Dear Nick:
Thanks a lot for your help.
Here is the mod file and test data, it works fine in PsN.
============================
$PROB POPPK MODEL
$INPUT C ID TIME AMT DV CMT EVID AGE SEX RACE SJC TJC WBC ALB
MTX ICRP IWGT RATE MDV IRP TSLD PTIM SMOK ETOH DIAB DROP
$DATA pktest.csv IGNORE=C
$SUBROUTINES ADVAN3 TRANS4
$PK
STDY=12
IF (ID.GT.14000.AND.ID.LT.15000) STDY=14
IF (ID.GT.15000) STDY=31
WHT=0
IF (RACE.EQ.1) WHT=1
BLK=0
IF (RACE.EQ.2) BLK=0
ASN=0
IF (RACE.EQ.3) ASN=1
OTH=0
IF (RACE.EQ.4.OR.RACE.EQ.2) OTH=1
TVV1 = THETA(1)*(IWGT/70)**THETA(9)
V1 = TVV1*EXP(ETA(1))
TVCL = THETA(2)
TVCL = TVCL*(IWGT/70)**THETA(10)*(AGE/35)**THETA(11)*(1+THETA(12)*SEX)
TVCL = TVCL*(1+THETA(13)*BLK)*(1+THETA(14)*ASN)*(1+THETA(15)*OTH)
TVCL = TVCL*(ICRP)**THETA(16)*(1+THETA(17)*IRP)*(1+THETA(18)*MTX)
TVCL = TVCL*(ALB/4.2)**THETA(19)*((SJC+1)/14)**THETA(20)*(TJC/23)**THETA(21)
TVCL = TVCL*(1+DIAB*THETA(22))*(1+SMOK*THETA(23))*(WBC/7.5)**THETA(24)
CL = TVCL*EXP(ETA(2))
K = CL/V1
TVQ = THETA(3)*(IWGT/70)**THETA(25)
Q = TVQ*EXP(ETA(3))
K12 = TVQ/TVV1
TVV2 = THETA(4)*(IWGT/70)**THETA(26)
V2 = TVV2*EXP(ETA(4))
K21 = TVQ/TVV2
S1 = V1 ; Dose = mg, Conc = ug/mL, Volume = L
$ERROR
W=SQRT(THETA(5)**2*F**2+THETA(6)**2)
IF (STDY.EQ.12) LOQ=0.2
IF (STDY.GT.12) LOQ=0.039
IF (F.GT.0) THEN
Y=F+W*EPS(1)
IPRED=F
IRES=DV-IPRED
IWRES=IRES/W
ELSE
Y=0
IPRED=0
IRES=0
IWRES=0
ENDIF
$THETA (0, 3.99) ;KEEP 1 : V
$THETA (0, 0.623) ;KEEP 2 : CL
$THETA (0, 0.229) ;KEEP 3 : Q
$THETA (0, 2.52) ;KEEP 4 : V2
$THETA (0.312) ;KEEP 5 : PROP ERR
$THETA (0 FIX) ;KEEP 6 : ADDITIVE ERR
$THETA (0 FIX) ;KEEP 7 : K23
$THETA (0 FIX) ;KEEP 8 : K32
$THETA (0.513) ;KEEP 9 : IWGT ON V
$THETA (0.512) ;KEEP 10 : IWGT ON CL
$THETA (-0.188) ;11 : AGE
$THETA (-1,0.114) ;12 : SEX
$THETA (0 FIX) ;13 : BLK
$THETA (-1, 0.0699) ;14 : ASN
$THETA (-1, 0.0193) ;15 : OTH
$THETA (0.0105) ;16 : ICRP
$THETA (-1, 0.333) ;17 : IRP
$THETA (-1, -0.0869) ;18 : MTX
$THETA (-0.769) ;19 : ALB
$THETA (0.0126) ;20 : SJC
$THETA (0 FIX) ;21 : TJC
$THETA (-1, 0.106) ;22 : DIAB
$THETA (-1, 0.0319) ;23 : SMOK
$THETA (0.037) ;24 : WBC
$THETA (0.555) ;KEEP 25 : IWGT ON Q
$THETA (0.528) ;KEEP 26 : IWGT ON V3
$OMEGA BLOCK(2) ; 1,2 : V - ETA1 CL-ETA2
0.131
0.0666 0.163
$OMEGA (0 FIX) ; 3: IIV - K12
$OMEGA (0.105) ; 4: IIV - K21
$SIGMA
1 FIX
$ESTIMATION MAXEVAL=0 PRINT=10 METHOD=1 INT NOABORT
;$COV PRINT=E MATRIX=S
$TABLE ID TIME DV WRES IRES CWRES IWRES IPRED ETA1 ETA2 ETA3 ETA4 EVID
NOPRINT ONEHEADER FILE=fit4.tab
$TABLE ID STDY ETA1 ETA2 ETA3 ETA4
CL V1 Q V2 TIME EVID NOPRINT NOAPPEND
ONEHEADER FILE=patab4
===========================data below
C,ID,TIME,AMT,DV,CMT,EVID,AGE,SEX,RACE,SJC,TJC,WBC,ALB,MTX,ICRP,IWGT,RATE,MDV,IRP,TSLD,PTIM,SMOK,ETOH,DIAB,USUBJID
.,12001,0,110,
