[GE users] SunGrid Engine & BLAST

Ron Chen ron_chen_123 at yahoo.com
Mon Jan 17 16:16:04 GMT 2005


See this "Reducing and Eliminating NFS Usage" HOWTO:

http://gridengine.sunsource.net/project/gridengine/howto/nfsreduce.html

 -Ron

--- Hrishikesh Deshmukh <hdeshmuk at gmail.com> wrote:
> I think i have now figured out few more things, the
> problem was of
> permissions though /usr/local/sge was owned by
> sgeadmin, the dirs
> inside were owned by root!(since remote dektop was
> used by root to
> copy them to exec. hosts).
> 
> So now sgeadmin owns /usr/local/sge and sub dirs in
> it.
> So when i run the ./install_execd again,i get the
> following error:
> Checking cell directory
> -----------------------
> 
> Cannot find required files. The following error was
> returned:
> 
> >common directory not found: default/common<
> 
> 
> Please make sure that you have installed the qmaster
> host before
> installing an execution host.
> 
> The installation procedure will only work if you use
> a shared
> directory (e.g. shared with NFS) for your
> installation.
> 
> The installation of the execution daemon will abort
> now.
> 
> So how does one make NFS mount/some shared dir on
> the i guess master host!
> 
> Thanks,
> Hrishi
> 
> 
> On Fri, 14 Jan 2005 20:05:33 -0500, Hrishikesh
> Deshmukh
> <hdeshmuk at gmail.com> wrote:
> > Could this be a problem,sgeadmin is sudo.
> > I downloaded the installation files on a machine
> and made the machine
> > the master by running the ./install_qmaster, then
> asked the SYS ADMIN
> > of the dept. to copy the installation dirs and
> files to all the
> > machines,its easy to do this using remote desktop.
> > Could this be causing some kind of permissions!!
> conflict, i think
> > sgeadmin owns the install dirs and files.
> > 
> > Just guessing about the critical error:resolving
> problems origin!!!
> > 
> > Thanks,
> > Hrishi
> > 
> > On Fri, 14 Jan 2005 14:56:18 -0500, Hrishikesh
> Deshmukh
> > <hdeshmuk at gmail.com> wrote:
> > > I kind of guess that! I really appreciate this
> help.
> > > I am installing sge as sgeadmind (sudo).
> > > I did define port 28 in /etc/services on master
> and execution host.
> > > I did sudo ./install_execd
> > >
> > > Hrishi
> > >
> > > On Fri, 14 Jan 2005 11:48:34 PST, Rayson Ho
> <raysonho at eseenet.com> wrote:
> > > > Just I came back from lunch :)
> > > >
> > > > Thanks for comparing the output!!
> > > >
> > > > So, commd on the exec hosts are not running,
> and since they need to bind to
> > > > ports below 1024, did you start execd as
> root??
> > > >
> > > > Also, "printenv COMMD_PORT" did not show
> anything, did you define the port
> > > > number for it as 28 in /etc/services??
> > > >
> > > > Rayson
> > > >
> > > >
> > > > >Here are the DIFFERENCES in the outputs for
> the cmd: netstat -an |
> > > > >grep 28
> > > > >on master host:
> > > > > ...
> > > > >tcp4       0      0  *.28                  
> *.*      LISTEN
> > > > >
> > > > >on (potential) executions host:
> > > > >udp4       0      0  *.3283                
> *.*
> > > > > 1104930 dgram       0      0        0 
> 1104fc0        0  1104b28
> > > > > 1104b28 dgram       0      0        0 
> 1104fc0        0  1104b60
> > > >
> > > >
> > > >
>
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