1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
|
#!/usr/bin/env python
# Copyright (c) 2005 The Regents of The University of Michigan
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met: redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer;
# redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution;
# neither the name of the copyright holders nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Authors: Ali Saidi
# Nathan Binkert
import os, os.path, re, sys
from os import environ as env, listdir
from os.path import basename, isdir, isfile, islink, join as joinpath
from filecmp import cmp as filecmp
from shutil import copyfile
progname = basename(sys.argv[0])
usage = """\
Usage:
%(progname)s [-c] [-e] [-f] [-q queue] [-v] <regexp>
-c clean directory if job can be run
-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
-v be verbose
%(progname)s -l [-v] <regexp>
-l list job names, don't submit
-v be verbose (list job parameters)
%(progname)s -h
-h display this help
""" % locals()
try:
import getopt
opts, args = getopt.getopt(sys.argv[1:], '-cd:efhlq:v')
except getopt.GetoptError:
sys.exit(usage)
clean = False
onlyecho = False
exprs = []
force = False
listonly = False
queue = ''
verbose = False
rootdir = re.sub(r'^/\.automount/', r'/n/', os.getcwd())
for opt,arg in opts:
if opt == '-c':
clean = True
if opt == '-d':
rootdir = arg
if opt == '-e':
onlyecho = True
if opt == '-f':
force = True
if opt == '-h':
print usage
sys.exit(0)
if opt == '-l':
listonly = True
if opt == '-q':
queue = arg
if opt == '-v':
verbose = True
basedir = joinpath(rootdir, 'Base')
linkdir = joinpath(rootdir, 'Link')
for arg in args:
exprs.append(re.compile(arg))
if not listonly and not onlyecho and isdir(linkdir):
print 'Checking for outdated files in Link directory'
entries = listdir(linkdir)
for entry in entries:
link = joinpath(linkdir, entry)
if not islink(link) or not isfile(link):
continue
base = joinpath(basedir, entry)
if not isfile(base) or not filecmp(link, base):
print 'Base/%s is different than Link/%s: copying' % (entry, entry)
copyfile(link, base)
import job, jobfile, pbs
test = jobfile.JobFile(joinpath(basedir, 'test.py'))
joblist = []
for jobname in test.jobs:
if not exprs:
joblist.append(jobname)
continue
for expr in exprs:
if expr.match(jobname):
joblist.append(jobname)
break
if listonly:
if verbose:
for jobname in joblist:
test.printinfo(jobname)
else:
for jobname in joblist:
print jobname
sys.exit(0)
if not onlyecho:
jl = []
for jobname in joblist:
if os.path.exists(jobname):
if not force:
if os.path.isfile(joinpath(jobname, '.success')):
continue
if os.path.isfile(joinpath(jobname, '.start')) and \
not os.path.isfile(joinpath(jobname, '.stop')):
continue
if not clean:
sys.exit('job directory not clean!')
job.cleandir(jobname)
else:
os.mkdir(jobname)
jl.append(jobname)
joblist = jl
for jobname in joblist:
jobdir = joinpath(rootdir, jobname)
if not onlyecho and not os.path.isdir(jobdir):
sys.exit('%s is not a directory. Cannot build job' % jobdir)
print >>sys.stderr, 'Job name: %s' % jobname
print >>sys.stderr, 'Job directory: %s' % jobdir
qsub = pbs.qsub()
qsub.pbshost = 'simpool.eecs.umich.edu'
qsub.stdout = joinpath(jobdir, 'jobout')
qsub.name = jobname
qsub.join = True
qsub.node_type = 'FAST'
qsub.onlyecho = onlyecho
qsub.env['ROOTDIR'] = rootdir
qsub.verbose = verbose
if len(queue):
qsub.queue = queue
qsub.do(joinpath(basedir, 'job.py'))
print >>sys.stderr, ''
|
