Fwd: [BioBrew Users] post installation?

Glen Otero gotero at linuxprophet.com
Wed Mar 3 11:38:25 EST 2004

I didn't see this message on the list yesterday after I posted it, so 
I'm sending it again.


Begin forwarded message:

> From: Glen Otero <gotero at linuxprophet.com>
> Date: March 2, 2004 9:33:52 AM PST
> To: Soumyadeep nandi <soumyadeep_nandi at yahoo.com>
> Cc: BioBrew-Users at bioinformatics.org
> Subject: Re: [BioBrew Users] post installation?
> Soumyadeep-
> I guess it's time to post the full BioBrew User's Guide. The User's 
> Guide I'm going to post is the one my company distributes with 
> clusters we install for people using Callident Rx, our base cluster 
> solution.  Except for the few extra steps noted in the BioBrew 1.0 
> README and Install Pictorial needed to get BioBrew up and running, the 
> manual contains all the goodies needed to prep you for world 
> domination. It has the answers to your questions about how to run mpi 
> jobs and testing the cluster with Linpack. Page 41 has information on 
> providing web access to the cluster. With regard to getting the bio 
> apps running, the directories only need be put into users' paths. Joe 
> Landman has some very useful scripts (run_mpibalst, run_mpiblastrc, 
> sge_mpiblast) for running mpiBLAST that I recommend people look into 
> and adapt for running mpiblast  in BioBrew. The scripts can be found 
> at http://downloads.scalableinformatics.com/.
> Hope this helps. Comments and suggestions on the manual and software 
> are encouraged.
> Glen
> On Mar 2, 2004, at 8:24 AM, Soumyadeep nandi wrote:
>> Hi Everybody,
>> Thrilled to have installed BioBrew. It looks like the
>> base for exactly what we want. Would like R etc...but
>> more of that later.
>> We are more or less familiar with all the (Bio)
>> packages that constitute BioBrew, and have run HMMER
>> using pvm strung over a cluster of workstations...but
>> We have never used Rocks. So though installation went
>> without any hiccups - the frontend and compute nodes
>> boot  smoothly, we cannot access anything easily : No
>> http access to the frontend for the homepage or (web)
>> blast. We identified the BioBrew packages to the
>> /opt/BioBrew
>> Can we have some pointers to:
>> 1. Setting up the lam-mpi and pvm environments
>> 2. Activating Apache to allow access to the frontend
>> 3. Testing the cluster
>> 4. Running the biobrew packages (Do we just have to
>> add the directories to the path?)
>> 5. Is there a x-windows based browser as part of the
>> frontend?
>> regards,
>> Soumyadeep Nandi
>> Bioinformatics Center
>> Jawaharlal Nehru University
>> New Delhi
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> Glen Otero, Ph.D.
> Linux Prophet
> 619.917.1772
Glen Otero, Ph.D.
Linux Prophet

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