AW: AW: Using nodelist file causes namd to hang

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Jun 20 2014 - 05:15:02 CDT

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> -----Ursprüngliche Nachricht-----
> Von: Douglas Houston [mailto:DouglasR.Houston_at_ed.ac.uk]
> Gesendet: Freitag, 20. Juni 2014 12:00
> An: Norman Geist
> Cc: Namd Mailing List
> Betreff: Re: AW: namd-l: Using nodelist file causes namd to hang
>
> Hi Norman,
>
> +idlepoll has made a big difference with CPUs at 100% on all nodes.
> That's with the following logging parameters:
>
> restartfreq 500
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
>
> 4 of the nodes (3,4,5,6) are identical, with each having 12 of the
> following cores split between 2 CPUs:
>
> vendor_id : GenuineIntel
> cpu family : 6
> model : 44
> model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
> stepping : 2
> cpu MHz : 1600.000
> cache size : 12288 KB
> physical id : 0
> siblings : 12
> core id : 0
>
> 2 of the nodes (1 & 2, on a different subnet) are identical, with each
> having 8 of the following cores split between 2 CPUs:
>
> vendor_id : GenuineIntel
> cpu family : 6
> model : 23
> model name : Intel(R) Xeon(R) CPU E5420 @ 2.50GHz
> stepping : 10
> cpu MHz : 2500.078
> cache size : 6144 KB
> physical id : 0
> siblings : 4
> core id : 0
>
> Adding itioc1 and 2 to the nodelist now seems to work with all CPUs
> still close to 100%. Is the message "Load balancer assumes all CPUs
> are same" a problem as 1&2 have slightly slower processors than 3-6?

Problem = slower, so your benchmark will point out ;)

>
> I will report the results of benchmarking when done.
>
> Thanks so much for all your help!
>
> cheers,
> Doug
>
>
> Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Fri, 20 Jun
> 2014 09:25:11 +0200:
>
> >> -----Ursprüngliche Nachricht-----
> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> >> Auftrag von Douglas Houston
> >> Gesendet: Donnerstag, 19. Juni 2014 19:25
> >> An: Norman Geist
> >> Cc: Namd Mailing List
> >> Betreff: Re: namd-l: Using nodelist file causes namd to hang
> >>
> >> Hi Norman,
> >>
> >> Switching off the firewalls using '/etc/init.d/iptables stop' on
> each
> >> node now allows everything to run, and for the log files, dcd file
> >> etc. to update.
> >>
> >
> > Finally ;)
> >
> >> However I'm seeing only 1% utilisation of each CPU. I thought
> perhaps
> >> running on only those nodes that share a subnet might help in case
> the
> >> link between the two subnets was causing a bottleneck but no luck,
> CPU
> >> usage is still no more than 5%.
> >>
> >> Is this behaviour expected? What sort of ethernet bandwidth should I
> >> need to fully utilise 48 cores across 4 nodes?
> >
> >
> > For this setup 1Gbit should be ok. Depending on system size of
> course.
> > For namd2 you might want to use +idlepoll.
> >
> >>
> >> Another issue is that the hard drive where the files are written is
> >> not inside any of the nodes but in a server on a different subnet.
> But
> >> I wouldn't have thought so much data is written that quickly to
> cause
> >> a problem?
> >
> > Usually this is not a problem if having reasonable output options
> like:
> >
> > Dcdfreq 1000
> > Restartfreq 100000
> > Outputenergies 1000
> >
> > Please benchmark your setup from 1 to 4 nodes and report the
> time/step or
> > ns/day so that I can see the full behavior. Also make sure you do not
> use
> > hyper threading cores. What CPU model do you have?
> >
> >>
> >> Or are there settings in my .conf file that could improve
> >> parallelisation?
> >>
> >> cheers,
> >> Doug
> >>
> >>
> >>
> >>
> >> Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Thu, 19 Jun
> >> 2014 12:09:43 +0200:
> >>
> >> >
> >> >> -----Ursprüngliche Nachricht-----
> >> >> Von: Douglas Houston [mailto:DouglasR.Houston_at_ed.ac.uk]
> >> >> Gesendet: Donnerstag, 19. Juni 2014 11:56
> >> >> An: Norman Geist
> >> >> Cc: Namd Mailing List
> >> >> Betreff: Re: AW: AW: AW: AW: namd-l: Using nodelist file causes
> namd
> >> to
> >> >> hang
> >> >>
> >> >> Thanks Norman,
> >> >>
> >> >> Not sure if this is relevant, but If I specify any one node in
> the
> >> >> nodelist file it runs OK, it only hangs if I have more than one
> node
> >> >> listed. Whether the node is on the same or different subnet seems
> to
> >> >> make no difference.
> >> >
> >> > Which pointed me to the local dns / or firewalls.
> >> >
> >> >>
> >> >> How do I check that all the nodes can reach each other over the
> >> >> network? I can ssh from one to the other OK (without password),
> what
> >> >> else should I check? We do have firewalls in place obviously but
> how
> >> >> can I tell if this is the problem?
> >> >
> >> > Easiest option is to turn off firewalls on two nodes and try with
> >> them, best
> >> > with only one process per node.
> >> >
> >> >>
> >> >> cheers,
> >> >> Doug
> >> >>
> >> >>
> >> >> Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Thu, 19
> Jun
> >> >> 2014 09:19:03 +0200:
> >> >>
> >> >> > The behavior you see let's me at least think, that indeed all
> the
> >> >> nodes can
> >> >> > connect to the "1st" node from which the job has been started
> as
> >> "all
> >> >> node
> >> >> > programs connected", but seem not be able to reach each other,
> so
> >> >> stuck.
> >> >> > This means that there's something weird with your network
> config
> >> and
> >> >> you
> >> >> > might want to check that all the nodes can reach each other
> over
> >> the
> >> >> network
> >> >> > you try to use, this may include possible firewall. This also
> >> still
> >> >> includes
> >> >> > that the hostnames of all nodes resolve to outgoing ip
> addresses
> >> as
> >> >> > explained before.
> >> >> >
> >> >> > 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: Mittwoch, 18. Juni 2014 14:58
> >> >> >> An: Norman Geist
> >> >> >> Cc: Namd Mailing List
> >> >> >> Betreff: Re: AW: AW: AW: namd-l: Using nodelist file causes
> namd
> >> to
> >> >> >> hang
> >> >> >>
> >> >> >> itioc1 and 2 are in a different physical location to 3, 4 5
> and
> >> 6,
> >> >> and
> >> >> >> presumably this means they're on a different subnet. Does this
> >> mean
> >> >> >> they can't be used?
> >> >> >>
> >> >> >> Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Wed,
> 18
> >> Jun
> >> >> >> 2014 14:52:29 +0200:
> >> >> >>
> >> >> >> > 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
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> _____________________________________________________
> >> >> >> 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

• Next message: Douglas Houston: "Re: AW: Using nodelist file causes namd to hang"
• Previous message: Norman Geist: "AW: Using nodelist file causes namd to hang"
• In reply to: Douglas Houston: "Re: AW: Using nodelist file causes namd to hang"
• Next in thread: Douglas Houston: "Re: AW: AW: Using nodelist file causes namd to hang"
• Reply: Douglas Houston: "Re: AW: AW: Using nodelist file causes namd to hang"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:31 CST