[BioBrew Users] Re: mpiformatdb error in BioBrew distribution

Glen Otero gotero at linuxprophet.com
Thu Feb 3 19:00:35 EST 2005


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 don't recommend the last option, but the others are no problem. Also, 
a new biobrew roll for Rocks 3.3 will be available next week as well.

Sorry for the screw up. Let me know which way you would like to go.

Glen

On Feb 3, 2005, at 11:45 AM, dayala at hpcf.upr.edu wrote:

> Hello Glen,
>
>      We are using BioBrew in our Rocks cluster.  I'm getting this very
> weird mistake when formatting a database with the mpiformatdb
> command.
>
> -----------------------------------------------------------
> # mpiformatdb -N 20 -i ecoli.nt -o T -p F -n ../ecoli.nt 
> mpiformatdb: error while loading shared libraries: libvmi20.so.0: 
> cannot
> open shared object file: No such file or directory 
> -----------------------------------------------------------
>
> The problem is that mpiformatdb is asking to be linked with this 
> library
> libvmi20.so.0 which is not part of the BioBrew rol.  When I execute  
> "#ldd
> mpiformatdb"  I get the line "libvmi20.so.0 => not found".  We have
> installed the ncbi toolkit 6.1.0 installed right now.  What is the
> problem? and more importantly, what is the solution to this problem?
> Thank you very much for your time and help.
>
> Daniel Ayala
>
>
Glen Otero Ph.D.
Linux Prophet

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