Re: AW: Using nodelist file causes namd to hang

From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Wed Apr 09 2014 - 04:28:37 CDT

The following command works on all of the nodes:

/usr/people/douglas/programs/NAMD_2.9_Linux-x86/charmrun +p12
/usr/people/douglas/programs/NAMD_2.9_Linux-x86/namd2 ++local mdrun.conf

Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Wed, 9 Apr
2014 07:21:40 +0200:

> Are you able to run this same binary manually on one of the nodes by using
> charmrun?
>
> Norman Geist.
>
>> -----Ursprüngliche Nachricht-----
>> Von: Douglas Houston [mailto:DouglasR.Houston_at_ed.ac.uk]
>> Gesendet: Dienstag, 8. April 2014 15:50
>> An: Norman Geist
>> Cc: Namd Mailing List
>> Betreff: Re: namd-l: Using nodelist file causes namd to hang
>>
>> 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.
>
>
>
> ---
> 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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