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-rwxr-xr-xutil/pbs/job.py2
-rwxr-xr-xutil/pbs/pbs.py26
-rwxr-xr-xutil/pbs/send.py29
3 files changed, 37 insertions, 20 deletions
diff --git a/util/pbs/job.py b/util/pbs/job.py
index fb375cf5d..0fd3b4f97 100755
--- a/util/pbs/job.py
+++ b/util/pbs/job.py
@@ -149,7 +149,7 @@ if __name__ == '__main__':
pbs_jobname = env['PBS_JOBNAME']
basedir = joinpath(rootdir, 'Base')
jobname = env.setdefault('JOBNAME', pbs_jobname)
- jobfile = env.setdefault('JOBFILE', joinpath(basedir, 'test.py'))
+ jobfile = env.setdefault('JOBFILE', joinpath(rootdir, 'Test.py'))
outdir = env.setdefault('OUTPUT_DIR', joinpath(rootdir, jobname))
env['POOLJOB'] = 'True'
diff --git a/util/pbs/pbs.py b/util/pbs/pbs.py
index ecacbeba2..292ddf1f9 100755
--- a/util/pbs/pbs.py
+++ b/util/pbs/pbs.py
@@ -91,19 +91,20 @@ class MyPOpen(object):
class qsub:
def __init__(self):
+ self.afterok = None
self.hold = False
self.join = False
self.keep_stdout = False
self.keep_stderr = False
- self.node_type = ''
+ self.node_type = None
self.mail_abort = False
self.mail_begin = False
self.mail_end = False
- self.name = ''
- self.stdout = ''
- self.priority = 0
- self.queue = ''
- self.pbshost = ''
+ self.name = None
+ self.stdout = None
+ self.priority = None
+ self.queue = None
+ self.pbshost = None
self.qsub = 'qsub'
self.env = {}
@@ -118,7 +119,7 @@ class qsub:
if self.hold:
self.cmd.append('-h')
- if len(self.stdout):
+ if self.stdout:
self.cmd.append('-olocalhost:' + self.stdout)
if self.keep_stdout and self.keep_stderr:
@@ -133,7 +134,7 @@ class qsub:
if self.join:
self.cmd.append('-joe')
- if len(self.node_type):
+ if self.node_type:
self.cmd.append('-lnodes=' + self.node_type)
if self.mail_abort or self.mail_begin or self.mail_end:
@@ -147,15 +148,18 @@ class qsub:
if len(flags):
self.cmd.append('-m ' + flags)
- if len(self.name):
+ if self.name:
self.cmd.append("-N%s" % self.name)
- if self.priority != 0:
+ if self.priority:
self.cmd.append('-p' + self.priority)
- if len(self.queue):
+ if self.queue:
self.cmd.append('-q' + self.queue)
+ if self.afterok:
+ self.cmd.append('-Wdepend=afterok:%s' % self.after)
+
self.cmd.extend(args)
self.script = script
self.command = ' '.join(self.cmd + [ self.script ])
diff --git a/util/pbs/send.py b/util/pbs/send.py
index 51eb8425e..d04f9066b 100755
--- a/util/pbs/send.py
+++ b/util/pbs/send.py
@@ -82,11 +82,11 @@ Usage:
-e only echo pbs command info, don't actually send the job
-f force the job to run regardless of state
-q <queue> submit job to the named queue
- -j <jobfile> specify the jobfile (default is <basedir>/test.py)
+ -j <jobfile> specify the jobfile (default is <rootdir>/Test.py)
-v be verbose
%(progname)s [-j <jobfile>] -l [-v] <regexp>
- -j <jobfile> specify the jobfile (default is <basedir>/test.py)
+ -j <jobfile> specify the jobfile (default is <rootdir>/Test.py)
-l list job names, don't submit
-v be verbose (list job parameters)
@@ -96,10 +96,11 @@ Usage:
try:
import getopt
- opts, args = getopt.getopt(sys.argv[1:], '-CRcd:efhj:lq:v')
+ opts, args = getopt.getopt(sys.argv[1:], '-Ccdefhj:lq:Rt:v')
except getopt.GetoptError:
sys.exit(usage)
+depend = False
clean = False
onlyecho = False
exprs = []
@@ -107,18 +108,19 @@ force = False
listonly = False
queue = ''
verbose = False
-jfile = 'Base/test.py'
+jfile = 'Test.py'
docpts = False
doruns = True
runflag = False
+node_type = 'FAST'
for opt,arg in opts:
if opt == '-C':
docpts = True
- if opt == '-R':
- runflag = True
if opt == '-c':
clean = True
+ if opt == '-d':
+ depend = True
if opt == '-e':
onlyecho = True
if opt == '-f':
@@ -132,6 +134,10 @@ for opt,arg in opts:
listonly = True
if opt == '-q':
queue = arg
+ if opt == '-R':
+ runflag = True
+ if opt == '-t':
+ node_type = arg
if opt == '-v':
verbose = True
@@ -149,6 +155,8 @@ conf = jobfile.JobFile(jfile)
if not listonly and not onlyecho and isdir(conf.linkdir):
if verbose:
print 'Checking for outdated files in Link directory'
+ if not isdir(conf.basedir):
+ os.mkdir(conf.basedir)
syncdir(conf.linkdir, conf.basedir)
jobnames = {}
@@ -237,6 +245,9 @@ namehack = NameHack()
for job in joblist:
jobdir = JobDir(joinpath(conf.rootdir, job.name))
+ if depend:
+ cptdir = JobDir(joinpath(conf.rootdir, job.checkpoint.name))
+ cptjob = cptdir.readval('.pbs_jobid')
if not onlyecho:
jobdir.create()
@@ -249,10 +260,12 @@ for job in joblist:
qsub.stdout = jobdir.file('jobout')
qsub.name = job.name[:15]
qsub.join = True
- qsub.node_type = 'FAST'
+ qsub.node_type = node_type
qsub.env['ROOTDIR'] = conf.rootdir
qsub.env['JOBNAME'] = job.name
- if len(queue):
+ if depend:
+ qsub.afterok = cptjob
+ if queue:
qsub.queue = queue
qsub.build(joinpath(progpath, 'job.py'))