Changes between Version 2 and Version 3 of jazz/mpdboot


Ignore:
Timestamp:
Jul 2, 2008, 1:33:14 AM (17 years ago)
Author:
jazz
Comment:

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  • jazz/mpdboot

    v2 v3  
    4141 * Reference Solution: [http://structbio.vanderbilt.edu/comp/soft/amber/start.php Getting started with AMBER]
    4242
    43 ==
     43== Configure mpd for normal user ==
     44
     45 * Fisrt, login as nornal user. Here we login with user id 'jazz'. Then exchange SSH public key to each computing node.
     46{{{
     47login as: jazz
     48jazz@bio-cluster-12's password:
     49jazz@bio-cluster-12:~$ for i in 11 10 09 08 07 06; do scp .ssh/id_rsa.pub bio-cluster-$i:.ssh/authorized_keys; done
     50}}}
     51 * setup .mpd.conf for each compute node in $HOME
     52{{{
     53jazz@bio-cluster-12:~$ echo "MPD_SECRETWORD=${user}$$" > ~/.mpd.conf
     54jazz@bio-cluster-12:~$ chmod 600 .mpd.conf
     55jazz@bio-cluster-12:~$ for i in 11 10 09 08 07 06
     56> do
     57> scp .mpd.conf bio-cluster-$i:.
     58> done
     59.mpd.conf                                     100%   21     0.0KB/s   00:00
     60.mpd.conf                                     100%   21     0.0KB/s   00:00
     61.mpd.conf                                     100%   21     0.0KB/s   00:00
     62.mpd.conf                                     100%   21     0.0KB/s   00:00
     63.mpd.conf                                     100%   21     0.0KB/s   00:00
     64.mpd.conf                                     100%   21     0.0KB/s   00:00
     65}}}
     66 * setup mpd.hosts on localhost
     67{{{
     68jazz@bio-cluster-12:~$ cat > mpd.hosts << EOF
     69> bio-cluster-11
     70> bio-cluster-10
     71> bio-cluster-09
     72> bio-cluster-08
     73> bio-cluster-07
     74> bio-cluster-06
     75> EOF
     76}}}
     77 * run '''mpdboot''' for 7 nodes and use '''mpdtrace''' to check the status of mpd process on each compute node. '''mpdringtest''' can test the speed of message passing.
     78{{{
     79jazz@bio-cluster-12:~$ mpdboot -n 7
     80jazz@bio-cluster-12:~$ mpdtrace -l
     81bio-cluster-12_54092 (140.129.162.12)
     82bio-cluster-08_38361 (10.220.202.223)
     83bio-cluster-09_52923 (10.220.202.222)
     84bio-cluster-11_33377 (10.220.202.220)
     85bio-cluster-10_33103 (10.220.202.221)
     86bio-cluster-06_59631 (10.220.202.225)
     87bio-cluster-07_59533 (10.220.202.224)
     88jazz@bio-cluster-12:~$ mpdringtest 100
     89time for 100 loops = 0.0729811191559 seconds
     90}}}
     91 *