12357Sktlim@umich.edu# Copyright (c) 2006 The Regents of The University of Michigan
22357Sktlim@umich.edu# All rights reserved.
32357Sktlim@umich.edu#
42357Sktlim@umich.edu# Redistribution and use in source and binary forms, with or without
52357Sktlim@umich.edu# modification, are permitted provided that the following conditions are
62357Sktlim@umich.edu# met: redistributions of source code must retain the above copyright
72357Sktlim@umich.edu# notice, this list of conditions and the following disclaimer;
82357Sktlim@umich.edu# redistributions in binary form must reproduce the above copyright
92357Sktlim@umich.edu# notice, this list of conditions and the following disclaimer in the
102357Sktlim@umich.edu# documentation and/or other materials provided with the distribution;
112357Sktlim@umich.edu# neither the name of the copyright holders nor the names of its
122357Sktlim@umich.edu# contributors may be used to endorse or promote products derived from
132357Sktlim@umich.edu# this software without specific prior written permission.
142357Sktlim@umich.edu#
152357Sktlim@umich.edu# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
162357Sktlim@umich.edu# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
172357Sktlim@umich.edu# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
182357Sktlim@umich.edu# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
192357Sktlim@umich.edu# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
202357Sktlim@umich.edu# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
212357Sktlim@umich.edu# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
222357Sktlim@umich.edu# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
232357Sktlim@umich.edu# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
242357Sktlim@umich.edu# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
252357Sktlim@umich.edu# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
262357Sktlim@umich.edu#
272357Sktlim@umich.edu# Authors: Kevin Lim
282357Sktlim@umich.edu
292357Sktlim@umich.eduimport os, popen2, re, sys
302357Sktlim@umich.edu
312357Sktlim@umich.educlass MyPOpen(object):
322357Sktlim@umich.edu    def __init__(self, cmd, input = None, output = None, bufsize = -1):
332357Sktlim@umich.edu        self.status = -1
342357Sktlim@umich.edu
352357Sktlim@umich.edu        if input is None:
362357Sktlim@umich.edu            p2c_read, p2c_write = os.pipe()
372357Sktlim@umich.edu            self.tochild = os.fdopen(p2c_write, 'w', bufsize)
382357Sktlim@umich.edu        else:
392357Sktlim@umich.edu            p2c_write = None
402357Sktlim@umich.edu            if isinstance(input, file):
412357Sktlim@umich.edu                p2c_read = input.fileno()
422357Sktlim@umich.edu            elif isinstance(input, str):
432357Sktlim@umich.edu                input = file(input, 'r')
442357Sktlim@umich.edu                p2c_read = input.fileno()
452357Sktlim@umich.edu            elif isinstance(input, int):
462357Sktlim@umich.edu                p2c_read = input
472357Sktlim@umich.edu            else:
482357Sktlim@umich.edu                raise AttributeError
492357Sktlim@umich.edu
502357Sktlim@umich.edu        if output is None:
512357Sktlim@umich.edu            c2p_read, c2p_write = os.pipe()
522357Sktlim@umich.edu            self.fromchild = os.fdopen(c2p_read, 'r', bufsize)
532357Sktlim@umich.edu        else:
542357Sktlim@umich.edu            c2p_read = None
552357Sktlim@umich.edu            if isinstance(output, file):
562357Sktlim@umich.edu                c2p_write = output.fileno()
572357Sktlim@umich.edu            elif isinstance(output, str):
582357Sktlim@umich.edu                output = file(output, 'w')
592357Sktlim@umich.edu                c2p_write = output.fileno()
602357Sktlim@umich.edu            elif isinstance(output, int):
612357Sktlim@umich.edu                c2p_write = output
622357Sktlim@umich.edu            else:
632357Sktlim@umich.edu                raise AttributeError
642357Sktlim@umich.edu
652357Sktlim@umich.edu        self.pid = os.fork()
662357Sktlim@umich.edu        if self.pid == 0:
672357Sktlim@umich.edu            os.dup2(p2c_read, sys.stdin.fileno())
682357Sktlim@umich.edu            os.dup2(c2p_write, sys.stdout.fileno())
692357Sktlim@umich.edu            os.dup2(c2p_write, sys.stderr.fileno())
702357Sktlim@umich.edu            try:
712357Sktlim@umich.edu                os.execvp(cmd[0], cmd)
722357Sktlim@umich.edu            finally:
732357Sktlim@umich.edu                os._exit(1)
742357Sktlim@umich.edu
752357Sktlim@umich.edu        os.close(p2c_read)
762357Sktlim@umich.edu        os.close(c2p_write)
772357Sktlim@umich.edu
782357Sktlim@umich.edu    def poll(self):
792357Sktlim@umich.edu        if self.status < 0:
802357Sktlim@umich.edu            pid, status = os.waitpid(self.pid, os.WNOHANG)
812357Sktlim@umich.edu            if pid == self.pid:
822357Sktlim@umich.edu                self.status = status
832357Sktlim@umich.edu        return self.status
842357Sktlim@umich.edu
852357Sktlim@umich.edu    def wait(self):
862357Sktlim@umich.edu        if self.status < 0:
872357Sktlim@umich.edu            pid, status = os.waitpid(self.pid, 0)
882357Sktlim@umich.edu            if pid == self.pid:
892357Sktlim@umich.edu                self.status = status
902357Sktlim@umich.edu        return self.status
912357Sktlim@umich.edu
922357Sktlim@umich.edu
932357Sktlim@umich.educlass oarsub:
942357Sktlim@umich.edu    def __init__(self):
952357Sktlim@umich.edu        self.walltime = None
962357Sktlim@umich.edu        self.queue = None
972357Sktlim@umich.edu        self.properties = None
982357Sktlim@umich.edu
992357Sktlim@umich.edu        # OAR 2.0 parameters only!