,1,1,19,0,4,7,13,10.7,4.1,0,2,54,5280,1,1,0,0,0,0,0,C0524T12100120379
.,12001,0, ,0,1,0,19,0,4,7,13,10.7,4.1,0,2,54, ,1,1,0,0,0,0,0,C0524T12100120379
C,12001,0.063, ,2.21433,1,0,19,0,4,7,13,10.7,4.1,0,2,54,
,0,1,0.063,0,0,0,0,C0524T12100120379
.,12001,15.927, ,0.72804,1,0,19,0,4,7,13,10.7,4.1,0,2,54,
,0,1,15.927,15.927,0,0,0,C0524T12100120379
.,12001,29.896, ,0,1,0,19,0,4,7,13,10.7,4.1,0,2,54,
,1,1,29.896,28,0,0,0,C0524T12100120379
.,12001,56.892, ,0,1,0,19,0,4,7,13,10.7,4.1,0,2,54,
,1,1,56.892,56,0,0,0,C0524T12100120379
.,12001,83.899, ,0,1,0,19,0,4,7,13,10.7,4.1,0,2,54,
,1,1,83.899,84,0,0,0,C0524T12100120379
.,12001,84.003,110,
,1,1,19,0,4,7,13,10.7,4.1,0,2,54,5280,1,1,0,84,0,0,0,C0524T12100120379
.,12001,84.066, ,31.83529,1,0,19,0,4,7,13,10.7,4.1,0,2,54,
,0,1,0.063,84,0,0,0,C0524T12100120379
.,12001,99.906, ,1.57552,1,0,19,0,4,7,13,10.7,4.1,0,2,54,
,0,1,15.903,98,0,0,0,C0524T12100120379
.,12001,113.899, ,0.39355,1,0,19,0,4,7,13,10.7,4.1,0,2,54,
,0,1,29.896,112,0,0,0,C0524T12100120379
.,12001,168.924, ,0,1,0,19,0,4,7,13,10.7,4.1,0,2,54,
,1,1,84.92,168,0,0,0,C0524T12100120379
.,12001,169.035,100,
,1,1,19,0,4,7,13,10.7,4.1,0,2,54,0,1,1,0,168,0,0,0,C0524T12100120379
.,12001,169.097, ,33.7706,1,0,19,0,4,7,13,10.7,4.1,0,2,54,
,0,1,0.063,168,0,0,0,C0524T12100120379
.,12001,252.924, ,0,1,0,19,0,4,7,13,10.7,4.1,0,2,54,
,1,1,83.889,252,0,0,0,C0524T12100120379
.,12001,253.038,100,
,1,1,19,0,4,7,13,10.7,4.1,0,2,54,4800,1,1,0,252,0,0,0,C0524T12100120379
.,12001,335.917, ,0,1,0,19,0,4,7,13,10.7,4.1,0,2,54,
,1,1,82.878,336,0,0,0,C0524T12100120379
.,12002,0,260,
,1,1,34,1,4,10,15,7.6,4.6,1,3.9,64.5,12480,1,0,0,0,0,0,0,C0524T12100120386
.,12002,0, ,0,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,1,0,0,0,0,0,0,C0524T12100120386
.,12002,0.063, ,5.7957,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,0,0,0.063,0,0,0,0,C0524T12100120386
.,12002,7.92, ,11.62571,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,0,0,7.92,7.92,0,0,0,C0524T12100120386
.,12002,27.913, ,0.23622,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,0,0,27.913,28,0,0,0,C0524T12100120386
.,12002,55.924, ,0.47727,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,0,0,55.924,56,0,0,0,C0524T12100120386
.,12002,83.906, ,0,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,1,0,83.906,84,0,0,0,C0524T12100120386
.,12002,84.01,260,
,1,1,34,1,4,10,15,7.6,4.6,1,3.9,64.5,12480,1,0,0,84,0,0,0,C0524T12100120386
.,12002,84.073, ,40.47069,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,0,0,0.063,84,0,0,0,C0524T12100120386
.,12002,97.903, ,8.58377,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,0,0,13.892,98,0,0,0,C0524T12100120386
.,12002,111.948, ,3.02214,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,0,0,27.938,112,0,0,0,C0524T12100120386
