Re: AW: Using nodelist file causes namd to hang

From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Tue Apr 08 2014 - 07:21:19 CDT

Hi Ramya, I am not running namd in a queue, or using qsub. My nodes
are ordinary Intel Linux workstations on an ethernet network (I
believe this is called a "Beowulf cluster"). I already have the
nodelist file in the working dir.

Quoting ramya narasimhan <ramya_jln_at_yahoo.co.in> on Tue, 8 Apr 2014
19:28:54 +0800 (SGT):

> Are you running in queue? Then give the command as these lines in *.sh file.
> #!/bin/bash
> #
> #$ -cwd
> #$ -j y
> #$ -S /bin/bash
> #$ -pe mpich 12
> #
> export namdroot=/path/NAMD_2.9_Linux-x86_64-ibverbs-smp
>
> $namdroot/charmrun +p12 ++remote-shell ssh ++nodelist nodelist
> ++verbose $namdroot/namd2 *.conf> *.log
>  Have the nodelist file in the woking dir.
> Submit the job as : qsub *.sh
>
> Dr.Ramya.L.
> On Tuesday, 8 April 2014 4:35 PM, Douglas Houston
> <DouglasR.Houston_at_ed.ac.uk> wrote:
>
> 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.

_____________________________________________________
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.

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:40 CST