[modeller_usage] Parallel Python (socket.error: (111, 'Connection refused')

[Laurence Cooke <>]

Hello,
I have password-less ssh and rsh (I've tried both; same
"Connection refused" error).  My home directory is NFS mounted to all
slave machines.  I successfully ran parallel python with Modeller9v7 in
the past with this setup but now since updating to Mod9v8 I'm not able
to run the same scripts.  It's been a while since I've used Modeller so
I'm not sure if the problem is due to updating Modeller or changes that
might have occurred in the computer configurations.  Again ssh and rsh
work seamlessly between all nodes without passwords.

Also:

I'm able to run the scripts using 'local_slave()'.
I updated to Modeller9v8 on all machines.
All nodes are correctly listed in the /etc/hosts files on all machines.
We do run other software apps that require password-less ssh and they
are working well.
Nodes are quad core processors.

Finally:

I included below the code I'm running as well as the Modeller output in
the *.slave files.

Any help would be greatly appreciated.


        Regards,

        Laurence Cooke
        Arizona Cancer Center
        Tucson, Arizona


        ******************************************
        Start Parallel Task Remote file (one node)
        ******************************************
        from modeller import *
        from modeller.parallel import *

        from buildmodeltask import BuildModelTask

        log.minimal()
        j = job()
        j.append(ssh_slave('slave1', ssh_command='ssh'))
        j.append(ssh_slave('slave1', ssh_command='ssh'))
        j.append(ssh_slave('slave1', ssh_command='ssh'))
        j.append(ssh_slave('slave1', ssh_command='ssh'))


        j.queue_task(BuildModelTask('alignment_1.ali','pdb','sequence_1'))
        j.queue_task(BuildModelTask('alignment_2.ali','pdb','sequence_2'))
        j.queue_task(BuildModelTask('alignment_3.ali','pdb','sequence_3'))
        j.queue_task(BuildModelTask('alignment_4.ali','pdb','sequence_4'))

        results = j.run_all_tasks()

        print "Done: ", results



        *****************************
        BuildModelTask file
        ******************************
        import random
        from modeller import *
        from modeller.parallel import task
        from modeller.automodel import *


        class BuildModelTask(task):
           def run(self,ali,pdb,unknown):
                env = environ(rand_seed=(random.randint(2,50000)*-1))
                env.io.hetatm = True
                a = automodel(env, alnfile=ali,
                              knowns=pdb, sequence=unknown,
                              assess_methods=(assess.DOPE,
        assess.GA341))
                a.starting_model = 1
                a.ending_model = 250
                a.make()


        *********************************
        *.slave0-4 files
        *********************************
        Slave startup: connect to master at 127.0.0.1:59941:0:LMTRWVLB
        Traceback (most recent call last):
          File "/usr/lib/modeller9v8/bin/modslave.py", line 27, in ?
            slaveloop(sys.argv[2])
          File
        "/usr/lib/python2.4/site-packages/modeller/parallel/slaveloop.py", line
        57, in slaveloop
            master.connect_back(host, port, identifier)
          File
        "/usr/lib/python2.4/site-packages/modeller/parallel/slave_communicator.py", line 15, in connect_back
            s.connect((host, port))
          File "<string>", line 1, in connect
        socket.error: (111, 'Connection refused')




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