From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Apr 08 2014 - 07:30:15 CDT
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
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