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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi Glen or anyone who knows,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I am testing ROCKS 3.3.0 w/ Biobrew roll on AMD Dual Opterons
w/ 2 gb ram. I’ve got a head node distributing a BLAST using mpiBLAST
to two compute nodes hooked together in a 10/100 switch (yes slow switch, but I’m
just testing things out until my new equipment comes in).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I don’t know if you have all seen it, but Glen has a
tutorial to run mpiBLAST using the Hs.seq.uniq collection w/ a sequence file called
IL2RA. I was wondering if any of you have followed the tutorial and ran a
mpiformatdb then a mpiblast, and if you knew how long it took (I know everyone’s
setup is different in hardware, # nodes, etc, so time will be different for
everyone, but I want a vague idea of if this was a “slow” or “fast”
process?)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I’m asking because I ran mpiblast 1.3 (which was
originally installed w/ BioBrew), and this particular search took about 43
seconds. When I upgraded to mpiblast 1.4, the search took an outrageously
greater amount of time (18minutes, 23s). I wonder what the discrepancy is
that caused this, as my setup has not changed other than upgrading to
1.4. I am also not sure if a search of this kind w/ this particular
sequence/DB combo is supposed to actually take this long on my equipment?
For all I know, the 43 seconds in my original setup w/ v1.3 could have been
wrong and too fast, and the time it took for v1.4 is more realistic in my hardware
configuration? Knowing the general speed you have encountered allows me to
investigate further into if v1.4 is indeed the problem, and then I can ask the
mpiBLAST user group.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Any ideas?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><br>
Thank you,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Ray<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Univ of CA-Davis<o:p></o:p></span></font></p>
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