[BioBrew Users] post installation?

Glen Otero gotero at linuxprophet.com
Tue Mar 2 12:33:52 EST 2004


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 

Hope this helps. Comments and suggestions on the manual and software 
are encouraged.


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

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