Re: AW: AW: Using nodelist file causes namd to hang

From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Tue Jun 24 2014 - 08:42:20 CDT

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Hi Norman,

My sysadmin isn't too happy with me leaving the firewalls off
(understandably so; these boxes have been hacked in the past). He is
asking if we know what port(s) namd wants to use, because if they are
defined we can set it up for that. Are there specific ports only that
we could leave open?

cheers,
Doug

Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Fri, 20 Jun
2014 12:15:02 +0200:

>
>> -----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
>
>
>

_____________________________________________________
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.

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This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:55 CST