1002357Sktlim@umich.edu        self.name = None
1012357Sktlim@umich.edu        self.afterok = None
1022357Sktlim@umich.edu        self.notify = None
1032357Sktlim@umich.edu        self.stderr = None
1042357Sktlim@umich.edu        self.stdout = None
1052357Sktlim@umich.edu
1062357Sktlim@umich.edu
1072357Sktlim@umich.edu        self.oarhost = None
1082357Sktlim@umich.edu        self.oarsub = 'oarsub'
1092357Sktlim@umich.edu
1102357Sktlim@umich.edu        self.jobid = re.compile('IdJob = (\S+)')
1112357Sktlim@umich.edu        #self.outfile = open("jobnames.dat", "a+")
1122357Sktlim@umich.edu
1132357Sktlim@umich.edu    def build(self, script, args = []):
1142357Sktlim@umich.edu        self.cmd = [ self.oarsub ]
1152357Sktlim@umich.edu
1162357Sktlim@umich.edu        print "args:", args
1172357Sktlim@umich.edu        print "script:", script
1182357Sktlim@umich.edu        if self.properties:
1192357Sktlim@umich.edu            self.cmd.append('-p"%s"' % self.properties )
1202357Sktlim@umich.edu
1212357Sktlim@umich.edu        if self.queue:
1222357Sktlim@umich.edu            self.cmd.append('-q "%s"' % self.queue)
1232357Sktlim@umich.edu
1242357Sktlim@umich.edu        if self.walltime:
1252357Sktlim@umich.edu            self.cmd.append('-l walltime=%s' % self.walltime)
1262357Sktlim@umich.edu
1272357Sktlim@umich.edu        if script[0] != "/":
1282357Sktlim@umich.edu            self.script = os.getcwd()
1292357Sktlim@umich.edu        else:
1302357Sktlim@umich.edu            self.script = script
1312357Sktlim@umich.edu
1322357Sktlim@umich.edu        self.cmd.extend(args)
1332357Sktlim@umich.edu        self.cmd.append(self.script)
1342357Sktlim@umich.edu        #cmd = [ 'ssh', '-x', self.oarhost,  '"cd %s; %s"' % (os.getcwd(), self.command) ]
1352357Sktlim@umich.edu        self.command = ' '.join(self.cmd)
1362357Sktlim@umich.edu
1372357Sktlim@umich.edu        print "command: [%s]" % self.command
1382357Sktlim@umich.edu
1392357Sktlim@umich.edu    def do(self):
1402357Sktlim@umich.edu        oar = MyPOpen(self.cmd)
1412357Sktlim@umich.edu        self.result = oar.fromchild.read()
1422357Sktlim@umich.edu        ec = oar.wait()
1432357Sktlim@umich.edu
1442357Sktlim@umich.edu        if ec != 0 and self.oarhost:
1452357Sktlim@umich.edu            pstdin, pstdout = os.popen4(self.command)
1462357Sktlim@umich.edu            self.result = pstdout.read()
1472357Sktlim@umich.edu
1482357Sktlim@umich.edu        jobid = self.jobid.match(self.result)
1492357Sktlim@umich.edu        if jobid == None:
1502357Sktlim@umich.edu            print "Couldn't get jobid from [%s]" % self.result
1512357Sktlim@umich.edu            sys.exit(1)
1522357Sktlim@umich.edu        else:
1532357Sktlim@umich.edu            #self.outfile.write("%d %s\n" %(int(jobid.group(1)), self.name));
1542357Sktlim@umich.edu            #self.outfile.flush()
1552357Sktlim@umich.edu            self.result = jobid.group(1)
1562357Sktlim@umich.edu
1572357Sktlim@umich.edu        return 0
1582357Sktlim@umich.edu
1592357Sktlim@umich.educlass qsub:
1602357Sktlim@umich.edu    def __init__(self):
1612357Sktlim@umich.edu        self.afterok = None
1622357Sktlim@umich.edu        self.hold = False
1632357Sktlim@umich.edu        self.join = False
1642357Sktlim@umich.edu        self.keep_stdout = False
1652357Sktlim@umich.edu        self.keep_stderr = False
1662357Sktlim@umich.edu        self.node_type = None
1672357Sktlim@umich.edu        self.mail_abort = False
1682357Sktlim@umich.edu        self.mail_begin = False
1692357Sktlim@umich.edu        self.mail_end = False
1702357Sktlim@umich.edu        self.name = None
1712357Sktlim@umich.edu        self.stdout = None
1722357Sktlim@umich.edu        self.priority = None
1732357Sktlim@umich.edu        self.queue = None
1742357Sktlim@umich.edu        self.pbshost = None
