[phenixbb] exporting results, reduce

Eric Williams ericwilliams at pobox.com
Sat Feb 8 14:13:15 PST 2014


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.

(My system is 32-bit Ubuntu 12.04 on Intel Xeon CPU X5470 @ 3.33GHz × 8
with 16GB RAM.)

Thanks. :)

Eric

On Fri, Jan 24, 2014 at 12:00 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  Hello,
>
> 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)?
>
> Thanks,
> Pavel
>
>
> On 1/24/14, 8:44 AM, jp d wrote:
>
>   hi,
> replying for the sake of posterity.
> the slow export/reduce seems to be related to a malformed input model.
> the segids are ok but there are  some different segids that have the same
> chain.
> setting the chain to empty for everything resolved the issue.
> Using the malformed chain model took 35 hours (if it finished).
> Using the no chain model took 5 hours.
> thanks
> jpd
>
>    ------------------------------
>  *From:* jp d <yoyoq at yahoo.com> <yoyoq at yahoo.com>
> *To:* PHENIX user mailing list <phenixbb at phenix-online.org><phenixbb at phenix-online.org>
> *Sent:* Friday, January 17, 2014 9:53 AM
> *Subject:* [phenixbb] exporting results, reduce
>
>   hi,
> we have a large complex at low resolution (7A) and just want
>  to see general conformational changes. Occasionally phenix
> gets stuck at 'Exporting Results' and top shows 'reduce' running
> and using lots of RAM . so much RAM that it starts using swap.
> is there  a way to bypass or limit the reduce step.
> thanks
> jpd
>
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