RE: Slow PRED in tables?
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: http://www.iconplc.com/
Quoted reply history
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
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