[Bioclusters] [mpiBLAST]how to "mpiformatdb nr"~~?THX~
Osborne, John
bioclusters@bioinformatics.org
Tue, 13 May 2003 16:21:12 -0400
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I'm not sure why you don't have an nr.dbs, I just started installing
mpiblast (taking most of the day so far)
and I did get an nr.dbs in my shared storage directory.
I have other problems though, for instance I get a 3 line (null).pal in my
shared storage directory instead of the
nr.pal it is looking for. Anyone know what happened with this?
In addition, when I run mpiformatdb and tell it to break it into 20 chunks
it creates 21, from 0 to 20.
Pretty annoying.
The other problem I ran into when I was running mpiformatdb (on nr, is there
preformatted stuff I can
download now?) is that it took really long. Sure enough, it was only
running on one machine and when I
peaked at the mpiformatdb.cpp I noticed there were no MPI_ function
calls...?! No big deal, but I find the
name of the program somewhat misleading.
Anybody solve these problems? I'm using 1.1.0. I actually tried using an
earlier version of mpiblast before but I couldn't get it to
compile. Still seems more promising than the non-MPI query splitting
variant I have been using in the past since each mini
database should be able to fit into RAM on our nodes.
-John
-----Original Message-----
From: kwLee [mailto:g912803@student.thu.edu.tw]
Sent: Monday, May 12, 2003 10:32 PM
To: bioclusters@bioinformatics.org
Subject: [Bioclusters] [mpiBLAST]how to "mpiformatdb nr"~~?THX~
i think i have installed mpiblast already
i can use "mpiformatdb" to format yeast.nt database into same fragment
then use "mpiblast blastn" to search sequence
so i try "nr" database
i have formated nr database(use mpiformat)
but when i use "mpiblast blastp" to search
it says that "ERROR opening...nr.dbs"
i don't know why it has no nr.dbs
THX~
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<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>I'm
not sure why you don't have an nr.dbs, I just started installing mpiblast
(taking most of the day so far)</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>and I
did get an nr.dbs in my shared storage directory.</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>I have
other problems though, for instance I get a 3 line (null).pal in my shared
storage directory instead of the</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>nr.pal
it is looking for. Anyone know what happened with
this?</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>In
addition, when I run mpiformatdb and tell it to break it into 20 chunks it
creates 21, from 0 to 20.</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>Pretty
annoying.</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>The
other problem I ran into when I was running mpiformatdb (on nr, is there
preformatted stuff I can</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff
size=2> download now?) is that it took really long. Sure enough, it
was only running on one machine and when I</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>peaked
at the mpiformatdb.cpp I noticed there were no MPI_ function
calls...?! No big deal, but I find the</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>name
of the program somewhat misleading.</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff
size=2>Anybody solve these problems? I'm using 1.1.0. I actually tried
using an earlier version of mpiblast before but I couldn't get it
to</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff
size=2>compile. Still seems more promising than the non-MPI query
splitting variant I have been using in the past since each
mini</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff
size=2>database should be able to fit into RAM on our nodes.</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff
size=2> -John</FONT></SPAN></DIV>
<DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> kwLee
[mailto:g912803@student.thu.edu.tw]<BR><B>Sent:</B> Monday, May 12, 2003 10:32
PM<BR><B>To:</B> bioclusters@bioinformatics.org<BR><B>Subject:</B>
[Bioclusters] [mpiBLAST]how to "mpiformatdb nr"~~?THX~<BR><BR></FONT></DIV>
<DIV><FONT size=2>i think i have installed mpiblast already</FONT></DIV>
<DIV>i can use "mpiformatdb" to format yeast.nt database into same
fragment</DIV>
<DIV>then use "mpiblast blastn" to search sequence</DIV>
<DIV>so i try "nr" database</DIV>
<DIV>i have formated nr database(use mpiformat)</DIV>
<DIV>but when i use "mpiblast blastp" to search</DIV>
<DIV>it says that "ERROR opening...nr.dbs"</DIV>
<DIV><FONT size=2>i don't know why it has no nr.dbs</FONT></DIV>
<DIV>THX~</DIV>
<DIV> </DIV></BLOCKQUOTE></BODY></HTML>
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