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 To: PHENIX user mailing list 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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_______________________________________________

hi, the rigid body refinement took 5 hours, not the reduce step. this is a run with chain problems and it never finished http://musso.ucsc.edu/exporting_reduce/verify_fail/ http://musso.ucsc.edu/exporting_reduce/verify_fail/withchain.pdb this is the pdb with no chain where refine took 5 hours and reduce finished normally http://musso.ucsc.edu/exporting_reduce/no_chain/ http://musso.ucsc.edu/exporting_reduce/no_chain/nochain.pdb this is a similar run with chain problems and it took 35 hours http://musso.ucsc.edu/exporting_reduce/oneproc/ thanks jpd ________________________________ From: Pavel Afonine To: [email protected] Sent: Friday, January 24, 2014 9:00 AM Subject: Re: [phenixbb] exporting results, reduce 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, phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Daniela, I will not be there, so don't count on me. Kris Kris F. Tesh, Ph. D. Department of Biology and Biochemistry University of Houston ________________________________ From: Daniela Stock To: PHENIX user mailing list Sent: Monday, February 10, 2014 2:50 PM Subject: [phenixbb] on approach Hi Pavel, I thought I give you a little earlier warning than last time. I will be in SF for the last days of the Biophysical Society meeting and then Katjusa and Dan's wedding. I will have some free time Monday Feb 24 or Tues 25 (flight leaves that evening) if you are free to go hiking : ). I was hoping to find out who else might be there, but don't know yet if Tassos or Dusan will be coming and I might ask Christine Gee (James Holton's wife) if she is free these days. Hope all is well. Don't worry if you are not there or are busy, but would be nice to see you. All the best, Daniela ______________________________________________________________________ The Victor Chang Cardiac Research Institute's Email is scanned by the MessageLabs Email Security System. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

oh no, what a nightmare. I am so sorry… well, obviously if anyone else is interested in discussing my refinement problems in the Berkeley Hills, you know where to find me. The more the merrier. See you around and apologies again, Daniela PS: any other comments to my personal e-mail please On 11 Feb 2014, at 8:21 am, lbetts0508 . mailto:[email protected]> wrote: You all are sending personal emails to the PHENIX bb. Just FYI Laurie On Mon, Feb 10, 2014 at 4:10 PM, Kris Tesh mailto:[email protected]> wrote: Daniela, I will not be there, so don't count on me. Kris Kris F. Tesh, Ph. D. Department of Biology and Biochemistry University of Houston From: Daniela Stock mailto:[email protected]> To: PHENIX user mailing list mailto:[email protected]> Sent: Monday, February 10, 2014 2:50 PM Subject: [phenixbb] on approach Hi Pavel, I thought I give you a little earlier warning than last time. I will be in SF for the last days of the Biophysical Society meeting and then Katjusa and Dan's wedding. I will have some free time Monday Feb 24 or Tues 25 (flight leaves that evening) if you are free to go hiking : ). I was hoping to find out who else might be there, but don't know yet if Tassos or Dusan will be coming and I might ask Christine Gee (James Holton's wife) if she is free these days. Hope all is well. Don't worry if you are not there or are busy, but would be nice to see you. All the best, Daniela ______________________________________________________________________ The Victor Chang Cardiac Research Institute's Email is scanned by the MessageLabs Email Security System. _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Scanned by Messagelabs *** _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb ______________________________________________________________________ The Victor Chang Cardiac Research Institute's Email is scanned by the MessageLabs Email Security System.