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diff --git a/util/batch/batch.py b/util/batch/batch.py
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+# Copyright (c) 2006 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: Kevin Lim
+
+import os, popen2, re, sys
+
+class MyPOpen(object):
+ def __init__(self, cmd, input = None, output = None, bufsize = -1):
+ self.status = -1
+
+ if input is None:
+ p2c_read, p2c_write = os.pipe()
+ self.tochild = os.fdopen(p2c_write, 'w', bufsize)
+ else:
+ p2c_write = None
+ if isinstance(input, file):
+ p2c_read = input.fileno()
+ elif isinstance(input, str):
+ input = file(input, 'r')
+ p2c_read = input.fileno()
+ elif isinstance(input, int):
+ p2c_read = input
+ else:
+ raise AttributeError
+
+ if output is None:
+ c2p_read, c2p_write = os.pipe()
+ self.fromchild = os.fdopen(c2p_read, 'r', bufsize)
+ else:
+ c2p_read = None
+ if isinstance(output, file):
+ c2p_write = output.fileno()
+ elif isinstance(output, str):
+ output = file(output, 'w')
+ c2p_write = output.fileno()
+ elif isinstance(output, int):
+ c2p_write = output
+ else:
+ raise AttributeError
+
+ self.pid = os.fork()
+ if self.pid == 0:
+ os.dup2(p2c_read, sys.stdin.fileno())
+ os.dup2(c2p_write, sys.stdout.fileno())
+ os.dup2(c2p_write, sys.stderr.fileno())
+ try:
+ os.execvp(cmd[0], cmd)
+ finally:
+ os._exit(1)
+
+ os.close(p2c_read)
+ os.close(c2p_write)
+
+ def poll(self):
+ if self.status < 0:
+ pid, status = os.waitpid(self.pid, os.WNOHANG)
+ if pid == self.pid:
+ self.status = status
+ return self.status
+
+ def wait(self):
+ if self.status < 0:
+ pid, status = os.waitpid(self.pid, 0)
+ if pid == self.pid:
+ self.status = status
+ return self.status
+
+
+class oarsub:
+ def __init__(self):
+ self.walltime = None
+ self.queue = None
+ self.properties = None
+
+ # OAR 2.0 parameters only!
+ self.name = None
+ self.afterok = None
+ self.notify = None
+ self.stderr = None
+ self.stdout = None
+
+
+ self.oarhost = None
+ self.oarsub = 'oarsub'
+
+ self.jobid = re.compile('IdJob = (\S+)')
+ #self.outfile = open("jobnames.dat", "a+")
+
+ def build(self, script, args = []):
+ self.cmd = [ self.oarsub ]
+
+ print "args:", args
+ print "script:", script
+ if self.properties:
+ self.cmd.append('-p"%s"' % self.properties )
+
+ if self.queue:
+ self.cmd.append('-q "%s"' % self.queue)
+
+ if self.walltime:
+ self.cmd.append('-l walltime=%s' % self.walltime)
+
+ if script[0] != "/":
+ self.script = os.getcwd()
+ else:
+ self.script = script
+
+ self.cmd.extend(args)
+ self.cmd.append(self.script)
+ #cmd = [ 'ssh', '-x', self.oarhost, '"cd %s; %s"' % (os.getcwd(), self.command) ]
+ self.command = ' '.join(self.cmd)
+
+ print "command: [%s]" % self.command
+
+ def do(self):
+ oar = MyPOpen(self.cmd)
+ self.result = oar.fromchild.read()
+ ec = oar.wait()
+
+ if ec != 0 and self.oarhost:
+ pstdin, pstdout = os.popen4(self.command)
+ self.result = pstdout.read()
+
+ jobid = self.jobid.match(self.result)
+ if jobid == None:
+ print "Couldn't get jobid from [%s]" % self.result
+ sys.exit(1)
+ else:
+ #self.outfile.write("%d %s\n" %(int(jobid.group(1)), self.name));
+ #self.outfile.flush()
+ self.result = jobid.group(1)
+
+ return 0
+
+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 = None
+ self.mail_abort = False
+ self.mail_begin = False
+ self.mail_end = False
+ self.name = None
+ self.stdout = None
+ self.priority = None
+ self.queue = None
+ self.pbshost = None
+ self.qsub = 'qsub'
+ self.env = {}
+
+ def build(self, script, args = []):
+ self.cmd = [ self.qsub ]
+
+ if self.env:
+ arg = '-v'
+ arg += ','.join([ '%s=%s' % i for i in self.env.iteritems() ])
+ self.cmd.append(arg)
+
+ if self.hold:
+ self.cmd.append('-h')
+
+ if self.stdout:
+ self.cmd.append('-olocalhost:' + self.stdout)
+
+ if self.keep_stdout and self.keep_stderr:
+ self.cmd.append('-koe')
+ elif self.keep_stdout:
+ self.cmd.append('-ko')
+ elif self.keep_stderr:
+ self.cmd.append('-ke')
+ else:
+ self.cmd.append('-kn')
+
+ if self.join:
+ self.cmd.append('-joe')
+
+ if self.node_type:
+ self.cmd.append('-lnodes=' + self.node_type)
+
+ if self.mail_abort or self.mail_begin or self.mail_end:
+ flags = ''
+ if self.mail_abort:
+ flags.append('a')
+ if self.mail_begin:
+ flags.append('b')
+ if self.mail_end:
+ flags.append('e')
+ if len(flags):
+ self.cmd.append('-m ' + flags)
+ else:
+ self.cmd.append('-mn')
+
+ if self.name:
+ self.cmd.append("-N%s" % self.name)
+
+ if self.priority:
+ self.cmd.append('-p' + self.priority)
+
+ if self.queue:
+ self.cmd.append('-q' + self.queue)
+
+ if self.afterok:
+ self.cmd.append('-Wdepend=afterok:%s' % self.afterok)
+
+ self.cmd.extend(args)
+ self.script = script
+ self.command = ' '.join(self.cmd + [ self.script ])
+
+ def do(self):
+ pbs = MyPOpen(self.cmd + [ self.script ])
+ self.result = pbs.fromchild.read()
+ ec = pbs.wait()
+
+ if ec != 0 and self.pbshost:
+ cmd = ' '.join(self.cmd + [ '-' ])
+ cmd = [ 'ssh', '-x', self.pbshost, cmd ]
+ self.command = ' '.join(cmd)
+ ssh = MyPOpen(cmd, input = self.script)
+ self.result = ssh.fromchild.read()
+ ec = ssh.wait()
+
+ return ec
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