[BioBrew Users] installed biobrew today...

Glen Otero gotero at linuxprophet.com
Fri Aug 22 13:46:21 EDT 2003

On Thursday, August 21, 2003, at 05:58  PM, kip wrote:

>> ...
>> These are both Rocks issues. How did you manage to set
>> hdc=scsi during  the partitioning? I'm assuming you
>> implemented a manual partitioning  scheme?
> I used the 'autopartition' scheme.  IIRC, when I installed
> BioBrew the first time, i was given the opportunity to edit
> the kernel boot arguments.  When I installed today, I wasn't
> given this option.

Some people make the mistake of querying for boot options and arguments 
like during a normal Linux installation.  BioBrew isn't designed to do 
that.  Typing anything other than 'frontend' at the 'boot:' prompt will 
dump you into a default Linux installation that will ultimately fail. 
It sounds like you looked for boot arguments the first time and got the 
default Linux install that failed and gave you the traceback error.

> I am planning on re-installing tomorrow, in any case.  Today
> I was focused on getting a complete system running; tomorrow
> I will spend more time tweaking.  My boss is out of town
> tomorrow, and my goal is to open the cluster for business as
> of Monday.

Good luck!
> I am incredibly impressed with Rocks/BioBrew so far.

Glad to hear it.  Tell your friends and colleagues.
> BTW: the installation instructions were a bit confusing in 2
> places.  (I am referring to the 'quick start', which is
> located at your download site).
> 1. networking (step 4): I was asked to fill in information
> for eth0, then for eth1.  Your instructions only refer to
> the eth1 config.

I should have mentioned a little more about eth0.  I glossed over it in 
step 3) by saying to 'accept the defaults for the next three screens'. 
One of those screens is the eth0 configuration screen.  The defaults do 
work for this step and it's the recommended way to go.
> 2. step 12: It is a bit confusing figuring out what actions
> are required.  I would recommend separating the instructive
> text from the 'action item' text.

Thanks for pointing that out.  I'll improve that.
> Also, I would recommend including some post-install steps:
> 1. how to add a user, and set password;

As root:

#useradd <username>
#passwd <username>

enter desired password twice when prompted

Be sure to tell new users that when they login that they should just 
hit <return> to accept the defaults (no passphrase) for their ssh keys; 
just like after you logged in as root the first time.

> 2. how to run MPI benchmark.

This I need to work on since BioBrew uses SGE and not PBS.  I'll get 
this out ASAP.

>> Rocks uses ext2 by default because the Rocks folks think
>> that ext3  performance is lame, and they're right for the
>> most part.  But you  should be able to select ext3 as the
>> filesystem if you manually  partition your frontend
>> drives.
>> Glen
> That is a good reason to stick with ext2.  I was under the
> impression that ext3 performance was comparable to ext2, but
> if ext2 is faster, then we will probably go with it.

Thanks for all the feedback!!


Glen Otero, Ph.D.
Linux Prophet

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