Re: [phenixbb] exporting results, reduce

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 mailto:[email protected]> 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 mailto:[email protected] *To:* PHENIX user mailing list mailto:[email protected] *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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