1752357Sktlim@umich.edu        self.qsub = 'qsub'
1762357Sktlim@umich.edu        self.env = {}
1772357Sktlim@umich.edu
1782357Sktlim@umich.edu    def build(self, script, args = []):
1792357Sktlim@umich.edu        self.cmd = [ self.qsub ]
1802357Sktlim@umich.edu
1812357Sktlim@umich.edu        if self.env:
1822357Sktlim@umich.edu            arg = '-v'
1832357Sktlim@umich.edu            arg += ','.join([ '%s=%s' % i for i in self.env.iteritems() ])
1842357Sktlim@umich.edu            self.cmd.append(arg)
1852357Sktlim@umich.edu
1862357Sktlim@umich.edu        if self.hold:
1872357Sktlim@umich.edu            self.cmd.append('-h')
1882357Sktlim@umich.edu
1892357Sktlim@umich.edu        if self.stdout:
1902357Sktlim@umich.edu            self.cmd.append('-olocalhost:' + self.stdout)
1912357Sktlim@umich.edu
1922357Sktlim@umich.edu        if self.keep_stdout and self.keep_stderr:
1932357Sktlim@umich.edu            self.cmd.append('-koe')
1942357Sktlim@umich.edu        elif self.keep_stdout:
1952357Sktlim@umich.edu            self.cmd.append('-ko')
1962357Sktlim@umich.edu        elif self.keep_stderr:
1972357Sktlim@umich.edu            self.cmd.append('-ke')
1982357Sktlim@umich.edu        else:
1992357Sktlim@umich.edu            self.cmd.append('-kn')
2002357Sktlim@umich.edu
2012357Sktlim@umich.edu        if self.join:
2022357Sktlim@umich.edu            self.cmd.append('-joe')
2032357Sktlim@umich.edu
2042357Sktlim@umich.edu        if self.node_type:
2052357Sktlim@umich.edu            self.cmd.append('-lnodes=' + self.node_type)
2062357Sktlim@umich.edu
2072357Sktlim@umich.edu        if self.mail_abort or self.mail_begin or self.mail_end:
2082357Sktlim@umich.edu            flags = ''
2092357Sktlim@umich.edu            if self.mail_abort:
2102357Sktlim@umich.edu                flags.append('a')
2112357Sktlim@umich.edu            if self.mail_begin:
2122357Sktlim@umich.edu                flags.append('b')
2132357Sktlim@umich.edu            if self.mail_end:
2142357Sktlim@umich.edu                flags.append('e')
2152357Sktlim@umich.edu            if len(flags):
2162357Sktlim@umich.edu                self.cmd.append('-m ' + flags)
2172357Sktlim@umich.edu        else:
2182357Sktlim@umich.edu            self.cmd.append('-mn')
2192357Sktlim@umich.edu
2202357Sktlim@umich.edu        if self.name:
2212357Sktlim@umich.edu            self.cmd.append("-N%s" % self.name)
2222357Sktlim@umich.edu
2232357Sktlim@umich.edu        if self.priority:
2242357Sktlim@umich.edu            self.cmd.append('-p' + self.priority)
2252357Sktlim@umich.edu
2262357Sktlim@umich.edu        if self.queue:
2272357Sktlim@umich.edu            self.cmd.append('-q' + self.queue)
2282357Sktlim@umich.edu
2292357Sktlim@umich.edu        if self.afterok:
2302357Sktlim@umich.edu            self.cmd.append('-Wdepend=afterok:%s' % self.afterok)
2312357Sktlim@umich.edu
2322357Sktlim@umich.edu        self.cmd.extend(args)
2332357Sktlim@umich.edu        self.script = script
2342357Sktlim@umich.edu        self.command = ' '.join(self.cmd + [ self.script ])
2352357Sktlim@umich.edu
2362357Sktlim@umich.edu    def do(self):
2372357Sktlim@umich.edu        pbs = MyPOpen(self.cmd + [ self.script ])
2382357Sktlim@umich.edu        self.result = pbs.fromchild.read()
2392357Sktlim@umich.edu        ec = pbs.wait()
2402357Sktlim@umich.edu
2412357Sktlim@umich.edu        if ec != 0 and self.pbshost:
2422357Sktlim@umich.edu            cmd = ' '.join(self.cmd + [ '-' ])
2432357Sktlim@umich.edu            cmd = [ 'ssh', '-x', self.pbshost, cmd ]
2442357Sktlim@umich.edu            self.command = ' '.join(cmd)
2452357Sktlim@umich.edu            ssh = MyPOpen(cmd, input = self.script)
2462357Sktlim@umich.edu            self.result = ssh.fromchild.read()
2472357Sktlim@umich.edu            ec = ssh.wait()
2482357Sktlim@umich.edu
2492357Sktlim@umich.edu        return ec
250