.,12002,167.938, ,0.25898,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,0,0,83.927,168,0,0,0,C0524T12100120386
.,12002,168.045,250,
,1,1,34,1,4,10,15,7.6,4.6,1,3.9,64.5,0,1,0,0,168,0,0,0,C0524T12100120386
.,12002,168.108, ,82.39627,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,0,0,0.063,168,0,0,0,C0524T12100120386
.,12002,251.927, ,0.38148,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,0,0,83.882,252,0,0,0,C0524T12100120386
.,12002,252.007,250,
,1,1,34,1,4,10,15,7.6,4.6,1,3.9,64.5,12000,1,0,0,252,0,0,0,C0524T12100120386
.,12002,335.92, ,0.32601,1,0,34,1,4,10,15,7.6,4.6,1,3.9,64.5,
,0,0,83.913,336,0,0,0,C0524T12100120386
.,12003,0,110,
,1,1,46,0,4,14,23,8,3.5,0,0.6,54,5280,1,0,0,0,0,0,0,C0524T12100120388
.,12003,0, ,0,1,0,46,0,4,14,23,8,3.5,0,0.6,54, ,1,0,0,0,0,0,0,C0524T12100120388
C,12003,0.063, ,4.50075,1,0,46,0,4,14,23,8,3.5,0,0.6,54,
,0,0,0.063,0,0,0,0,C0524T12100120388
.,12003,8.965, ,1.32628,1,0,46,0,4,14,23,8,3.5,0,0.6,54,
,0,0,8.965,8.965,0,0,0,C0524T12100120388
.,12003,27.892, ,0,1,0,46,0,4,14,23,8,3.5,0,0.6,54,
,1,0,27.892,28,0,0,0,C0524T12100120388
.,12003,55.92, ,0,1,0,46,0,4,14,23,8,3.5,0,0.6,54,
,1,0,55.92,56,0,0,0,C0524T12100120388
.,12003,83.872, ,0,1,0,46,0,4,14,23,8,3.5,0,0.6,54,
,1,0,83.872,84,0,0,0,C0524T12100120388
.,12003,84.007,110,
,1,1,46,0,4,14,23,8,3.5,0,0.6,54,5280,1,0,0,84,0,0,0,C0524T12100120388
.,12003,84.069, ,25.48774,1,0,46,0,4,14,23,8,3.5,0,0.6,54,
,0,0,0.063,84,0,0,0,C0524T12100120388
.,12003,97.868, ,0.68514,1,0,46,0,4,14,23,8,3.5,0,0.6,54,
,0,0,13.861,98,0,0,0,C0524T12100120388
.,12003,111.889, ,0,1,0,46,0,4,14,23,8,3.5,0,0.6,54,
,1,0,27.882,112,0,0,0,C0524T12100120388
.,12003,167.906, ,0,1,0,46,0,4,14,23,8,3.5,0,0.6,54,
,1,0,83.899,168,0,0,0,C0524T12100120388
.,12003,168.007,120,
,1,1,46,0,4,14,23,8,3.5,0,0.6,54,0,1,0,0,168,0,0,0,C0524T12100120388
.,12003,168.069, ,38.7479,1,0,46,0,4,14,23,8,3.5,0,0.6,54,
,0,0,0.063,168,0,0,0,C0524T12100120388
.,12003,251.892, ,0,1,0,46,0,4,14,23,8,3.5,0,0.6,54,
,1,0,83.885,252,0,0,0,C0524T12100120388
.,12003,251.976,120,
,1,1,46,0,4,14,23,8,3.5,0,0.6,54,5760,1,0,0,252,0,0,0,C0524T12100120388
.,12003,335.885, ,0,1,0,46,0,4,14,23,8,3.5,0,0.6,54,
,1,0,83.91,336,0,0,0,C0524T12100120388
===================================================
-----Original Message-----
From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On
Behalf Of Nick Holford
Sent: Friday, October 26, 2012 10:23 PM
To: 'nmusers'
Subject: [NMusers] Re: WFN problem
Sam,
Please send me the run4.mod control stream and a sample of data so I can
investigate.
Impossible to help you without any further information :-)
Nick
On 27/10/2012 4:35 p.m., Sam Liao wrote:
Dear Nick:
I have encounter a problem using nmgo in WFN.
