From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Jun 18 2014 - 07:52:29 CDT
Look the line with the <----
> >> Charmrun> adding client 0: "itioc3", IP:129.215.237.179
> >> Charmrun> adding client 1: "itioc4", IP:129.215.237.180
> >> Charmrun> adding client 2: "itioc5", IP:129.215.237.186
> >> Charmrun> adding client 3: "itioc6", IP:129.215.237.187
> >> Charmrun> adding client 4: "itioc1", IP:129.215.137.21 <-----
> >> Charmrun> adding client 5: "itioc2", IP:129.215.137.123 <-----
> >> Charmrun> adding client 6: "itioc3", IP:129.215.237.179
> >> Charmrun> adding client 7: "itioc4", IP:129.215.237.180
This nodes don't seem to use the same network as the other nodes!
Something is definitely weird with your network config.
Also:
> 129.215.137.123 itioc2.bch.ed.ac.uk itioc2
> 129.215.137.21 n3
Is again different from what could be seen above. (137/237)
This doesn't look continues and might be an error.
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: Douglas Houston [mailto:DouglasR.Houston_at_ed.ac.uk]
> Gesendet: Mittwoch, 18. Juni 2014 14:24
> An: Norman Geist
> Cc: Namd Mailing List
> Betreff: Re: AW: AW: namd-l: Using nodelist file causes namd to hang
>
> Here is an example of what /etc/hosts contains:
>
> # Do not remove the following line, or various programs
> # that require network functionality will fail.
> 127.0.0.1 localhost.localdomain localhost
> 129.215.137.123 itioc2.bch.ed.ac.uk itioc2
> ::1 localhost6.localdomain6 localhost6
> 129.215.137.21 n3
>
> I'm not sure I can see anything wrong with it?
>
>
>
> Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Mon, 16 Jun
> 2014 09:19:28 +0200:
>
> > This may be related to an unsuitable local dns setup. Please check
> that in
> > all the nodes "/etc/hosts" the hostname of the node does not point to
> a
> > loopback address similar to 127.0.0.1 but too the outgoing IP. I've
> written
> > another thread about that somewhen.
> >
> > Norman Geist.
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: Douglas Houston [mailto:DouglasR.Houston_at_ed.ac.uk]
> >> Gesendet: Freitag, 13. Juni 2014 19:17
> >> An: Norman Geist
> >> Cc: Namd Mailing List
> >> Betreff: Re: AW: namd-l: Using nodelist file causes namd to hang
> >>
> >> Hi Norman,
> >>
> >> I have made some progress, I now get:
> >>
> >> [douglas_at_itioc1 200ns]$
> >> /usr/people/douglas/programs/NAMD_2.9_Linux-x86/charmrun +p8
> >> /usr/people/douglas/programs/NAMD_2.9_Linux-x86/namd2 ++verbose
> >> mdrun.conf
> >> Charmrun> charmrun started...
> >> Charmrun> using ./nodelist as nodesfile
> >> Charmrun> adding client 0: "itioc3", IP:129.215.237.179
> >> Charmrun> adding client 1: "itioc4", IP:129.215.237.180
> >> Charmrun> adding client 2: "itioc5", IP:129.215.237.186
> >> Charmrun> adding client 3: "itioc6", IP:129.215.237.187
> >> Charmrun> adding client 4: "itioc1", IP:129.215.137.21
> >> Charmrun> adding client 5: "itioc2", IP:129.215.137.123
> >> Charmrun> adding client 6: "itioc3", IP:129.215.237.179
> >> Charmrun> adding client 7: "itioc4", IP:129.215.237.180
> >> Charmrun> Charmrun = 129.215.137.21, port = 54043
> >> start_nodes_rsh
> >> Charmrun> Sending "0 129.215.137.21 54043 24199 0" to client 0.
> >> Charmrun> find the node program
> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-x86/namd2" at
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/unfold_MD_Cks1pep
> >> _par36_Skp2complex/200ns" for
> >> 0.
> >> Charmrun> Starting ssh itioc3 -l douglas /bin/sh -f
> >> Charmrun> remote shell (itioc3:0) started
> >> Charmrun> Sending "1 129.215.137.21 54043 24199 0" to client 1.
> >> Charmrun> find the node program
> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-x86/namd2" at
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/unfold_MD_Cks1pep
> >> _par36_Skp2complex/200ns" for
> >> 1.
> >> Charmrun> Starting ssh itioc4 -l douglas /bin/sh -f
> >> Charmrun> remote shell (itioc4:1) started
> >> Charmrun> Sending "2 129.215.137.21 54043 24199 0" to client 2.
> >> Charmrun> find the node program
> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-x86/namd2" at
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/unfold_MD_Cks1pep
> >> _par36_Skp2complex/200ns" for
> >> 2.
> >> Charmrun> Starting ssh itioc5 -l douglas /bin/sh -f
> >> Charmrun> remote shell (itioc5:2) started
> >> Charmrun> Sending "3 129.215.137.21 54043 24199 0" to client 3.
> >> Charmrun> find the node program
> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-x86/namd2" at
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/unfold_MD_Cks1pep
> >> _par36_Skp2complex/200ns" for
> >> 3.
> >> Charmrun> Starting ssh itioc6 -l douglas /bin/sh -f
> >> Charmrun> remote shell (itioc6:3) started
> >> Charmrun> Sending "4 129.215.137.21 54043 24199 0" to client 4.
> >> Charmrun> find the node program
> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-x86/namd2" at
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/unfold_MD_Cks1pep
> >> _par36_Skp2complex/200ns" for
> >> 4.
> >> Charmrun> Starting ssh itioc1 -l douglas /bin/sh -f
> >> Charmrun> remote shell (itioc1:4) started
> >> Charmrun> Sending "5 129.215.137.21 54043 24199 0" to client 5.
> >> Charmrun> find the node program
> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-x86/namd2" at
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/unfold_MD_Cks1pep
> >> _par36_Skp2complex/200ns" for
> >> 5.
> >> Charmrun> Starting ssh itioc2 -l douglas /bin/sh -f
> >> Charmrun> remote shell (itioc2:5) started
> >> Charmrun> Sending "6 129.215.137.21 54043 24199 0" to client 6.
> >> Charmrun> find the node program
> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-x86/namd2" at
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/unfold_MD_Cks1pep
> >> _par36_Skp2complex/200ns" for
> >> 6.
> >> Charmrun> Starting ssh itioc3 -l douglas /bin/sh -f
> >> Charmrun> remote shell (itioc3:6) started
> >> Charmrun> Sending "7 129.215.137.21 54043 24199 0" to client 7.
