[phenixbb] exporting results, reduce

[Pavel Afonine]

Hi Eric,

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.

Pavel


On 2/8/14, 2:13 PM, Eric Williams wrote:
> 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 
> <mailto: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> <mailto:yoyoq at yahoo.com>
>>     *To:* PHENIX user mailing list <phenixbb at phenix-online.org>
>>     <mailto: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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>>
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