def main():
if len(sys.argv) != 2:
print "usage: psub PBS_SCRIPT"
sys.exit()
if sys.argv[1] == "-h" or sys.argv[1] == "--help":
print "usage: psub PBS_SCRIPT"
sys.exit()
qsubstr = open(sys.argv[1], "r").read()
job = pbs.Job(qsubstr=qsubstr)
job.submit()
def submit(self):
"""Submit a PBS job for this VASP relaxation"""
# first, check if the job has already been submitted and is not completed
db = pbs.JobDB()
print "rundir", self.calcdir
id = db.select_regex_id("rundir", self.calcdir)
print "id:", id
sys.stdout.flush()
if id != []:
for j in id:
job = db.select_job(j)
# taskstatus = ["Incomplete","Complete","Continued","Check","Error:.*","Aborted"]
# jobstatus = ["C","Q","R","E","W","H","M"]
if job["jobstatus"] != "C":
print "JobID:", job["jobid"], " Jobstatus:", job["jobstatus"], " Not submitting."
sys.stdout.flush()
return
#elif job["taskstatus"] in ["Complete", "Check"] or re.match( "Error:.*", job["taskstatus"]):
# print "JobID:", job["jobid"], " Taskstatus:", job["taskstatus"], " Not submitting."
# sys.stdout.flush()
# return
# second, only submit a job if relaxation status is "incomplete"
# construct the Relax object
relaxation = vasp.Relax(self.calcdir, self.run_settings())
# check the current status
(status, task) = relaxation.status()
if status == "complete":
print "Status:", status, " Not submitting."
sys.stdout.flush()
# ensure job marked as complete in db
if self.auto:
for j in id:
job = db.select_job(j)
if job["taskstatus"] == "Incomplete":
try:
pbs.complete_job(jobid=j)
except (pbs.PBSError, pbs.JobDBError, pbs.EligibilityError) as e:
print str(e)
sys.stdout.flush()
# ensure results report written
if not os.path.isfile(os.path.join(self.calcdir, "properties.calc.json")):
self.report()
return
elif status == "not_converging":
print "Status:", status, " Not submitting."
sys.stdout.flush()
return
elif status != "incomplete":
raise vaspwrapper.VaspWrapperError("unexpected relaxation status: '" + status + "' and task: '" + task + "'")
sys.stdout.flush()
return
print "Preparing to submit a VASP relaxation PBS job"
sys.stdout.flush()
# cd to configdir, submit jobs from configdir, then cd back to currdir
currdir = os.getcwd()
os.chdir(self.calcdir)
# determine the number of atoms in the configuration
print " Counting atoms in the POSCAR"
sys.stdout.flush()
pos = vasp.io.Poscar(os.path.join(self.configdir,"POS"))
N = len(pos.basis)
print " Constructing a PBS job"
sys.stdout.flush()
# construct a pbs.Job
job = pbs.Job(name=casm.jobname(self.configdir),\
account=self.settings["account"],\
nodes=int(math.ceil(float(N)/float(self.settings["atom_per_proc"])/float(self.settings["ppn"]))),\
ppn=int(self.settings["ppn"]),\
walltime=self.settings["walltime"],\
pmem=self.settings["pmem"],\
qos=self.settings["qos"],\
queue=self.settings["queue"],\
message=self.settings["message"],\
email=self.settings["email"],\
priority=self.settings["priority"],\
command="python -c \"import casm.vaspwrapper; casm.vaspwrapper.Relax('" + self.configdir + "').run()\"",\
auto=self.auto)
print " Submitting"
sys.stdout.flush()
# submit the job
job.submit()
# return to current directory
os.chdir(currdir)
print "CASM VASPWrapper relaxation PBS job submission complete\n"
sys.stdout.flush()
sys.stdout.write(line)
db = pbs.JobDB()
#initialize Relax object and begin relaxation
cmd = "python -c \"import quantumespresso; relaxation=quantumespresso.Relax('" + relaxdir + "');relaxation.settings['" + "infilename" + "']='" + case[
"infilename"] + "';relaxation.settings['" + "outfilename" + "']='" + case[
"outfilename"] + "';relaxation.run();\"\n"
job = pbs.Job(name="casm_unit_test",\
account=None,\
nodes=1,\
ppn=2,\
walltime="1:00:00",\
pmem=None,\
qos=None,\
queue="batch",\
message=None,\
email=None,\
priority=0,\
command=cmd,\
auto=True)
os.chdir(relaxdir)
job.submit()
os.chdir(curr)
db.update()
id = db.select_regex_id("rundir", relaxdir)
j = db.select_job(id[-1])
while (j["jobstatus"] == "Q" or j["jobstatus"] == "R"):
time.sleep(10)
db.update()
def submit(self): #pylint: disable=too-many-statements
"""Submit a PBS job for this SeqQuest relaxation"""
print "Submitting..."
print "Configuration:", self.configname
# first, check if the job has already been submitted and is not completed
db = pbs.JobDB()
print "Calculation directory:", self.calcdir
id = db.select_regex_id("rundir", self.calcdir)
print "JobID:", id
sys.stdout.flush()
if id != []:
for j in id:
job = db.select_job(j)
if job["jobstatus"] != "C":
print "JobID:", job["jobid"], " Jobstatus:", job[
"jobstatus"], " Not submitting."