> >> Charmrun> find the node program
> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-x86/namd2" at
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/unfold_MD_Cks1pep
> >> _par36_Skp2complex/200ns" for
> >> 7.
> >> Charmrun> Starting ssh itioc4 -l douglas /bin/sh -f
> >> Charmrun> remote shell (itioc4:7) started
> >> Charmrun> node programs all started
> >> Charmrun remote shell(itioc3.6)> remote responding...
> >> Charmrun remote shell(itioc3.0)> remote responding...
> >> Charmrun remote shell(itioc3.6)> starting node-program...
> >> Charmrun remote shell(itioc3.0)> starting node-program...
> >> Charmrun remote shell(itioc3.6)> rsh phase successful.
> >> Charmrun remote shell(itioc3.0)> rsh phase successful.
> >> Charmrun remote shell(itioc4.1)> remote responding...
> >> Charmrun remote shell(itioc4.1)> starting node-program...
> >> Charmrun remote shell(itioc4.1)> rsh phase successful.
> >> Charmrun remote shell(itioc4.7)> remote responding...
> >> Charmrun remote shell(itioc4.7)> starting node-program...
> >> Charmrun remote shell(itioc4.7)> rsh phase successful.
> >> Charmrun remote shell(itioc1.4)> remote responding...
> >> Charmrun remote shell(itioc1.4)> starting node-program...
> >> Charmrun remote shell(itioc1.4)> rsh phase successful.
> >> Charmrun remote shell(itioc6.3)> remote responding...
> >> Charmrun remote shell(itioc6.3)> starting node-program...
> >> Charmrun remote shell(itioc6.3)> rsh phase successful.
> >> Charmrun remote shell(itioc5.2)> remote responding...
> >> Charmrun remote shell(itioc5.2)> starting node-program...
> >> Charmrun remote shell(itioc5.2)> rsh phase successful.
> >> Charmrun remote shell(itioc2.5)> remote responding...
> >> Charmrun remote shell(itioc2.5)> starting node-program...
> >> Charmrun remote shell(itioc2.5)> rsh phase successful.
> >> Charmrun> Waiting for 0-th client to connect.
> >> Charmrun> Waiting for 1-th client to connect.
> >> Charmrun> Waiting for 2-th client to connect.
> >> Charmrun> Waiting for 3-th client to connect.
> >> Charmrun> Waiting for 4-th client to connect.
> >> Charmrun> Waiting for 5-th client to connect.
> >> Charmrun> client 0 connected (IP=129.215.237.179 data_port=45304)
> >> Charmrun> client 6 connected (IP=129.215.237.179 data_port=54685)
> >> Charmrun> client 4 connected (IP=129.215.137.21 data_port=49908)
> >> Charmrun> client 5 connected (IP=129.215.137.123 data_port=40205)
> >> Charmrun> client 1 connected (IP=129.215.237.180 data_port=47847)
> >> Charmrun> client 7 connected (IP=129.215.237.180 data_port=45521)
> >> Charmrun> Waiting for 6-th client to connect.
> >> Charmrun> client 2 connected (IP=129.215.237.186 data_port=52855)
> >> Charmrun> Waiting for 7-th client to connect.
> >> Charmrun> client 3 connected (IP=129.215.237.187 data_port=50052)
> >> Charmrun> All clients connected.
> >> Charmrun> IP tables sent.
> >> Charmrun> node programs all connected
> >> Charmrun> started all node programs in 1.805 seconds.
> >> Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
> >> Charm++> scheduler running in netpoll mode.
> >> CharmLB> Load balancer assumes all CPUs are same.
> >>
> >>
> >> Output to terminal halts at this point. All node processors are
> >> running but nothing is written to disk. I see others have had this
> >> problem before:
> >>
> >> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-
> >> 2012/3776.html
> >>
> >> I tried your suggestion of running charmrun with the debug option.
> >> This causes 8 xterm windows to open, each with the following:
> >>
> >> GNU gdb (GDB) Fedora (7.2-16.fc14)
> >> Copyright (C) 2010 Free Software Foundation, Inc.
> >> License GPLv3+: GNU GPL version 3 or later
> >> <http://gnu.org/licenses/gpl.html>
> >> This is free software: you are free to change and redistribute it.
> >> There is NO WARRANTY, to the extent permitted by law. Type "show
> >> copying"
> >> and "show warranty" for details.
> >> This GDB was configured as "x86_64-redhat-linux-gnu".
> >> For bug reporting instructions, please see:
> >> <http://www.gnu.org/software/gdb/bugs/>...
> >> Reading symbols from
> >> /usr/people/douglas/programs/NAMD_2.9_Linux-x86/namd2...(no
> debugging
> >> symbols found)...done.
> >> (gdb)
> >>
> >>
> >> What should I try next?
> >>
> >> cheers,
> >> Doug
> >>
> >>
> >> Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Mon, 2 Jun
> >> 2014 13:31:08 +0200:
> >>
> >> > The error with "HOST IDENTIFICATION HAS CHANGED" means, that the
> >> entries in
> >> > "known_hosts" are no more true. Therefore it would be easier to
> >> delete ALL
> >> > the "known_hosts" entries from all nodes and recreate them by
> sshing
> >> to each
> >> > other and to localhost and 127.0.0.1. It might be easier if the
> nodes
> >> would
> >> > share the same identification which can be done by mirroring the
> >> "~/.ssh"
> >> > folder to all nodes after the clean-up
> >> >
> >> > Norman Geist.
> >> >
> >> >
> >> >> -----Ursprüngliche Nachricht-----
> >> >> Von: Douglas Houston [mailto:DouglasR.Houston_at_ed.ac.uk]
> >> >> Gesendet: Montag, 2. Juni 2014 13:26
> >> >> An: Norman Geist
> >> >> Betreff: Re: AW: AW: AW: namd-l: Using nodelist file causes namd
> to
> >> >> hang
> >> >>
> >> >> Hi Norman,
> >> >>
> >> >> My .ssh/known_hosts contains one line for each of the itioc
> nodes,
> >> >> plus one line for 127.0.0.1 and one line for localhost.
> >> >>
> >> >> Could you clarify which entries exactly I should delete in this
> >> file,
> >> >> and also what you mean by "start over"?
> >> >>
> >> >> cheers,
> >> >> Doug
> >> >>
> >> >>
> >> >> Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Mon, 2
> Jun
> >> >> 2014 13:06:30 +0200:
> >> >>
> >> >> > Easiest way is to delete all the nodes "known_hosts" entries
> and
> >> >> start over.
