[Bioclusters] mpiBLAST

[Osborne, John]

Hi Joe,

I wrote an email earlier for another thread where I described some of the
problems I ran
into.  In short I was complaining about:

1)mpiformatdb creating 21 database fragments when I tell it to create 20, or
19 when I tell it to create 18... ie)n0 to n20 when I ask for just 20

2)The (null).pal file in my shared storage directory (created by
mpiformatdb).  I think the
file is also incorrect since it contains a line like this:
DBLIST (null).00 (null).01 ... (null).20

3)The misleading name of mpiformatdb which doesn't actually have an MPI
library calls (I grepped
for MPI_).  This is just a pet peeve because I was upset at how long the
format took.  :)

Right now I have it running, but with it doesn't produce any output and
lamclean hasn't killed
the process on the first node (it has been trying for >5 minute now).
Speaking of the first node,
are we supposed to set up n0 as our master node?  Is that why I get 21
fragments when I say divide
it into 20 pieces?

 -John



-----Original Message-----
From: Joe Landman [mailto:landman@scalableinformatics.com]
Sent: Tuesday, May 13, 2003 7:57 PM
To: biocluster
Subject: RE: [Bioclusters] mpiBLAST


On Tue, 2003-05-13 at 17:27, Osborne, John wrote:
> RedHat 7.2 with the 2.4.19 kernel (SMP)
> 
> I can get it to compile, but I have issues running it.

If you are stuck trying to run it, please let us know what the errors
you are getting are.

Would it help if I wrote a more detailed step-by-step, complete with
examples?


-- 
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615

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