print qsub_args
os.system(qsub_args)
sys.exit(1)
partsize = int(os.environ['COBALT_PARTSIZE'])
partition = os.environ['COBALT_PARTNAME']
jobid = int(os.environ['COBALT_JOBID'])
print 'Nodes per job: %d' % npj
print 'MPI tasks per node: %d' % ppn
print 'Number of sub-block jobs: %d' % njobs
print 'Number of nodes: %d' % nodes
blocks = get_bootable_blocks(partition, nodes)
print 'Available blocks: %s' % blocks
boot_blocks(blocks)
# start sub-block jobs with background runjob helper processes
jobs = []
logs = []
# Lets make each job a tuple struct like
# (jobdir, bxv, v, rc).
for job, (block, corner, shape) in zip(jobdirs, block_corner_iter(blocks,
npj)):
print job, (block, corner, shape)
os.chdir(os.path.join(scratch, job[0]))
log = open('gbrelax.out', 'a')
locargs = '--block %s --corner %s --shape %s' % (block, corner, shape)
# runjob_args = ('python %s -n %d -p %d %s' % (locargs, npj*ppn, ppn, envargs)).split()
pyargs = 'python /home/lambert/pymodules/imeall/imeall/run_dyn.py -rc {rc} -i_v {i_v} -i_bxv {i_bxv} '.format(
rc=job[1], i_v=job[2], i_bxv=job[3])
njobs = 1
nodes = npj*njobs
job_xyz = glob.glob('feb*.xyz')[0]
bulk = Atoms(job_xyz)
line=[]
for at in bulk:
line.append( FixedLine(at.index, (0,0,1)) )
bulk.set_constraint(line)
hostname, ip = get_hostname_ip()
partsize, partition, job_name = get_cobalt_info()
blocks = get_bootable_blocks(partition, nodes)
print('Available blocks: %s' % blocks)
boot_blocks(blocks)
block, corner, shape = list(block_corner_iter(blocks, npj))[0]
print block, corner, shape
vasp_client = VaspClient(client_id=0,
kpts =[16,16,1],
amix = 0.01,
amin = 0.001,
bmix = 0.001,
amix_mag = 0.01,
bmix_mag = 0.001,
npj=npj,
ppn=ppn,
block=block,
corner=corner,
exe = '/home/avazquez/public/install/bin/cp2k.psmp' # '/soft/applications/cp2k/cp2k.psmp-2.5'
envargs = '--envs OMP_NUM_THREADS=%d BG_SMP_FAST_WAKEUP=YES BG_THREADLAYOUT=1 OMP_WAIT_POLICY=ACTIVE' % threads
# ACTUAL CODE
if 'COBALT_PARTSIZE' not in os.environ:
print('Not running under control of cobalt. Launching qsub...')
qsub_args = 'qsub -A %s -n %d -t %d -q %s --mode script --disable_preboot %s' % (acct, nodes, time, queue, sys.argv[0])
print(qsub_args)
os.system(qsub_args)
sys.exit(1)
partsize = int(os.environ['COBALT_PARTSIZE'])
partition = os.environ['COBALT_PARTNAME']
jobid = int(os.environ['COBALT_JOBID'])
# blocks = get_bootable_blocks(partition, nodes)
boot_blocks([partition])
print("partition: %s" % partition)
if os.path.exists('%s-1.restart' % jobstem):
# use restart as input
input_file = '%s-1.restart' % jobstem
else:
# files needed: inp and xyz
input_file = jobstem + '.inp'
# locargs = '--block %s' % blocks[0]
runjob_args = ('runjob --np %d -p %d --block %s %s : %s %s' % (nodes*ppn, ppn, partition, envargs, exe, input_file)).split()
print(' '.join(runjob_args))
job = subprocess.Popen(runjob_args)
# wait for all background jobs to finish
job.wait()