> >> >> >
> >> >> >
> >> >> > Norman Geist.
> >> >> >
> >> >> >> -----Ursprüngliche Nachricht-----
> >> >> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-
> l_at_ks.uiuc.edu]
> >> Im
> >> >> >> Auftrag von Douglas Houston
> >> >> >> Gesendet: Montag, 2. Juni 2014 11:51
> >> >> >> An: Namd Mailing List
> >> >> >> Betreff: Re: AW: AW: namd-l: Using nodelist file causes namd
> to
> >> hang
> >> >> >>
> >> >> >> Sorry for the long delay but I ran out of time to continue
> >> >> >> troubleshooting this, until now.
> >> >> >>
> >> >> >> To recap, I have 6 nodes. When I'm logged in to e.g. itioc6 I
> can
> >> >> ssh
> >> >> >> to localhost, 127.0.0.1, and 129.215.237.187 (itioc6's IP
> >> address).
> >> >> >> But if I login to e.g. itioc1, I can't ssh to localhost (see
> >> error
> >> >> >> message below). If I change the key in
> ~douglas/.ssh/known_hosts
> >> to
> >> >> >> make this work on itioc1 it stops working on itioc6.
> >> >> >>
> >> >> >> It looks like I can only have one working "localhost" or
> >> "127.0.0.1"
> >> >> >> key in the known_hosts file, but as I understand it I need all
> my
> >> >> >> itioc nodes to each have one. How can I achieve this?
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Wed,
> 9
> >> Apr
> >> >> >> 2014 12:53:50 +0200:
> >> >> >>
> >> >> >> > This may be a hint. Your nodes must not only be able to
> logon
> >> to
> >> >> all
> >> >> >> nodes
> >> >> >> > without password, but should also be able to logon to
> >> themselves
> >> >> via
> >> >> >> own IP
> >> >> >> > address, localhost and 127.0.0.1
> >> >> >> >
> >> >> >> > You may want to delete the wrong entries in
> ~/.ssh/known_hosts
> >> on
> >> >> the
> >> >> >> nodes,
> >> >> >> > and recreate by ssh to the targets mentioned above.
> >> >> >> >
> >> >> >> > Norman Geist.
> >> >> >> >
> >> >> >> >
> >> >> >> >> -----Ursprüngliche Nachricht-----
> >> >> >> >> Von: Douglas Houston [mailto:DouglasR.Houston_at_ed.ac.uk]
> >> >> >> >> Gesendet: Mittwoch, 9. April 2014 12:42
> >> >> >> >> An: Norman Geist
> >> >> >> >> Betreff: Re: AW: namd-l: Using nodelist file causes namd to
> >> hang
> >> >> >> >>
> >> >> >> >> The same command without the ++local causes the nodelist
> file
> >> to
> >> >> be
> >> >> >> >> used, I have already posed the output from this.
> >> >> >> >>
> >> >> >> >> If I delete the nodelist file, the same command without the
> >> >> ++local
> >> >> >> >> (which causes the file /usr/people/douglas/.nodelist to be
> >> used)
> >> >> >> >> outputs:
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> Charmrun> charmrun started...
> >> >> >> >> Charmrun> using /usr/people/douglas/.nodelist as nodesfile
> >> >> >> >> Charmrun> adding client 0: "localhost", IP:127.0.0.1
> >> >> >> >> Charmrun> Charmrun = 129.215.237.187, port = 35909
> >> >> >> >> start_nodes_rsh
> >> >> >> >> Charmrun> Sending "0 129.215.237.187 35909 27843 0" to
> client
> >> 0.
> >> >> >> >> Charmrun> find the node program
> >> >> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-x86/namd2" at
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> " for
> >> >> >> >> 0.
> >> >> >> >> Charmrun> Starting ssh localhost -l douglas /bin/sh -f
> >> >> >> >> Charmrun> remote shell (localhost:0) started
> >> >> >> >> Charmrun> node programs all started
> >> >> >> >> @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
> >> >> >> >> @ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @
> >> >> >> >> @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
> >> >> >> >> IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
> >> >> >> >> Someone could be eavesdropping on you right now (man-in-
> the-
> >> >> middle
> >> >> >> >> attack)!
> >> >> >> >> It is also possible that the RSA host key has just been
> >> changed.
> >> >> >> >> The fingerprint for the RSA key sent by the remote host is
> >> >> >> >> 99:cb:e0:0a:77:8b:61:fd:19:01:57:93:ec:93:99:63.
> >> >> >> >> Please contact your system administrator.
> >> >> >> >> Add correct host key in
> /usr/people/douglas/.ssh/known_hosts
> >> to
> >> >> get
> >> >> >> >> rid of this message.
> >> >> >> >> Offending key in /usr/people/douglas/.ssh/known_hosts:47
> >> >> >> >> RSA host key for localhost has changed and you have
> requested
> >> >> strict
> >> >> >> >> checking.
> >> >> >> >> Host key verification failed.
> >> >> >> >> Charmrun> Error 255 returned from rsh (localhost:0)
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> The file /usr/people/douglas/.nodelist contains:
> >> >> >> >> group main
> >> >> >> >> host localhost
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on
> Wed,
> >> 9
> >> >> Apr
> >> >> >> >> 2014 12:28:51 +0200:
> >> >> >> >>
> >> >> >> >> > Please try the same command without ++local and see if it
> >> still
> >> >> >> >> works.
> >> >> >> >> >
> >> >> >> >> >> -----Ursprüngliche Nachricht-----
> >> >> >> >> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-
> >> >> l_at_ks.uiuc.edu]
> >> >> >> Im
> >> >> >> >> >> Auftrag von Douglas Houston
> >> >> >> >> >> Gesendet: Mittwoch, 9. April 2014 11:49
> >> >> >> >> >> An: ramya narasimhan
> >> >> >> >> >> Cc: Namd Mailing List
> >> >> >> >> >> Betreff: Re: namd-l: Using nodelist file causes namd to
> >> hang
> >> >> >> >> >>
> >> >> >> >> >> The result is the same whichever order the nodes are
> >> present
> >> >> in
> >> >> >> the
> >> >> >> >> >> list.
> >> >> >> >> >>
> >> >> >> >> >> What exactly is Charmrun waiting for at the "Waiting for
> 0-
> >> th
> >> >> >> client
> >> >> >> >> >> to connect." stage? Presumably the 0th client is the
> first
> >> in
> >> >> >> >> >> nodelist, and that a process is supposed to start on
> that
> >> >> node,
> >> >> >> then
> >> >> >> >> >> "connect" to Charmrun on the host machine?
