Douglas: Thank you for sharing your code and data with me. When PRED, WRES, or RES are requested, NONMEM calls the weighted residual routine PRRES, which calculates PRED, WRES, and RES together. Your problem has a large number of data per subject (up to 1544) , and evaluating WRES requires some matrix algebra on up to a 1544x1544 matrix, which can take time to compute for each subject. The standard method of calculating WRES in NONMEM 7.3 and lower versions is inefficient, and I have made it more efficient for a future version of nonmem 7.4, so your TABLE step will calculate in 15 minutes. Meantime, in recently released NONMEM 7.3, you can use the WRESCHOL option, and the $TABLE step was calculated in 3 minutes.
Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Email: [email protected]<mailto:[email protected]> Web: www.iconplc.com<http://www.iconplc.com/> From: [email protected] [mailto:[email protected]] On Behalf Of Eleveld, DJ Sent: Tuesday, January 28, 2014 9:19 AM To: [email protected] Subject: [NMusers] Slow PRED in tables? Hello everyone, I have a curious problem with slow PRED calculations in tables. The estimations are reasonably fast, 471 seconds for 23 iterations. If there is no PRED in any tables then NONMEM finishes a moment after the message about elapsed estimation time. But if is PRED in a table then it takes an extremely long time to return, I waited more than 10 hours before I broke off the run. If convergence of the algorithm is reasonably fast I get the impression that the differential equations are not problematic (it is $DES solved with ADVAN13 TOL=9). In fact if I restart the run with all $OMEGA to (0 FIXED) - to force all ETAs to zero - and do a MAX=0 run then it is quite fast. I would expect calculating PRED would be simply setting ETA=0 and solving the differential equations just once. Am I missing anything in how PRED in a table is calculated? Has anyone seen this kind of thing before? Any advice or tips? Warm regards, Douglas Eleveld ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. <br /><br /> ICON plc made the following annotations. ------------------------------------------------------------------------------ This e-mail transmission may contain confidential or legally privileged information that is intended only for the individual or entity named in the e-mail address. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or reliance upon the contents of this e-mail is strictly prohibited. If you have received this e-mail transmission in error, please reply to the sender, so that ICON plc can arrange for proper delivery, and then please delete the message. Thank You, ICON plc South County Business Park Leopardstown Dublin 18 Ireland Registered number: 145835
