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])
runjob_args = ('runjob %s -n %d -p %d %s : %s' %
(locargs, 1, 1, envargs, pyargs)).split()
print ' '.join(runjob_args)
jobs.append(subprocess.Popen(runjob_args, stdout=log))
logs.append(log)
# wait for all background jobs to finish, then flush their logs
for (job, log) in zip(jobs, logs):
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,
shape=shape,
exe = vasp,
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,
shape=shape,
exe=vasp,
assert nodes == partsize
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 = []
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))
log = open('%d.vasp.stdout' % jobid, 'w')
locargs = '--block %s --corner %s --shape %s' % (block, corner, shape)
runjob_args = ('runjob %s -n %d -p %d %s : %s' % (locargs, npj*ppn, ppn, envargs, vasp)).split()
print ' '.join(runjob_args)
print
jobs.append(subprocess.Popen(runjob_args, stdout=log))
logs.append(log)
# wait for all background jobs to finish, then flush their logs
for (job, log) in zip(jobs, logs):
job.wait()
job_name, os.path.splitext(os.path.basename(sys.argv[0]))[0])
except KeyError:
# Not running under cobalt, so let's qsub ourselves
print 'NOT RUNNING COBALT'
qsub_args = 'qsub -A %s -n %d -t %d -q %s --mode script --disable_preboot %s' % \
(acct, nodes, runtime, queue, ' '.join(sys.argv))
print qsub_args
os.system(qsub_args)
sys.exit(1)
blocks = get_bootable_blocks(partition, nodes)
print('Available blocks: %s' % blocks)
boot_blocks(blocks)
qm_subblocks = [
(i, bcs) for (i, bcs) in enumerate(block_corner_iter(blocks, qm_npj))
]
print 'qm_subblocks', qm_subblocks
qm_clients = [
VaspClient(client_id, qm_exe, qm_env, qm_npj, qm_ppn, block, corner,
shape, jobname, **vasp_args)
for client_id, (block, corner, shape) in qm_subblocks
]
else:
qm_clients = []
hostname, ip = '<dummy>', 0
print 'FEN hostname: %s' % hostname
print 'FEN server IP: %s' % ip
print 'QM nodes per job: %r' % qm_npj
print 'QM MPI tasks per node: %r' % qm_ppn
os.system(qsub_args)
sys.exit(1)
if args.block !='0':
block = args.block
corner = args.corner
shape = args.shape
else:
#no block information available need to grab this.
partsize = int(os.environ['COBALT_PARTSIZE'])
partition = os.environ['COBALT_PARTNAME']
jobid = int(os.environ['COBALT_JOBID'])
blocks = get_bootable_blocks(partition, nodes)
print 'Available blocks: %s' % blocks
boot_blocks(blocks)
print block_corner_iter(blocks, nodes)
for b, c, s in block_corner_iter(blocks,nodes):
block, corner, shape = b, c, s
#Running this script on it's own so need to boot blocks
npj = int(args.npj)
ppn = int(args.ppn)
hostname, ip = get_hostname_ip()
reference_file = 'ref_slab.xyz' # Reference file for Nye tensor
continuation = args.continuation # If true, restart form last frame of most recent *.traj.xyz file
test_mode = False
classical = False # If true, do classical MD instead of QM/MM
sim_T = 300.0*units.kB # Simulation temperature
rescale_velo = True # Rescale velocities to 2*sim_T
timestep = 1.0*units.fs # Timestep (NB: time base units are not fs!)
cutoff_skin = 2.0*units.Ang # Amount by which potential cutoff is increased
partsize, partition, job_name = get_cobalt_info()
jobname = '%s.%s' % (job_name, os.path.splitext(os.path.basename(sys.argv[0]))[0])
except KeyError:
# Not running under cobalt, so let's qsub ourselves
print 'NOT RUNNING COBALT'
qsub_args = 'qsub -A %s -n %d -t %d -q %s --mode script --disable_preboot %s' % \
(acct, nodes, runtime, queue, ' '.join(sys.argv))
print qsub_args
os.system(qsub_args)
sys.exit(1)
blocks = get_bootable_blocks(partition, nodes)
print('Available blocks: %s' % blocks)
boot_blocks(blocks)
qm_subblocks = [(i, bcs) for (i, bcs) in enumerate(block_corner_iter(blocks, qm_npj)) ]
print 'qm_subblocks', qm_subblocks
qm_clients = [VaspClient(client_id, qm_exe, qm_env, qm_npj, qm_ppn, block, corner, shape, jobname,
**vasp_args) for client_id, (block, corner, shape) in qm_subblocks]
else:
qm_clients = []
hostname, ip = '<dummy>', 0
print 'FEN hostname: %s' % hostname
print 'FEN server IP: %s' % ip
print 'QM nodes per job: %r' % qm_npj
print 'QM MPI tasks per node: %r' % qm_ppn
print 'Number of QM jobs: %d' % n_qm_jobs
print 'Total number of sub-block jobs: %d' % njobs
print 'Total number of nodes: %d' % nodes
# ******* End of parameters *************