> >> >> >> >> >
> >> >> >> >> > Charmrun is just spawning the namd processes and now is
> >> waiting
> >> >> >> for
> >> >> >> >> them to
> >> >> >> >> > start to talk.
> >> >> >> >> >
> >> >> >> >> >>
> >> >> >> >> >> Using the command top I see no evidence of anything new
> >> >> starting
> >> >> >> on
> >> >> >> >> >> the node, despite all the "starting node-program" and
> "rsh
> >> >> phase
> >> >> >> >> >> successful" messages that are output.
> >> >> >> >> >>
> >> >> >> >> >> Using "ps -u douglas" on the node shows a whole bunch of
> >> tcsh
> >> >> and
> >> >> >> sh
> >> >> >> >> >> shells and sleep processes starting then dying but
> nothing
> >> >> else.
> >> >> >> >> >>
> >> >> >> >> >> What does the line "Sending "0 129.215.237.187 57453
> 26737
> >> 0"
> >> >> to
> >> >> >> >> >> client 0" mean? How is this "sending" achieved? I see
> "port
> >> >> >> 57453"
> >> >> >> >> is
> >> >> >> >> >> mentioned in the output ...
> >> >> >> >> >
> >> >> >> >> > Seems like being part of the parallel startup, where the
> >> >> spawned
> >> >> >> >> processes
> >> >> >> >> > get the information about each other.
> >> >> >> >> >
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> Quoting ramya narasimhan <ramya_jln_at_yahoo.co.in> on Wed,
> 9
> >> Apr
> >> >> >> 2014
> >> >> >> >> >> 11:51:52 +0800 (SGT):
> >> >> >> >> >>
> >> >> >> >> >> > Just change the hostname [IP of the system] order in
> the
> >> >> >> >> >> > nodefile, so that the 0-th client will be itioc5
> instead
> >> >> >> >> of itioc1.
> >> >> >> >> >> > To find whether the problem is with nodes.
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> > Dr. Ramya.L.
> >> >> >> >> >> > On Tuesday, 8 April 2014 7:23 PM, Douglas Houston
> >> >> >> >> >> > <DouglasR.Houston_at_ed.ac.uk> wrote:
> >> >> >> >> >> >
> >> >> >> >> >> > Yes, with ping all the nodes resolve to full hostnames
> >> and
> >> >> IP
> >> >> >> >> >> > addresses. I tried putting IP addresses into nodelist
> >> >> instead
> >> >> >> of
> >> >> >> >> >> > hostnames but it still times out at "Waiting for 0-th
> >> client
> >> >> to
> >> >> >> >> >> connect"
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> > Quoting Norman Geist <norman.geist_at_uni-greifswald.de>
> on
> >> >> Tue, 8
> >> >> >> >> Apr
> >> >> >> >> >> > 2014 14:30:15 +0200:
> >> >> >> >> >> >
> >> >> >> >> >> >> On all the nodes? Otherwise try a nodelist with IP
> >> adresses
> >> >> >> >> instead
> >> >> >> >> >> of
> >> >> >> >> >> >> hostnames. If that works, you got a problem with
> local
> >> DNS.
> >> >> >> >> >> >>
> >> >> >> >> >> >> Norman Geist.
> >> >> >> >> >> >>
> >> >> >> >> >> >>
> >> >> >> >> >> >>> -----Ursprüngliche Nachricht-----
> >> >> >> >> >> >>> Von: Douglas Houston
> [mailto:DouglasR.Houston_at_ed.ac.uk]
> >> >> >> >> >> >>> Gesendet: Dienstag, 8. April 2014 14:14
> >> >> >> >> >> >>> An: Norman Geist
> >> >> >> >> >> >>> Cc: Namd Mailing List
> >> >> >> >> >> >>> Betreff: Re: AW: AW: namd-l: Using nodelist file
> causes
> >> >> namd
> >> >> >> to
> >> >> >> >> >> hang
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> Thanks Norman. I had found that thread after my
> >> searches
> >> >> but
> >> >> >> it
> >> >> >> >> did
> >> >> >> >> >> >>> not seem to apply to my problem.
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> "You can check this while doing a ping to the
> hostname,
> >> >> while
> >> >> >> >> you
> >> >> >> >> >> are
> >> >> >> >> >> >>> logged in at a compute node "ping hostname". If this
> >> >> returns
> >> >> >> an
> >> >> >> >> >> >>> 127.x.x.x address, your local DNS configuration is
> not
> >> >> >> suitable
> >> >> >> >> for
> >> >> >> >> >> >>> charmrun"
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> My ping returns the full name and IP address of the
> >> node,
> >> >> not
> >> >> >> >> >> >>> 127.x.x.x.
> >> >> >> >> >> >>>
> >> >> >> >> >> >>>
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> Quoting Norman Geist <norman.geist_at_uni-
> greifswald.de>
> >> on
> >> >> Tue,
> >> >> >> 8
> >> >> >> >> Apr
> >> >> >> >> >> >>> 2014 13:22:41 +0200:
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> > Now I remember that I already posted a solution
> for
> >> this
> >> >> >> some
> >> >> >> >> >> weeks
> >> >> >> >> >> >>> ago, you
> >> >> >> >> >> >>> > could have found it by using google.de. Maybe this
> >> helps
> >> >> >> you.
> >> >> >> >> >> >>> >
> >> >> >> >> >> >>> >
> >> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-
> >> >> >> l.2012-
> >> >> >> >> >> >>> 2013/2645.html
> >> >> >> >> >> >>> >
> >> >> >> >> >> >>> > Norman Geist.
> >> >> >> >> >> >>> >
> >> >> >> >> >> >>> >
> >> >> >> >> >> >>> >> -----Ursprüngliche Nachricht-----
> >> >> >> >> >> >>> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-
> >> >> >> >> l_at_ks.uiuc.edu]
> >> >> >> >> >> Im
> >> >> >> >> >> >>> >> Auftrag von Douglas Houston
> >> >> >> >> >> >>> >> Gesendet: Dienstag, 8. April 2014 12:53
> >> >> >> >> >> >>> >> An: Norman Geist
> >> >> >> >> >> >>> >> Cc: Namd Mailing List
> >> >> >> >> >> >>> >> Betreff: Re: AW: namd-l: Using nodelist file
> causes
> >> >> namd
> >> >> >> to
> >> >> >> >> hang
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>> >> Thanks for the tip Norman, but if I change my
> >> command
> >> >> to
> >> >> >> the
> >> >> >> >> >> >>> following
> >> >> >> >> >> >>> >> it still hangs at the same point:
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>> >> /usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/charmrun
> >> >> >> +p12
> >> >> >> >> >> >>> >> ++remote-shell ssh
> >> >> >> >> >> >>> >> /usr/people/douglas/programs/NAMD_2.9_Linux-
> >> x86/namd2
> >> >> >> >> ++verbose
> >> >> >> >> >> >>> >> mdrun.conf
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>> >> Quoting Norman Geist <norman.geist_at_uni-
> >> greifswald.de>
> >> >> on
> >> >> >> Tue,
> >> >> >> >> 8
> >> >> >> >> >> Apr
> >> >> >> >> >> >>> >> 2014 12:06:03 +0200:
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>> >> > Try the charmrun option "++remote-shell ssh".
