Subject: CHARMm with LAM-MPI

From: Fdo Danilo Gonzalez Nilo <[email-masked]>
Date: Wed, 3 Jul 2002 17:37:47 -0400 (CLT)

Hi all,

We are testing CHARMm in cluster enviroment with LAM-MPI. 
Any body know some program to check all CPU in cluster? (some thing like 
"top" command )

Thanks a lot,

Danilo Gonzalez N.           

University of Santiago de Chile
Faculty of Chemistry and Biology, Computational Chemistry Lab.         
Casilla 40, Correo 33, Santiago, Chile      Fono: (562) 681 1542 Anexo:799
E-mail : [email-masked]            Fax : (562) 681 2108           
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From: "David E. Konerding" <[email-masked]>
Date: Wed, 03 Jul 2002 19:35:14 -0700

>Any body know some program to check all CPU in cluster? (some thing like 

What sort of status check do you want?  Is your goal to find a set of 
free CPUs on which to
run CHARMm?  In that, the best solution is one which actually ensures 
that the machines are
free, rather than using some ad-hoc mechanism such as load (which is 
inaccurate due to disk-waits,
and time smoothing).  Queuing systems such as OpenPBS, Maui, and Sun 
Grid Engine are designed to
do this and they do it fairly well, as long as users respect the queue 
system (there's nothing quite so bad as
a user who knows the queue policy and insists on logging into a node 
manually to run their job, which typically
screws up any scaling you hoped to get using MPI).

An alternative, which is easy to set up and works well in many 
situations is the gexec/gstat/gmond combo of programs
> from ganglia.sourceforge.net.  The "gstat" command quickly tells you the 
state of nodes, and the gexec command can make it quite easy
to generate an MPICH mpi host list file (presumably also useful with 
LAM/MPI).

CLUSTER INFORMATION
       Name: unspecified
      Hosts: 13
Gexec Hosts: 12
 Dead Hosts: 0
  Localtime: Wed Jul  3 19:36:45 2002

CLUSTER HOSTS
Hostname                     LOAD                       CPU              
Gexec
 CPUs (Procs/Total) [     1,     5, 15min] [  User,  Nice, System, Idle]

client09.hanalei
    2 (    0/   38) [  0.00,  0.02,  0.51] [   0.0,   0.0,   0.0, 100.0] ON
client15.hanalei
    2 (    2/   38) [  0.00,  0.00,  0.00] [   0.0,   0.0,   0.0, 100.0] ON
client10.hanalei
    2 (    1/   42) [  0.96,  1.12,  1.94] [  50.0,   0.0,   0.0,  50.0] ON
client11.hanalei
    2 (    1/   41) [  0.98,  0.97,  0.99] [  49.8,   0.0,   0.1,  50.1] ON
client14.hanalei
    2 (    1/   41) [  0.99,  0.97,  0.98] [  49.3,   0.0,   0.1,  50.6] ON
client07.hanalei
    2 (    1/   41) [  1.00,  1.00,  1.00] [  49.2,   0.0,   0.5,  50.3] ON
client13.hanalei
    2 (    3/   44) [  1.02,  1.00,  1.03] [  32.7,   0.0,  16.7,  50.6] ON
client12.hanalei
    2 (    3/   44) [  1.97,  1.99,  2.00] [  99.4,   0.0,   0.0,   0.0] ON
workstation7.hanalei
    1 (    0/   53) [  0.99,  0.97,  0.91] [   0.0,   0.0,   0.0, 100.0] ON
client08.hanalei
    2 (    2/   48) [  2.04,  2.03,  2.06] [  58.4,   0.0,  38.4,   2.9] ON
client01.hanalei
    2 (    2/   45) [  2.05,  2.02,  2.01] [  97.9,   0.0,   0.2,   1.3] ON
client02.hanalei
    2 (    2/   44) [  2.12,  2.03,  2.00] [  96.9,   0.0,   0.6,   2.7] ON