For one run4.mod, when I used the 'nmgo run4', the program fail to run. When I
check the run4.nm7 folder, the run4.mod was copied only partially and stop.
Other run.mod were running fine. But I cannot tell what is the problem with
this run4.mod. It can run in PsN without problem.
Any suggestion I would be really appreciate.
Best regards,
Sam
-----Original Message-----
From: owner-nmus...@globomaxnm.com
[mailto:owner-nmus...@globomaxnm.com] On Behalf Of Nick Holford
Sent: Sunday, August 12, 2012 1:56 PM
To: nmusers
Subject: Re: [NMusers] Intel vs AMD
Mark,
I think you may not be fully appreciating the terms of the agreement when you say
"it is generally accepted that Intel continues to impair the optimization on AMD
CPU".Under the terms of the agreement (which you provide below) it is perfectly OK
for Intel to optimize their compilers for Intel CPUs without including any optimization
for AMD CPUs.
Furthermore they are not required to provide any optimization for AMD CPus.
Therefore, unless Intel don't know how to optimize compilers you must expect
the Intel compiler to perform better on an Intel CPU.
This issue might (or might not) be relevant to Martin's query about
'differences'. He does not specify the kind of difference e.g. faster?
more accurate?. It may be possible to choose compiler options that produce
identical numerical results on both CPUs but at the price of speed.
Rik Schoemaker suggested using these Intel compiler options /nologo
/nbs /w /Gs /fp:strict to obtain consistent numerical results
(http://www.cognigencorp.com/nonmem/current/2011-May/3266.html) with different
NONMEM 7 versions across different operating systems. Perhaps these options
would ensure numerical consistency across different CPU types.
Best wishes,
Nick
On 13/08/2012 8:27 a.m., Mark Sale - Next Level Solutions wrote:
Martin
Yes, the results can be different. Intel has been accused of
"crippling" the executable when the Intel compiler is used on AMD
CPUs
http://www.agner.org/optimize/blog/read.php?i=49
by turning off all optimization - they actually pretty much admitted
this in the lawsuit - but explained that it was for the benefit of
the customer - sort of like in the 1980's when Microsoft pretty much
disabled WordPerfect with every new OS release.
and yes, different optimization setting will give different results,
32 bit will also give different results from 64 bit. Sometimes the
phase of the moon, or the users astrological sign makes a different
as well ;-) Below is from the settlement:
Intel shall not include any Artificial Performance Impairment in any
Intel product or require any Third Party to include an Artificial
Performance Impairment in the Third Party’s product. As used in this
Section 2.3, “_Artificial Performance Impairment_” means an
affirmative engineering or design action by Intel (but not a failure
to act) that (i) degrades the performance or operation of a Specified
AMD product, (ii) is not a consequence of an Intel Product Benefit
and
(iii) is made intentionally to degrade the performance or operation
of a Specified AMD Product. For purposes of this Section 2.3,
“_Product Benefit_” shall mean any benefit, advantage, or improvement
in terms of performance, operation, price, cost, manufacturability,
reliability, compatibility, or ability to operate or enhance the
operation of another product.
In no circumstances shall this Section 2.3 impose or be construed to
impose any obligation on Intel to (i) take any act that would provide
a Product Benefit to any AMD or other non-Intel product, either when
such AMD or non-Intel product is used alone or in combination with
any other product, (ii) optimize any products for Specified AMD
Products, or (iii) provide any technical information, documents, or know how to
AMD.
But, it is generally accepted that Intel continues to impair the
optimization on AMD CPU.
So, to answer your question, I don't think there is any way to insure
consistent results between Intel and AMD CPUs.
Mark
Mark Sale MD
President, Next Level Solutions, LLC
www.NextLevelSolns.com <http://www.NextLevelSolns.com>
919-846-9185
A carbon-neutral company
See our real time solar energy production at:
http://enlighten.enphaseenergy.com/public/systems/aSDz2458
--
Nick Holford, Professor Clinical Pharmacology
First World Conference on Pharmacometrics, 5-7 September 2012 Seoul,
Korea http://www.go-wcop.org
Dept Pharmacology & Clinical Pharmacology, Bldg 505 Room 202D
University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New
Zealand
tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53
email: n.holf...@auckland.ac.nz
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
--
Nick Holford, Professor Clinical Pharmacology Dept Pharmacology & Clinical
Pharmacology, Bldg 503 Room 302A University of Auckland,85 Park Rd,Private Bag
92019,Auckland,New Zealand
tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53
email: n.holf...@auckland.ac.nz
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
