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espsite.py.example.SLURMsherlock
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espsite.py.example.SLURMsherlock
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# cluster-dependent definitions
# espresso.py will make use of all "self" variables in config class
import os
class config:
def __init__(self):
self.scratch = '/local-scratch/'+os.getenv('USER')
if not os.path.exists(self.scratch):
self.scratch = '/tmp'
self.submitdir = os.getenv('SLURM_SUBMIT_DIR')
self.batch = self.submitdir!=None
#we typically run batch jobs without openmp threads here
if self.batch:
os.putenv('OMP_NUM_THREADS','1')
#check for batch
if self.batch:
self.jobid = os.getenv('SLURM_JOBID')
nodefile = self.submitdir+'/nodefile.'+self.jobid
uniqnodefile = self.submitdir+'/uniqnodefile.'+self.jobid
os.system('scontrol show hostnames $SLURM_JOB_NODELIST >'+uniqnodefile)
taskspernode = os.getenv('SLURM_TASKS_PER_NODE')
xtaskspernode = taskspernode.find('(')
if xtaskspernode > -1:
taskspernode = taskspernode[:xtaskspernode]
os.system("awk '{for(i=0;i<"+taskspernode+";i++)print}' "+uniqnodefile+" >"+nodefile)
f = open(nodefile, 'r')
procs = [x.strip() for x in f.readlines()]
f.close()
self.procs = procs
nprocs = len(procs)
self.nprocs = nprocs
p = os.popen('wc -l <'+uniqnodefile, 'r')
nnodes = p.readline().strip()
p.close()
self.perHostMpiExec = 'mpiexec -machinefile '+uniqnodefile+' -np '+nnodes
self.perProcMpiExec = 'mpiexec -machinefile '+nodefile+' -np '+str(nprocs)+' -wdir %s %s'
self.perSpecProcMpiExec = 'mpiexec -machinefile %s -np %d -wdir %s %s'
def do_perProcMpiExec(self, workdir, program):
return os.popen2(self.perProcMpiExec % (workdir, program))
def do_perProcMpiExec_outputonly(self, workdir, program):
return os.popen(self.perProcMpiExec % (workdir, program), 'r')
def runonly_perProcMpiExec(self, workdir, program):
os.system(self.perProcMpiExec % (workdir, program))
def do_perSpecProcMpiExec(self, machinefile, nproc, workdir, program):
return os.popen3(self.perSpecProcMpiExec % (machinefile, nproc, workdir, program))