[BioBrew Users] Re: mpiformatdb error in BioBrew distribution (fwd)

[Bioinformatics.Org Sysadmin]

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---------- Forwarded message ----------
Date: Fri, 4 Feb 2005 12:58:02 -0800
From: Glen Otero <gotero at linuxprophet.com>
To: The Virtual BioBrew Think Tank <BioBrew-Users at bioinformatics.org>
Subject: Re: [BioBrew Users] Re: mpiformatdb error in BioBrew distribution


On Feb 3, 2005, at 5:01 PM, Humberto Ortiz Zuazaga wrote:

> Glen Otero <gotero at linuxprophet.com> wrote:
>
>> I know what the problem is. Packages on the roll were built with vmi
>> and mpich-vmi, which are in the BioBrew distro, but aren't included in
>> Rocks. That's my mistake. There are several solutions: 1) You could
>> use the new biobrew roll for Rocks 3.1 which will be available next
>> week; 2) you could rebuild the ncbitools package from SRPM, which I
>> could provide you; 3) or I could provide the vmi and vmi-mpich
>> sources.
>
> I vote for #2. I saw a couple of ncbitools srpms on bioinformatics.org,
> but didn't know which to build, or if it would try to pull in the vmi
> libraries at build time.

I can make the ncbitools srpm available early next week. I'm traveling 
right now.

> Speaking of missing RPMS, did you find an rpm
> for the modules package?

Yes. It's included in the BioBrew 3.1 release and I included your 
changes to the z-biomodules.sh{csh} files. Thanks again for those!

> We finally got air conditioning installed, so
> we're likely to bring our cluster up into production mode in the next
> couple of weeks. It would be terrific if we could bring up ROCKS 3.3 
> and
> a BioBrew roll.

That's great! The BioBrew roll for Rocks 3.3-x86 will be available next 
week too. I was careful to build it without vmi this time : ) The 
releases and rolls are completed, including BioBrew for Opteron, so I'm 
just waiting for them to be uploaded to the Bioinformatics.org servers. 
A BioBrew roll for Rocks-3.3-x86_64 should be ready soon.

Too avoid any more roll/package building snafus like this, I'm going to 
make all the SRPMs I used available. The SRPMs are included in the 
rolls this time. I will also upload the SRPMs to the Bioinformatics.org 
website. A formal announcement will be released to this (and other) 
lists next week.

How big is the cluster you're bringing up? Are there any apps you would 
like to see go into BioBrew?

Glen

>
> -- 
> Humberto Ortiz Zuazaga
> Programmer-Archaeologist
> High Performance Computing facility
> University of Puerto Rico
> http://www.hpcf.upr.edu/~humberto/
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>
Glen Otero Ph.D.
Linux Prophet