> >> >> >> >> >> >>> >> >
> >> >> >> >> >> >>> >> > Norman Geist.
> >> >> >> >> >> >>> >> >
> >> >> >> >> >> >>> >> >> -----Ursprüngliche Nachricht-----
> >> >> >> >> >> >>> >> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-
> namd-
> >> >> >> >> >> l_at_ks.uiuc.edu]
> >> >> >> >> >> >>> Im
> >> >> >> >> >> >>> >> >> Auftrag von Douglas Houston
> >> >> >> >> >> >>> >> >> Gesendet: Dienstag, 8. April 2014 11:30
> >> >> >> >> >> >>> >> >> An: namd-l_at_ks.uiuc.edu
> >> >> >> >> >> >>> >> >> Betreff: namd-l: Using nodelist file causes
> namd
> >> to
> >> >> >> hang
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> I have two nodes connected via ethernet:
> itioc5
> >> and
> >> >> >> itioc1
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> I have the following in my nodelist file:
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> group main
> >> >> >> >> >> >>> >> >> host itioc1
> >> >> >> >> >> >>> >> >> host itioc5
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> I am using the following command:
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> /usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> >> x86/charmrun
> >> >> >> >> +p12
> >> >> >> >> >> >>> >> >> /usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2
> >> >> >> >> >> ++verbose
> >> >> >> >> >> >>> >> >> mdrun.conf
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> I get the following output:
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> Charmrun> charmrun started...
> >> >> >> >> >> >>> >> >> Charmrun> using ./nodelist as nodesfile
> >> >> >> >> >> >>> >> >> Charmrun> adding client 0: "itioc1",
> >> >> IP:129.215.137.21
> >> >> >> >> >> >>> >> >> Charmrun> adding client 1: "itioc5",
> >> >> IP:129.215.237.186
> >> >> >> >> >> >>> >> >> Charmrun> adding client 2: "itioc1",
> >> >> IP:129.215.137.21
> >> >> >> >> >> >>> >> >> Charmrun> adding client 3: "itioc5",
> >> >> IP:129.215.237.186
> >> >> >> >> >> >>> >> >> Charmrun> adding client 4: "itioc1",
> >> >> IP:129.215.137.21
> >> >> >> >> >> >>> >> >> Charmrun> adding client 5: "itioc5",
> >> >> IP:129.215.237.186
> >> >> >> >> >> >>> >> >> Charmrun> adding client 6: "itioc1",
> >> >> IP:129.215.137.21
> >> >> >> >> >> >>> >> >> Charmrun> adding client 7: "itioc5",
> >> >> IP:129.215.237.186
> >> >> >> >> >> >>> >> >> Charmrun> adding client 8: "itioc1",
> >> >> IP:129.215.137.21
> >> >> >> >> >> >>> >> >> Charmrun> adding client 9: "itioc5",
> >> >> IP:129.215.237.186
> >> >> >> >> >> >>> >> >> Charmrun> adding client 10: "itioc1",
> >> >> IP:129.215.137.21
> >> >> >> >> >> >>> >> >> Charmrun> adding client 11: "itioc5",
> >> >> >> IP:129.215.237.186
> >> >> >> >> >> >>> >> >> Charmrun> Charmrun = 129.215.237.187, port =
> >> 58330
> >> >> >> >> >> >>> >> >> start_nodes_rsh
> >> >> >> >> >> >>> >> >> Charmrun> Sending "0 129.215.237.187 58330
> 19205
> >> 0"
> >> >> to
> >> >> >> >> client
> >> >> >> >> >> 0.
> >> >> >> >> >> >>> >> >> Charmrun> find the node program
> >> >> >> >> >> >>> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2"
> >> >> >> at
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> >> >>> >> >> " for
> >> >> >> >> >> >>> >> >> 0.
> >> >> >> >> >> >>> >> >> Charmrun> Starting ssh itioc1 -l douglas
> /bin/sh
> >> -f
> >> >> >> >> >> >>> >> >> Charmrun> remote shell (itioc1:0) started
> >> >> >> >> >> >>> >> >> Charmrun> Sending "1 129.215.237.187 58330
> 19205
> >> 0"
> >> >> to
> >> >> >> >> client
> >> >> >> >> >> 1.
> >> >> >> >> >> >>> >> >> Charmrun> find the node program
> >> >> >> >> >> >>> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2"
> >> >> >> at
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> >> >>> >> >> " for
> >> >> >> >> >> >>> >> >> 1.
> >> >> >> >> >> >>> >> >> Charmrun> Starting ssh itioc5 -l douglas
> /bin/sh
> >> -f
> >> >> >> >> >> >>> >> >> Charmrun> remote shell (itioc5:1) started
> >> >> >> >> >> >>> >> >> Charmrun> Sending "2 129.215.237.187 58330
> 19205
> >> 0"
> >> >> to
> >> >> >> >> client
> >> >> >> >> >> 2.
> >> >> >> >> >> >>> >> >> Charmrun> find the node program
> >> >> >> >> >> >>> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2"
> >> >> >> at
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> >> >>> >> >> " for
> >> >> >> >> >> >>> >> >> 2.
> >> >> >> >> >> >>> >> >> Charmrun> Starting ssh itioc1 -l douglas
> /bin/sh
> >> -f
> >> >> >> >> >> >>> >> >> Charmrun> remote shell (itioc1:2) started
> >> >> >> >> >> >>> >> >> Charmrun> Sending "3 129.215.237.187 58330
> 19205
> >> 0"
> >> >> to
> >> >> >> >> client
> >> >> >> >> >> 3.
> >> >> >> >> >> >>> >> >> Charmrun> find the node program
> >> >> >> >> >> >>> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2"
> >> >> >> at
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> >> >>> >> >> " for
> >> >> >> >> >> >>> >> >> 3.
