def do_process_fetch(workdir, test=False):
engine = create_engine(engine_file)
Session = sessionmaker(bind=engine)
session = Session()
clusters = Clusters()
job = get_job_from_workdir(session, workdir)
cluster, shell = clusters.get_cluster(job.cluster_name)
print(job)
print(job.status, job.name, job.id, job.workdir)
#if job.status == "S": return
rsync_return_code = cluster.pull(shell, job)
assert (rsync_return_code == 0)
if test:
chemtime, target_chemtime = test_workdir(job)
print chemtime, target_chemtime
# If the simulation hasn't started yet, skip
if not (chemtime and target_chemtime): return
# If the target chemtime hasn't been achieved, don't stop
if not (chemtime == target_chemtime): return
# Stop the simulation if complete
return
if job.status == "S": return
cluster.cancel(shell, job.cluster_id)
print("Stopping", job)
job.status = "S" # Stopped
session.add(job)
session.commit()
def process_resubmit(args):
engine = create_engine(engine_file)
Session = sessionmaker(bind=engine)
session = Session()
clusters = Clusters()
if True:
print("Checking")
jobs = [job for job in session.query(Job).order_by(Job.id) if job.status != "S"]
print("Found {} jobs to checkon".format(len(jobs)))
for job in jobs :
if job.status == "S": continue
if args.cluster and not job.cluster_name.lower().startswith(args.cluster): continue
print job
cluster, shell = clusters.get_cluster(job.cluster_name)
if not shell: continue
status = cluster.get_status(shell, job)
job.status = status
print("Before:",status, job.id)
if os.path.exists("{}/confout.gro".format(job.local_workdir)):
job.status = "S"
if job.status == "C":
job = cluster.submit(shell, job)
print("After:", job.status, job.id)
session.add(job)
session.commit()
def do_process_fetch(workdir, test=False):
engine = create_engine(engine_file)
Session = sessionmaker(bind=engine)
session = Session()
clusters = Clusters()
job = get_job_from_workdir(session, workdir)
cluster, shell = clusters.get_cluster(job.cluster_name)
print(job)
print(job.status, job.name, job.id, job.workdir)
#if job.status == "S": return
rsync_return_code = cluster.pull(shell, job)
assert(rsync_return_code==0)
if test:
chemtime, target_chemtime = test_workdir(job)
print chemtime, target_chemtime
# If the simulation hasn't started yet, skip
if not (chemtime and target_chemtime): return
# If the target chemtime hasn't been achieved, don't stop
if not (chemtime == target_chemtime): return
# Stop the simulation if complete
return
if job.status == "S": return
cluster.cancel(shell, job.cluster_id)
print("Stopping", job)
job.status = "S" # Stopped
session.add(job)
session.commit()
def process_resubmit(args):
engine = create_engine(engine_file)
Session = sessionmaker(bind=engine)
session = Session()
clusters = Clusters()
if True:
print("Checking")
jobs = [
job for job in session.query(Job).order_by(Job.id)
if job.status != "S"
]
print("Found {} jobs to checkon".format(len(jobs)))
for job in jobs:
if job.status == "S": continue
if args.clusters and not job.cluster_name.lower() in args.clusters:
continue
print job
cluster, shell = clusters.get_cluster(job.cluster_name)
if not shell: continue
status = cluster.get_status(shell, job)
job.status = status
print("Before:", status, job.id)
if os.path.exists("{}/confout.gro".format(job.local_workdir)):
job.status = "S"
if job.status == "C":
job = cluster.submit(shell, job)
print("After:", job.status, job.id)
session.add(job)
session.commit()
def main():
args = parse_args()
engine = create_engine(engine_file)
Session = sessionmaker(bind=engine)
session = Session()
clusters = Clusters()
job = get_job_from_workdir(session, args.workdir)
print job
cluster, shell = clusters.get_cluster(job.cluster_name)
print cluster, shell
return_code = cluster.delete(shell, job)
assert (return_code == 0)
def main():
args = parse_args()
engine = create_engine(engine_file)
Session = sessionmaker(bind=engine)
session = Session()
clusters = Clusters()
job = get_job_from_workdir(session, args.workdir)
print job
cluster, shell = clusters.get_cluster(job.cluster_name)
print cluster, shell
rsync_return_code = cluster.push(shell, job)
assert(rsync_return_code==0)
def main():
args = parse_args()
engine = create_engine(engine_file)
Session = sessionmaker(bind=engine)
session = Session()
clusters = Clusters()
for workdir in args.workdir:
job = get_job_from_workdir(session, workdir)
print job
cluster, shell = clusters.get_cluster(job.cluster_name)
print cluster, shell
cluster.cancel(shell, job)
job.status = "S" # Stopped
session.add(job)
session.commit()
def test_rsync():
f = "data/M2__monomer__charmm36__charmm22stprot__tip3p__strand_bilayer__run_1.tpr"
clusters = Clusters()
names = clusters.clusters.keys()
names = ["jade", "arcus", "biowulf"]
for name in names:
