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Hi Eric,<br>
<br>
this sounds very odd. Reduce used to take from a second or a few to
max a minute to run. I know this because I used to run Reduce for
all PDB entries quite regularly in the past. So if this sudden
change is confirmed than this is something to worry about.
Developers at Duke may comment on this.<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 2/8/14, 2:13 PM, Eric Williams
wrote:<br>
</div>
<blockquote
cite="mid:CANZF9CXM=KLoxxTkit-CZOnWLPf9Xy_iNJQZz6fxCRLeK_hneQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>
<div>I'm finding that Reduce in dev-1616 is taking from 10 to
30 seconds to run (approximately). Does that sound about
right? If not, do you have any suggestions for speeding it
up? That might not seem like a long time, but I'm running it
on the entire PDB, so every second added to the average
processing time adds a whole day to the complete run.<br>
<br>
(My system is 32-bit Ubuntu 12.04 on Intel Xeon CPU X5470 @
3.33GHz × 8 with 16GB RAM.)<br>
<br>
</div>
Thanks. :)<br>
<br>
</div>
Eric<br>
<div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Jan 24, 2014 at 12:00
PM, Pavel Afonine <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px
0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hello,<br>
<br>
usually Reduce takes from a fraction of a second
to seconds to run (provided I understand correctly
that Jeff fixed all problems related to "reduce
runs forever"). I wonder how PDB file should look
like so Reduce runs hours. Could you please send
me PDB file (off mailing list, to my email
directly)?<br>
<br>
Thanks,<br>
Pavel
<div>
<div class="h5"><br>
<br>
<div>On 1/24/14, 8:44 AM, jp d wrote:<br>
</div>
<blockquote type="cite">
<div
style="font-size:10pt;font-family:HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida
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<div>
<div>
<div
style="font-size:10pt;font-family:HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida
Grande,sans-serif">hi, <br>
replying for the sake of posterity.<br>
the slow export/reduce seems to be
related to a malformed input model.<br>
the segids are ok but there are
some different segids that have the
same chain.<br>
setting the chain to empty for
everything resolved the issue.<br>
Using the malformed chain model took
35 hours (if it finished).<br
clear="none">
Using the no chain model took 5
hours.<br clear="none">
<div><span>thanks<br>
jpd<br clear="none">
</span></div>
<div><br clear="none">
</div>
<div
style="font-family:HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida
Grande,sans-serif;font-size:10pt">
<div
style="font-family:HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida
Grande,sans-serif;font-size:12pt">
<div>
<div dir="ltr">
<hr size="1"> <font
face="Arial"> <b><span
style="font-weight:bold">From:</span></b>
jp d <a
moz-do-not-send="true"
href="mailto:yoyoq@yahoo.com"
target="_blank"><yoyoq@yahoo.com></a><br
clear="none">
<b><span
style="font-weight:bold">To:</span></b>
PHENIX user mailing list <a
moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org"
target="_blank"><phenixbb@phenix-online.org></a>
<br clear="none">
<b><span
style="font-weight:bold">Sent:</span></b>
Friday, January 17, 2014
9:53 AM<br clear="none">
<b><span
style="font-weight:bold">Subject:</span></b>
[phenixbb] exporting
results, reduce<br
clear="none">
</font> </div>
<div><br clear="none">
<div>
<div>
<div
style="font-size:10pt;font-family:HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida
Grande,sans-serif">
<div>hi,</div>
<div>we have a large
complex at low
resolution (7A) and
just want <br
clear="none">
</div>
<div
style="font-style:normal;font-size:13.3333px;background-color:transparent;font-family:HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida
Grande,sans-serif">to
see general
conformational
changes.
Occasionally phenix</div>
<div
style="font-style:normal;font-size:13.3333px;background-color:transparent;font-family:HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida
Grande,sans-serif">gets
stuck at 'Exporting
Results' and top
shows 'reduce'
running</div>
<div
style="font-style:normal;font-size:13.3333px;background-color:transparent;font-family:HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida
Grande,sans-serif">and
using lots of RAM .
so much RAM that it
starts using swap.</div>
<div
style="font-style:normal;font-size:13.3333px;background-color:transparent;font-family:HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida
Grande,sans-serif">is
there a way to
bypass or limit the
reduce step.</div>
<div
style="font-style:normal;font-size:13.3333px;background-color:transparent;font-family:HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida
Grande,sans-serif">thanks</div>
<div
style="font-style:normal;font-size:13.3333px;background-color:transparent;font-family:HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida
Grande,sans-serif">jpd<br
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