> >> >> >> >> >> >>> >> >> Charmrun> Starting ssh itioc5 -l douglas
> /bin/sh
> >> -f
> >> >> >> >> >> >>> >> >> Charmrun> remote shell (itioc5:3) started
> >> >> >> >> >> >>> >> >> Charmrun> Sending "4 129.215.237.187 58330
> 19205
> >> 0"
> >> >> to
> >> >> >> >> client
> >> >> >> >> >> 4.
> >> >> >> >> >> >>> >> >> Charmrun> find the node program
> >> >> >> >> >> >>> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2"
> >> >> >> at
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> >> >>> >> >> " for
> >> >> >> >> >> >>> >> >> 4.
> >> >> >> >> >> >>> >> >> Charmrun> Starting ssh itioc1 -l douglas
> /bin/sh
> >> -f
> >> >> >> >> >> >>> >> >> Charmrun> remote shell (itioc1:4) started
> >> >> >> >> >> >>> >> >> Charmrun> Sending "5 129.215.237.187 58330
> 19205
> >> 0"
> >> >> to
> >> >> >> >> client
> >> >> >> >> >> 5.
> >> >> >> >> >> >>> >> >> Charmrun> find the node program
> >> >> >> >> >> >>> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2"
> >> >> >> at
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> >> >>> >> >> " for
> >> >> >> >> >> >>> >> >> 5.
> >> >> >> >> >> >>> >> >> Charmrun> Starting ssh itioc5 -l douglas
> /bin/sh
> >> -f
> >> >> >> >> >> >>> >> >> Charmrun> remote shell (itioc5:5) started
> >> >> >> >> >> >>> >> >> Charmrun> Sending "6 129.215.237.187 58330
> 19205
> >> 0"
> >> >> to
> >> >> >> >> client
> >> >> >> >> >> 6.
> >> >> >> >> >> >>> >> >> Charmrun> find the node program
> >> >> >> >> >> >>> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2"
> >> >> >> at
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> >> >>> >> >> " for
> >> >> >> >> >> >>> >> >> 6.
> >> >> >> >> >> >>> >> >> Charmrun> Starting ssh itioc1 -l douglas
> /bin/sh
> >> -f
> >> >> >> >> >> >>> >> >> Charmrun> remote shell (itioc1:6) started
> >> >> >> >> >> >>> >> >> Charmrun> Sending "7 129.215.237.187 58330
> 19205
> >> 0"
> >> >> to
> >> >> >> >> client
> >> >> >> >> >> 7.
> >> >> >> >> >> >>> >> >> Charmrun> find the node program
> >> >> >> >> >> >>> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2"
> >> >> >> at
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> >> >>> >> >> " for
> >> >> >> >> >> >>> >> >> 7.
> >> >> >> >> >> >>> >> >> Charmrun> Starting ssh itioc5 -l douglas
> /bin/sh
> >> -f
> >> >> >> >> >> >>> >> >> Charmrun> remote shell (itioc5:7) started
> >> >> >> >> >> >>> >> >> Charmrun> Sending "8 129.215.237.187 58330
> 19205
> >> 0"
> >> >> to
> >> >> >> >> client
> >> >> >> >> >> 8.
> >> >> >> >> >> >>> >> >> Charmrun> find the node program
> >> >> >> >> >> >>> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2"
> >> >> >> at
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> >> >>> >> >> " for
> >> >> >> >> >> >>> >> >> 8.
> >> >> >> >> >> >>> >> >> Charmrun> Starting ssh itioc1 -l douglas
> /bin/sh
> >> -f
> >> >> >> >> >> >>> >> >> Charmrun> remote shell (itioc1:8) started
> >> >> >> >> >> >>> >> >> Charmrun> Sending "9 129.215.237.187 58330
> 19205
> >> 0"
> >> >> to
> >> >> >> >> client
> >> >> >> >> >> 9.
> >> >> >> >> >> >>> >> >> Charmrun> find the node program
> >> >> >> >> >> >>> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2"
> >> >> >> at
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> >> >>> >> >> " for
> >> >> >> >> >> >>> >> >> 9.
> >> >> >> >> >> >>> >> >> Charmrun> Starting ssh itioc5 -l douglas
> /bin/sh
> >> -f
> >> >> >> >> >> >>> >> >> Charmrun> remote shell (itioc5:9) started
> >> >> >> >> >> >>> >> >> Charmrun> Sending "10 129.215.237.187 58330
> 19205
> >> 0"
> >> >> to
> >> >> >> >> >> client
> >> >> >> >> >> >>> 10.
> >> >> >> >> >> >>> >> >> Charmrun> find the node program
> >> >> >> >> >> >>> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2"
> >> >> >> at
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> >> >>> >> >> " for
> >> >> >> >> >> >>> >> >> 10.
> >> >> >> >> >> >>> >> >> Charmrun> Starting ssh itioc1 -l douglas
> /bin/sh
> >> -f
> >> >> >> >> >> >>> >> >> Charmrun> remote shell (itioc1:10) started
> >> >> >> >> >> >>> >> >> Charmrun> Sending "11 129.215.237.187 58330
> 19205
> >> 0"
> >> >> to
> >> >> >> >> >> client
> >> >> >> >> >> >>> 11.
> >> >> >> >> >> >>> >> >> Charmrun> find the node program
> >> >> >> >> >> >>> >> >> "/usr/people/douglas/programs/NAMD_2.9_Linux-
> >> >> x86/namd2"
> >> >> >> at
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> "/usr/people/douglas/projects/UPS/targets/SCF/2AST/MD/parallelise_itioc
> >> >> >> >> >> >>> >> >> " for
> >> >> >> >> >> >>> >> >> 11.
> >> >> >> >> >> >>> >> >> Charmrun> Starting ssh itioc5 -l douglas
> /bin/sh
> >> -f
> >> >> >> >> >> >>> >> >> Charmrun> remote shell (itioc5:11) started
> >> >> >> >> >> >>> >> >> Charmrun> node programs all started
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.3)> remote
> >> >> responding...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.5)> remote
> >> >> responding...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.3)> starting
> node-
> >> >> >> program...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.5)> starting
> node-
> >> >> >> program...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.3)> rsh phase
> >> >> successful.
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.5)> rsh phase
> >> >> successful.
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.9)> remote
> >> >> responding...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.7)> remote
> >> >> responding...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.11)> remote
> >> >> responding...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.1)> remote
> >> >> responding...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.9)> starting
> node-
> >> >> >> program...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.7)> starting
> node-
> >> >> >> program...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.9)> rsh phase
> >> >> successful.
