<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 href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br>
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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>
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<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>
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<hr size="1"> <font face="Arial"> <b><span style="font-weight:bold">From:</span></b>
jp d <a 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 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">
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<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 clear="none">
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