATH.SUBMIT+'/'+'output.slurm')
self.checkpoint()
# prepare sbatch arguments
unix.run('sbatch '
+ '--job-name=%s ' % PAR.SUBTITLE
+ '--output %s ' % (PATH.SUBMIT+'/'+'output.log')
+ '--ntasks-per-node=%d ' % PAR.NODESIZE
+ '--nodes=%d ' % 1
+ '--time=%d ' % PAR.WALLTIME
+ findpath('system') +'/'+ 'slurm/wrapper_sbatch '
+ PATH.OUTPUT)
def submit(self, workflow):
""" Submits workflow
"""
unix.mkdir(PATH.OUTPUT)
unix.cd(PATH.OUTPUT)
self.checkpoint()
# if not exists(PATH.SUBMIT + '/' + 'scratch'):
# unix.ln(PATH.SCRATCH, PATH.SUBMIT + '/' + 'scratch')
node = 1 #PAR.NTASK/4
ntask_per_node = 4
unix.run('sbatch ' + '%s ' % PAR.SLURMARGS +
'--job-name=%s ' % PAR.TITLE + '--output=%s ' %
(PATH.WORKDIR + '/' + 'output.log') + '--nodes %d ' % node +
'--ntasks-per-node=%d ' % ntask_per_node +
'--gres=gpu:%d ' % PAR.NGPU + '--time=%d ' % PAR.WALLTIME +
findpath('seisflows.system') + '/' + 'wrappers/submit ' +
PATH.OUTPUT)
def submit(self, workflow):
""" Submits workflow
"""
unix.mkdir(PATH.OUTPUT)
unix.cd(PATH.OUTPUT)
unix.mkdir(PATH.SUBMIT+'/'+'output.lsf')
self.checkpoint()
# prepare bsub arguments
unix.run('bsub '
+ '%s ' % PAR.LSFARGS
+ '-J %s ' % PAR.TITLE
+ '-o %s ' % (PATH.SUBMIT+'/'+'output.log')
+ '-n %d ' % PAR.NTASK
+ '-e %s ' % (PATH.SUBMIT+'/'+'error.log')
+ '-W %d:00 ' % PAR.WALLTIME
+ findpath('seisflows.system') +'/'+ 'wrappers/submit '
+ PATH.OUTPUT)
def hostlist(self):
with open(PATH.SYSTEM + '/' + 'hostlist', 'w') as f:
unix.run('scontrol show hostname $SLURM_JOB_NODEFILE', stdout=f)
with open(PATH.SYSTEM + '/' + 'hostlist', 'r') as f:
return [line.strip() for line in f.readlines()]