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.7)> rsh phase
> >> >> successful.
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.11)> starting
> node-
> >> >> >> program...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.1)> starting
> node-
> >> >> >> program...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.11)> rsh phase
> >> >> successful.
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc5.1)> rsh phase
> >> >> successful.
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.10)> remote
> >> >> responding...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.0)> remote
> >> >> responding...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.4)> remote
> >> >> responding...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.10)> starting
> node-
> >> >> >> program...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.10)> rsh phase
> >> >> successful.
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.0)> starting
> node-
> >> >> >> program...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.0)> rsh phase
> >> >> successful.
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.4)> starting
> node-
> >> >> >> program...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.4)> rsh phase
> >> >> successful.
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.2)> remote
> >> >> responding...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.6)> remote
> >> >> responding...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.8)> remote
> >> >> responding...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.2)> starting
> node-
> >> >> >> program...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.2)> rsh phase
> >> >> successful.
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.6)> starting
> node-
> >> >> >> program...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.6)> rsh phase
> >> >> successful.
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.8)> starting
> node-
> >> >> >> program...
> >> >> >> >> >> >>> >> >> Charmrun remote shell(itioc1.8)> rsh phase
> >> >> successful.
> >> >> >> >> >> >>> >> >> Charmrun> Waiting for 0-th client to connect.
> >> >> >> >> >> >>> >> >> Charmrun> error 0 attaching to node:
> >> >> >> >> >> >>> >> >> Timeout waiting for node-program to connect
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> I'm not sure but I think the "Starting ssh
> itioc5
> >> -l
> >> >> >> >> douglas
> >> >> >> >> >> >>> /bin/sh
> >> >> >> >> >> >>> >> >> -f" lines has something to do with it. If I
> run
> >> the
> >> >> >> >> command
> >> >> >> >> >> "ssh
> >> >> >> >> >> >>> >> >> itioc5 -l douglas /bin/sh -f" it also hangs.
> If I
> >> >> run
> >> >> >> "ssh
> >> >> >> >> >> itioc5
> >> >> >> >> >> >>> -l
> >> >> >> >> >> >>> >> >> douglas" then it logs me in just fine (without
> >> >> asking
> >> >> >> for
> >> >> >> >> a
> >> >> >> >> >> >>> >> password).
> >> >> >> >> >> >>> >> >> Similarly the command "ssh itioc5 -l douglas -
> f
> >> pwd"
> >> >> >> works
> >> >> >> >> >> fine,
> >> >> >> >> >> >>> >> with
> >> >> >> >> >> >>> >> >> the expected directory name returned.
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> What exactly is happening at the "Waiting for
> 0-
> >> th
> >> >> >> client
> >> >> >> >> to
> >> >> >> >> >> >>> >> connect."
> >> >> >> >> >> >>> >> >> stage?
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> Many thanks in advance for your thoughts.
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> cheers,
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> Doug
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >>
> >> >> _____________________________________________________
> >> >> >> >> >> >>> >> >> Dr. Douglas R. Houston
> >> >> >> >> >> >>> >> >> Lecturer
> >> >> >> >> >> >>> >> >> Institute of Structural and Molecular Biology
> >> >> >> >> >> >>> >> >> Room 3.23, Michael Swann Building
> >> >> >> >> >> >>> >> >> King's Buildings
> >> >> >> >> >> >>> >> >> University of Edinburgh
> >> >> >> >> >> >>> >> >> Edinburgh, EH9 3JR, UK
> >> >> >> >> >> >>> >> >> Tel. 0131 650 7358
> >> >> >> >> >> >>> >> >> http://tinyurl.com/douglasrhouston
> >> >> >> >> >> >>> >> >>
> >> >> >> >> >> >>> >> >> --
> >> >> >> >> >> >>> >> >> The University of Edinburgh is a charitable
> body,
> >> >> >> >> registered
> >> >> >> >> >> in
> >> >> >> >> >> >>> >> >> Scotland, with registration number SC005336.
> >> >> >> >> >> >>> >> >
> >> >> >> >> >> >>> >> >
> >> >> >> >> >> >>> >> >
> >> >> >> >> >> >>> >> > ---
> >> >> >> >> >> >>> >> > Diese E-Mail ist frei von Viren und Malware,
> denn
> >> der
> >> >> >> >> avast!
> >> >> >> >> >> >>> >> > Antivirus Schutz ist aktiv.
> >> >> >> >> >> >>> >> > http://www.avast.com
> >> >> >> >> >> >
> >> >> >> >> >> >>> >> >
> >> >> >> >> >> >>> >> >
> >> >> >> >> >> >>> >> >
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>> >>
> >> _____________________________________________________
> >> >> >> >> >> >>> >> Dr. Douglas R. Houston
> >> >> >> >> >> >>> >> Lecturer
> >> >> >> >> >> >>> >> Institute of Structural and Molecular Biology
> >> >> >> >> >> >>> >> Room 3.23, Michael Swann Building
> >> >> >> >> >> >>> >> King's Buildings
> >> >> >> >> >> >>> >> University of Edinburgh
> >> >> >> >> >> >>> >> Edinburgh, EH9 3JR, UK
> >> >> >> >> >> >>> >> Tel. 0131 650 7358
> >> >> >> >> >> >>> >> http://tinyurl.com/douglasrhouston
> >> >> >> >> >> >>> >>
> >> >> >> >> >> >>> >> --
> >> >> >> >> >> >>> >> The University of Edinburgh is a charitable body,
> >> >> >> registered
> >> >> >> >> in
> >> >> >> >> >> >>> >> Scotland, with registration number SC005336.
> >> >> >> >> >> >>> >
> >> >> >> >> >> >>> >
> >> >> >> >> >> >>> >
> >> >> >> >> >> >>> > ---
> >> >> >> >> >> >>> > Diese E-Mail ist frei von Viren und Malware, denn
> der
> >> >> >> avast!
> >> >> >> >> >> >>> > Antivirus Schutz ist aktiv.