sys.stdout.flush()
return
# second, only submit a job if relaxation status is "incomplete"
# construct the Relax object
relaxation = seqquest.Relax(self.calcdir, self.run_settings())
# check the current status
(status, task) = relaxation.status()
if status == "complete":
print "Status:", status, " Not submitting."
sys.stdout.flush()
# ensure job marked as complete in db
if self.auto:
for j in id:
job = db.select_job(j)
if job["taskstatus"] == "Incomplete":
try:
pbs.complete_job(jobid=j)
except (pbs.PBSError, pbs.JobDBError,
pbs.EligibilityError) as e:
print str(e)
sys.stdout.flush()
# ensure results report written
if not os.path.isfile(
os.path.join(self.calcdir, "properties.calc.json")):
self.finalize()
return
elif status == "not_converging":
print "Status:", status, " Not submitting."
sys.stdout.flush()
return
elif status != "incomplete":
raise questwrapper.QuestWrapperError(
"unexpected relaxation status: '" + status + "' and task: '" +
task + "'")
# This code can never be reached...
# sys.stdout.flush()
# return
print "Preparing to submit a SeqQuest relaxation PBS job"
sys.stdout.flush()
# cd to configdir, submit jobs from configdir, then cd back to currdir
currdir = os.getcwd()
os.chdir(self.calcdir)
# determine the number of atoms in the configuration
print "Counting atoms in the POSCAR"
sys.stdout.flush()
geom = seqquest.seqquest_io.Geom.POS(
os.path.join(self.configdir, "POS"))
N = len(geom.basis)
# construct command to be run
cmd = ""
if self.settings["preamble"] is not None:
# Append any instructions given in the 'preamble' file, if given
preamble = self.casm_directories.settings_path_crawl(
self.settings["preamble"], self.configname, self.clex)
with open(preamble) as my_preamble:
cmd += "".join(my_preamble) + "\n"
if self.settings["prerun"] is not None:
cmd += self.settings["prerun"] + "\n"
cmd += "python -c \"import casm.vaspwrapper; casm.vaspwrapper.Relax('" + self.configdir + "').run()\"\n"
if self.settings["postrun"] is not None:
cmd += self.settings["postrun"] + "\n"
print "Constructing a PBS job"
sys.stdout.flush()
# construct a pbs.Job
job = pbs.Job(name=casm.jobname(self.configdir),\
account=self.settings["account"],\
nodes=int(math.ceil(float(N)/float(self.settings["atom_per_proc"])/float(self.settings["ppn"]))),\
ppn=int(self.settings["ppn"]),\
walltime=self.settings["walltime"],\
pmem=self.settings["pmem"],\
qos=self.settings["qos"],\
queue=self.settings["queue"],\
message=self.settings["message"],\
email=self.settings["email"],\
priority=self.settings["priority"],\
command=cmd,\
auto=self.auto)
print "Submitting"
sys.stdout.flush()
# submit the job
job.submit()
self.report_status("submitted")
# return to current directory
os.chdir(currdir)
print "CASM QuestWrapper relaxation PBS job submission complete\n"
sys.stdout.flush()
def test_run_single(self):
"""
Test vasp.Relax.run()
"""
curr = os.getcwd()
cases = self.cases["run_single"]
for case in cases:
# do tests
# load Relax directory
filesdir = join(fixtures.projects_dir, case["proj"])
if os.path.isdir(join(filesdir, "relaxdir")):
shutil.rmtree(join(filesdir, "relaxdir"))
shutil.copytree(filesdir, join(filesdir, "relaxdir"))
relaxdir = join(filesdir, "relaxdir")
##CREATE POTCAR##
if "VASP_POTENTIAL_DIR" not in os.environ.keys():
print "NO SPECIFIED ENVIRONMENT VARIABLE VASP_POTENTIAL_DIR\n"
print "USING DEFAULT OF $HOME/vasp_potentials\n"
vasp_pot = "$HOME/vasp_potentials"
else:
vasp_pot = os.environ["VASP_POTENTIAL_DIR"].encode(
'ascii', 'ignore')
with open(join(relaxdir, "POTCAR"), 'wb') as wfd:
for f in case["potcars"]:
with open(join(join(vasp_pot, f), "POTCAR"), 'rb') as fd:
shutil.copyfileobj(fd, wfd)
fd.close()
wfd.close()
print "Relax dir is", relaxdir
db = pbs.JobDB()
#initialize Relax object and begin relaxation
cmd = "python -c \"import vasp; relaxation=vasp.Relax('" + relaxdir + "');relaxation.run();\"\n"
job = pbs.Job(name="casm_unit_test",\
account=None,\
nodes=1,\
ppn=2,\
walltime="1:00:00",\
pmem=None,\
qos=None,\
queue="batch",\
message=None,\
email=None,\
priority=0,\
command=cmd,\
auto=True)
os.chdir(relaxdir)
job.submit()
os.chdir(curr)
db.update()
id = db.select_regex_id("rundir", relaxdir)
j = db.select_job(id[-1])
while j["jobstatus"] == "Q":
time.sleep(10)
db.update()
j = db.select_job(id[-1])
while j["jobstatus"] == "R":
time.sleep(10)
db.update()
j = db.select_job(id[-1])
self.assertTrue(exists(join(relaxdir, "run.final/OUTCAR")))
if relaxdir == join(filesdir, "relaxdir"):
shutil.rmtree(relaxdir)
print "done!"