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
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
|
#! /usr/bin/env python
# Copyright (c) 2004-2005 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.
import sys
import os
import re
import time
import optparse
import pexpect
progname = os.path.basename(sys.argv[0])
usage = "%prog [options] command [command arguments]"
optparser = optparse.OptionParser(usage=usage)
optparser.allow_interspersed_args=False
optparser.add_option('-e', dest='stderr_file',
help='command stderr output file')
optparser.add_option('-o', dest='stdout_file',
help='command stdout output file')
optparser.add_option('-l', dest='save_log', action='store_true',
help='save qsub output log file')
optparser.add_option('-N', dest='job_name',
help='qsub job name')
optparser.add_option('-q', dest='dest_queue',
help='qsub destination queue')
optparser.add_option('--qwait', dest='qsub_timeout', type='int',
help='qsub queue wait timeout', default=30*60)
optparser.add_option('-t', dest='cmd_timeout', type='int',
help='command execution timeout', default=600*60)
(options, cmd) = optparser.parse_args()
if cmd == []:
print >>sys.stderr, "%s: missing command" % progname
sys.exit(1)
# If we want to do this, need to add check here to make sure cmd[0] is
# a valid PBS job name, else qsub will die on us.
#
#if not options.job_name:
# options.job_name = cmd[0]
cwd = os.getcwd()
# Deal with systems where /n is a symlink to /.automount
if cwd.startswith('/.automount/'):
cwd = cwd.replace('/.automount/', '/n/', 1)
if not cwd.startswith('/n/poolfs/'):
print >>sys.stderr, "Error: current directory must be under /n/poolfs."
sys.exit(1)
# The Shell class wraps pexpect.spawn with some handy functions that
# assume the thing on the other end is a Bourne/bash shell.
class Shell(pexpect.spawn):
# Regexp to match the shell prompt. We change the prompt to
# something fixed and distinctive to make it easier to match
# reliably.
prompt_re = re.compile('qdo\$ ')
def __init__(self, cmd):
# initialize base pexpect.spawn object
try:
pexpect.spawn.__init__(self, cmd)
except pexpect.ExceptionPexpect, exc:
print "%s:" % progname, exc
sys.exit(1)
# full_output accumulates the full output of the session
self.full_output = ""
self.quick_timeout = 15
# wait for a prompt, then change it
try:
self.expect('\$ ', options.qsub_timeout)
except pexpect.TIMEOUT:
print >>sys.stderr, "%s: qsub timed out." % progname
self.kill(9)
self.close(wait=True)
sys.exit(1)
self.do_command('unset PROMPT_COMMAND; PS1="qdo$ "')
# version of expect that updates full_output too
def expect(self, regexp, timeout = -1):
pexpect.spawn.expect(self, regexp, timeout)
self.full_output += self.before + self.after
# Just issue a command and wait for the next prompt.
# Returns a string containing the output of the command.
def do_bare_command(self, cmd, timeout = -1):
global full_output
self.sendline(cmd)
# read back the echo of the command
self.readline()
# wait for the next prompt
self.expect(self.prompt_re, timeout)
output = self.before.rstrip()
return output
# Issue a command, then query its exit status.
# Returns a (string, int) tuple with the command output and the status.
def do_command(self, cmd, timeout = -1):
# do the command itself
output = self.do_bare_command(cmd, timeout)
# collect status
status = int(self.do_bare_command("echo $?", self.quick_timeout))
return (output, status)
# Check to see if the given directory exists.
def dir_exists(self, dirname):
(output, status) = shell.do_command('[ -d %s ]' % dirname,
self.quick_timeout)
return status == 0
# Spawn the interactive pool job.
# Hack to do link on poolfs... disabled for now since
# compiler/linker/library versioning problems between poolfs and
# nodes. May never work since poolfs is x86-64 and nodes are 32-bit.
if False and len(cmd) > 50:
shell_cmd = 'ssh -t poolfs /bin/sh -l'
print "%s: running %s on poolfs" % (progname, cmd[0])
else:
shell_cmd = 'qsub -I -S /bin/sh'
if options.job_name:
shell_cmd += ' -N "%s"' % options.job_name
if options.dest_queue:
shell_cmd += ' -q ' + options.dest_queue
shell = Shell(shell_cmd)
try:
# chdir to cwd
(output, status) = shell.do_command('cd ' + cwd)
if status != 0:
raise OSError, "Can't chdir to %s" % cwd
# wacky hack: sometimes scons will create an output directory then
# fork a job to generate files in that directory, and the job will
# get run before the directory creation propagates through NFS.
# This hack looks for a '-o' option indicating an output file and
# waits for the corresponding directory to appear if necessary.
try:
if 'cc' in cmd[0] or 'g++' in cmd[0]:
output_dir = os.path.dirname(cmd[cmd.index('-o')+1])
elif 'm5' in cmd[0]:
output_dir = cmd[cmd.index('-d')+1]
else:
output_dir = None
except (ValueError, IndexError):
# no big deal if there's no '-o'/'-d' or if it's the final argument
output_dir = None
if output_dir:
secs_waited = 0
while not shell.dir_exists(output_dir) and secs_waited < 90:
time.sleep(5)
secs_waited += 5
if secs_waited > 30:
print "waited", secs_waited, "seconds for", output_dir
# run command
if options.stdout_file:
cmd += ['>', options.stdout_file]
if options.stderr_file:
cmd += ['2>', options.stderr_file]
try:
(output, status) = shell.do_command(' '.join(cmd), options.cmd_timeout)
except pexpect.TIMEOUT:
print >>sys.stderr, "%s: command timed out after %d seconds." \
% (progname, options.cmd_timeout)
shell.sendline('~.') # qsub/ssh termination escape sequence
shell.close(wait=True)
status = 3
if output:
print output
finally:
# end job
if shell.isalive():
shell.sendline('exit')
shell.expect('qsub: job .* completed\r\n')
shell.close(wait=True)
# if there was an error, log the output even if not requested
if status != 0 or options.save_log:
log = file('qdo-log.' + str(os.getpid()), 'w')
log.write(shell.full_output)
log.close()
del shell
sys.exit(status)
|
