Better pool job handling

util/pbs/job.py:
    the default jobfile is now Test.py in the root of the jobs directory
util/pbs/pbs.py:
    Clean up the qsub options handling and add job dependencies
util/pbs/send.py:
    the default jobfile is now Test.py in the root of the jobs directory
    add a flag to depend on your checkpoint
    add a flag to specify your node type
    create the base directory if it doesn't exist

--HG--
extra : convert_revision : dfffa4a5b0e68b2550a28fbb06b9d6a208ea1f2e

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'
 

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 ])

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'))