[Beowulf] RE: [Bioclusters] FPGAin bioinformatics clusters (again?)

Mike Davis jmdavis at mail2.vcu.edu
Tue Jan 17 09:37:10 EST 2006


Folder is a convenient term. Yes it is a directory. I am a Mac, Vax, 
Mainframe, Irix, Sun OS,  Solaris, Linux, and occasionally HPUX person.

In regard to your  second point, this is an example of a problem in 
bioinformatics. The program is written for all of the data to be in one 
directory without sub dirs. It is a structure that works with smaller 
sample sizes. But the assembly of a genome (even for a bacteria) winds 
up being large numbers of sequence files from many lab and BLAST runs.

The ultimate solution is to rewrite the program so that it will deal 
with its data being distributed in a directory.

Mike Davis




Eugen Leitl wrote:

>On Mon, Jan 16, 2006 at 06:43:42PM -0500, Mike Davis wrote:
>
>  
>
>>sequences (which it wants to be in one folder). A quiz for  the Unix 
>>geeks out there, what happens when a folder has 50,000 files in it. Can 
>>you say SLOOOOOOOOOWWWW?
>>    
>>
>
>Unix doesn't have folders. Are you a Mac person, perchance? 
>
>You also seem to be using the wrong file system.
>
>If your application is needing 50 k files in one
>directory, your application should not be needng 50 k files
>in one directory. One trivial fix is to organize it
>into subdirectories, using parts of file name or hashes
>as prefix.
>
>  
>
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