> >> >> >> >> >> >>> > http://www.avast.com
> >> >> >> >> >> >>> >
> >> >> >> >> >> >>> >
> >> >> >> >> >> >>> >
> >> >> >> >> >> >>>
> >> >> >> >> >> >>>
> >> >> >> >> >> >>>
> >> >> >> >> >> >>>
> >> >> >> >> >> >>>
> _____________________________________________________
> >> >> >> >> >> >>> Dr. Douglas R. Houston
> >> >> >> >> >> >>> Lecturer
> >> >> >> >> >> >>> Institute of Structural and Molecular Biology
> >> >> >> >> >> >>> Room 3.23, Michael Swann Building
> >> >> >> >> >> >>> King's Buildings
> >> >> >> >> >> >>> University of Edinburgh
> >> >> >> >> >> >>> Edinburgh, EH9 3JR, UK
> >> >> >> >> >> >>> Tel. 0131 650 7358
> >> >> >> >> >> >>> http://tinyurl.com/douglasrhouston
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> --
> >> >> >> >> >> >>> The University of Edinburgh is a charitable body,
> >> >> registered
> >> >> >> in
> >> >> >> >> >> >>> Scotland, with registration number SC005336.
> >> >> >> >> >> >>
> >> >> >> >> >> >>
> >> >> >> >> >> >>
> >> >> >> >> >> >> ---
> >> >> >> >> >> >> Diese E-Mail ist frei von Viren und Malware, denn der
> >> >> avast!
> >> >> >> >> >> >> Antivirus Schutz ist aktiv.
> >> >> >> >> >> >> http://www.avast.com
> >> >> >> >> >> >>
> >> >> >> >> >> >>
> >> >> >> >> >> >>
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> > _____________________________________________________
> >> >> >> >> >> > Dr. Douglas R. Houston
> >> >> >> >> >> > Lecturer
> >> >> >> >> >> > Institute of Structural and Molecular Biology
> >> >> >> >> >> > Room 3.23, Michael Swann Building
> >> >> >> >> >> > King's Buildings
> >> >> >> >> >> > University of Edinburgh
> >> >> >> >> >> > Edinburgh, EH9 3JR, UK
> >> >> >> >> >> > Tel. 0131 650 7358
> >> >> >> >> >> > http://tinyurl.com/douglasrhouston
> >> >> >> >> >> >
> >> >> >> >> >> > --
> >> >> >> >> >> > The University of Edinburgh is a charitable body,
> >> registered
> >> >> in
> >> >> >> >> >> > Scotland, with registration number SC005336.
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> _____________________________________________________
> >> >> >> >> >> Dr. Douglas R. Houston
> >> >> >> >> >> Lecturer
> >> >> >> >> >> Institute of Structural and Molecular Biology
> >> >> >> >> >> Room 3.23, Michael Swann Building
> >> >> >> >> >> King's Buildings
> >> >> >> >> >> University of Edinburgh
> >> >> >> >> >> Edinburgh, EH9 3JR, UK
> >> >> >> >> >> Tel. 0131 650 7358
> >> >> >> >> >> http://tinyurl.com/douglasrhouston
> >> >> >> >> >>
> >> >> >> >> >> --
> >> >> >> >> >> The University of Edinburgh is a charitable body,
> >> registered
> >> >> in
> >> >> >> >> >> Scotland, with registration number SC005336.
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> > ---
> >> >> >> >> > Diese E-Mail ist frei von Viren und Malware, denn der
> avast!
> >> >> >> >> > Antivirus Schutz ist aktiv.
> >> >> >> >> > http://www.avast.com
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> _____________________________________________________
> >> >> >> >> Dr. Douglas R. Houston
> >> >> >> >> Lecturer
> >> >> >> >> Institute of Structural and Molecular Biology
> >> >> >> >> Room 3.23, Michael Swann Building
> >> >> >> >> King's Buildings
> >> >> >> >> University of Edinburgh
> >> >> >> >> Edinburgh, EH9 3JR, UK
> >> >> >> >> Tel. 0131 650 7358
> >> >> >> >> http://tinyurl.com/douglasrhouston
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> The University of Edinburgh is a charitable body,
> registered
> >> in
> >> >> >> >> Scotland, with registration number SC005336.
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > ---
> >> >> >> > Diese E-Mail ist frei von Viren und Malware, denn der avast!
> >> >> >> > Antivirus Schutz ist aktiv.
> >> >> >> > http://www.avast.com
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> _____________________________________________________
> >> >> >> Dr. Douglas R. Houston
> >> >> >> Lecturer
> >> >> >> Institute of Structural and Molecular Biology
> >> >> >> Room 3.23, Michael Swann Building
> >> >> >> King's Buildings
> >> >> >> University of Edinburgh
> >> >> >> Edinburgh, EH9 3JR, UK
> >> >> >> Tel. 0131 650 7358
> >> >> >> http://tinyurl.com/douglasrhouston
> >> >> >>
> >> >> >> --
> >> >> >> The University of Edinburgh is a charitable body, registered
> in
> >> >> >> Scotland, with registration number SC005336.
> >> >> >
> >> >> >
> >> >> >
> >> >> > ---
> >> >> > Diese E-Mail ist frei von Viren und Malware, denn der avast!
> >> >> > Antivirus Schutz ist aktiv.
> >> >> > http://www.avast.com
> >> >> >
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> _____________________________________________________
> >> >> Dr. Douglas R. Houston
> >> >> Lecturer
> >> >> Institute of Structural and Molecular Biology
> >> >> Room 3.23, Michael Swann Building
> >> >> King's Buildings
> >> >> University of Edinburgh
> >> >> Edinburgh, EH9 3JR, UK
> >> >> Tel. 0131 650 7358
> >> >> http://tinyurl.com/douglasrhouston
> >> >>
> >> >> --
> >> >> The University of Edinburgh is a charitable body, registered in
> >> >> Scotland, with registration number SC005336.
> >> >
> >> >
> >> >
> >> > ---
> >> > Diese E-Mail ist frei von Viren und Malware, denn der avast!
> >> > Antivirus Schutz ist aktiv.
> >> > http://www.avast.com
> >> >
> >> >
> >> >
> >>
> >>
> >>
> >>
> >> _____________________________________________________
> >> Dr. Douglas R. Houston
> >> Lecturer
> >> Institute of Structural and Molecular Biology
> >> Room 3.23, Michael Swann Building
> >> King's Buildings
> >> University of Edinburgh
> >> Edinburgh, EH9 3JR, UK
> >> Tel. 0131 650 7358
> >> http://tinyurl.com/douglasrhouston
> >>
> >> --
> >> The University of Edinburgh is a charitable body, registered in
> >> Scotland, with registration number SC005336.
> >>
> >
> >
> >
> > ---
> > Diese E-Mail ist frei von Viren und Malware, denn der avast!
> > Antivirus Schutz ist aktiv.
> > http://www.avast.com
> >
> >
> >
> >
>
>
>
>
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Institute of Structural and Molecular Biology
> Room 3.23, Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
> http://tinyurl.com/douglasrhouston
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
--- Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv. http://www.avast.com
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:52 CST