cluster, shell = clusters.get_cluster(name)
print cluster
output = "{}.tpr".format(name)
cluster.test_push(shell, f, "/tmp/topol.tpr", verbose=False)
cluster.test_pull(shell, "/tmp/topol.tpr", output, verbose=False)
desired = md5sum(f)
actual = md5sum(output)
print desired, actual
np.testing.assert_equal(actual, desired)
print("Testing complete, closing down")
def test_rsync():
f = "data/M2__monomer__charmm36__charmm22stprot__tip3p__strand_bilayer__run_1.tpr"
clusters = Clusters()
names = clusters.clusters.keys()
names = ["jade", "arcus", "biowulf"]
for name in names:
cluster, shell = clusters.get_cluster(name)
print cluster
output = "{}.tpr".format(name)
cluster.test_push(shell, f, "/tmp/topol.tpr", verbose=False)
cluster.test_pull(shell, "/tmp/topol.tpr", output, verbose=False)
desired = md5sum(f)
actual = md5sum(output)
print desired, actual
np.testing.assert_equal(actual, desired)
print("Testing complete, closing down")
def process_fetch(args):
engine = create_engine(engine_file)
Session = sessionmaker(bind=engine)
session = Session()
clusters = Clusters()
if True:
print("Fetching")
jobs = [job for job in session.query(Job).order_by(Job.id)]
print(dir(jobs[0]))
for i, job in enumerate(jobs) :
if job.status == "S": continue
if not job.cluster_name.lower().startswith(args.cluster): continue
print(i+1, len(jobs), job)
cluster, shell = clusters.get_cluster(job.cluster_name)
if not shell: continue
rsync_return_code = cluster.pull(shell, job)
def process_fetch(args):
engine = create_engine(engine_file)
Session = sessionmaker(bind=engine)
session = Session()
clusters = Clusters()
if True:
print("Fetching")
jobs = [job for job in session.query(Job).order_by(Job.id)]
print(dir(jobs[0]))
for i, job in enumerate(jobs):
if job.status == "S": continue
if not job.cluster_name.lower() in args.clusters: continue
print(i + 1, len(jobs), job)
cluster, shell = clusters.get_cluster(job.cluster_name)
if not shell: continue
rsync_return_code = cluster.pull(shell, job)
def main():
args = parse_args()
engine = create_engine(engine_file)
Session = sessionmaker(bind=engine)
session = Session()
clusters = Clusters()
for workdir in args.workdir:
job = get_job_from_workdir(session, workdir)
print(workdir,job)
if not args.refresh: continue
cluster, shell = clusters.get_cluster(job.cluster_name)
print cluster, shell
actual, desired = job.status, cluster.get_status(shell, job)
print "actual =", actual, "desired =", desired
if actual == desired : continue
def main():
args = parse_args()
engine = create_engine(engine_file)
Session = sessionmaker(bind=engine)
session = Session()
clusters = Clusters()
for workdir in args.workdir:
job = get_job_from_workdir(session, workdir)
print(workdir, job)
if not args.refresh: continue
cluster, shell = clusters.get_cluster(job.cluster_name)
print cluster, shell
actual, desired = job.status, cluster.get_status(shell, job)
print "actual =", actual, "desired =", desired
if actual == desired: continue
def main():
args = parse_args()
engine = create_engine(engine_file)
Session = sessionmaker(bind=engine)
session = Session()
clusters = Clusters()
for workdir in args.workdir:
print(workdir)
job = get_job_from_workdir(session, workdir)
if not job: continue
if not args.dry:
cluster, shell = clusters.get_cluster(job.cluster_name)
print(cluster, shell)
cluster.cancel(shell, job)
job.status = "S" # Stopped
session.add(job)
session.commit()
def main():
args = parse_args()
print(args.workdir)
engine = create_engine(engine_file)
Job.metadata.create_all(engine)
Session = sessionmaker(bind=engine)
session = Session()
if args.workdir == [] and os.path.exists("workdir"): args.workdir = ["workdir"]
# Restore an existing workdir
if len(args.workdir):
for workdir in args.workdir:
job = get_job_from_workdir(session, workdir)
print job
if job.status == "Q" or job.status == "R" or job.status == "PD":
print("Job already running or queued")
return
cluster, shell = Clusters().get_cluster(job.cluster_name)
job = cluster.submit(shell, job, duration=args.duration, nodes=args.nodes, partition=args.partition, ntasks_per_node=args.ntasks_per_node)
status = cluster.get_status(shell, job)
job.status = status
if args.partition and job.partition != args.partition: job.partition = args.partition
if args.nodes and job.nodes != args.nodes: job.nodes = args.nodes
session.add(job)
session.commit()
# Create a brand-new workdir
else:
cluster, shell = Clusters().get_cluster(args.cluster)
job = create(args.topol, cluster, shell, args.jobname, args.duration, args.nodes, args.processes, args.script, args.partition, ntasks_per_node=args.ntasks_per_node)
assert(job)
print job
status = cluster.get_status(shell, job)
print status
if not job.cluster_id:
job = cluster.submit(shell, job)
print status
session.add(job)
session.commit()