Wings for NONMEM Download
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for NONMEM 7.2 ONLY |
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for NONMEM 7.1 ONLY |
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for NONMEM VI ONLY |
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for
NONMEM V ONLY |
Download Instructions
The download file
is named wfnNnn.exe. The "N" is the major
version and the "nn" is the minor
version number. It is an executable zip archive file. The default
directory for wfn7 is to extract the files into is C:\nm720\wfn7. You
may choose a different home directory instead of C:\nm720\wfn7 when you
execute wfnNnn.exe. Please read Installation instructions carefully.
The instructions include information on uninstalling wfn.
Upgrading
If you are upgrading
from an earlier version you may re-install by overwriting your previous
installation. Simply run wfnNnn.exe and unzip the files into the %wfnhome% directory that you are already using. Note
that this will not change %wfnhome%\bin\wfn.bat which you may have modified during your original
installation. You do not need to uninstall wfn.
Sometimes an upgrade will involve a change to wfn.bat
(known as wfnauto.bat prior
to version 400) and this will be indicated in the version
notes. If
you are upgrading and if your currently installed version is older than
the last version (700) that required a change to wfn.bat then you
must create (or re-create) wfn.bat . In this case you should make a new wfn.bat
by modifying %wfnhome%\bin\wfn.txt
as necessary (see Installation ) and saving it as %wfnhome%\bin\wfn.bat.
Please email to receive notification of future updates to WFN.
Version Notes
01 June 2011
Version 720
This
version is for use only with NONMEM 7.2. It does not work with NONMEM 7.1.
NONMEM 7.2 has a number of optional arguments to the
nmfe72.bat command e.g.
nmfe72 infile
outfile [-background] [-PARAFILE=file.pnm] [-licfile=filename] [-prsame] [-prdefault] [-prcompile] [-trskip] [-rundir=dirname][-runpdir=dirname] [-nmexec=filename] [-xmloff]
The wfn7 commands for executing NONMEM remain simple
with just one argument (the runname) e.g.
nmgo runname
Optional arguments for NONMEM 7.2 should be
specified in an environment variable called ARGS7 e.g.
set ARGS7=-prdefault
The prdefault value will
restore the usual behavior of previous versions of NONMEM and skip the dynamic
resizing process (which may add a substantial overhead to total runtimes). It
is suggested that this command be added at the start of the wfn.bat file (see wfn.txt). The ARGS7 variable can be changed at any time before
running wfn7 commands that execute NONMEM (e.g. nmgo, nmbs, nmgosim).
Both file (fpi) and
message passing interfaces (mpi) have been tested
with wfn7. The parafiles (wfn_fpi2.pnm, wfn_mpi2.pnm,
wfn_fpi8.pnm, wfn_mpi8.pnm) in the %wfnhome%\run folder may be used as templates.
Set the ARGS7 variable to the parafile
name before running NONMEM e.g. if you have a two core computer with MPICH2
installed enter these commands:
set ARGS7=-parafile=wfn_mp2.pnm
nmgo theopd
Note that the quotation marks around the parafile argument are required. The parafile
must be put in the same folder as the run control stream file used by WFN. Do
not use the nmexec option because WFN uses that to
create a NONMEM executable using the runname. See Installation for
examples of testing fpi and mpi
methods.
Other Changes
Formatting of nmobj command no longer attempts
to show results when run folder does not contain a .smy
file.
nmbs command now allows runnames with %NMCTL% extension e.g. nmbs theopd.ctl 1 1000 or nmbs theopd 1 1000 are equivalent
Bug in nminstall.bat
for installing updates has been fixed. The installation destination directory
is created if it does not already exist.
20 June 2010
Version 703
This version if for NONMEM 7.1. It does not work with NONMEM
7.2.
The wfn7 nmbs command now reports the results from all estimation
methods used for a given problem instead of just the first estimation method.
The nminstall command has been changed to support the NONMEM
version update process. The revised nminstall.txt
should be used to create an updated nminstall.bat
file in the wfn7 directory.
A bug in adding EPS estimates to the *.smr file when
there is more than 1 sub-problem has been fixed. A bug when a comment followed
$OMEGA in forming the header line for the *.smr file has been fixed.
A bug has been fixed (again) for reporting the
estimation method. Version 702 reported FOCE when it should have been FOCEI. A
bug in the nmretbl
command introduced in version 701 has been fixed.
14 February 2010
Version 702/616
Users of Monolix can
create a model building table from Monolix projects
with the mlxmbt
command. The format of the output is the same as that used with the nmmbt command. Note: When Monolix is
asked to compute the log likelihood it adds a constant term equal to Obs*ln(2*pi) that is not added by NONMEM. The Monolix
derived Obj value reported by the mlxmbt command
can be converted to the equivalent value computed by NONMEM by subtracting Obs*ln(2*pi) from the Monolix value.
Unfortunately Monolix does not save the number of
observations (Obs) so this cannot currently be done
automatically by mlxmbt.
WFN Version 702 and 616 have an improved model
building summary table format. The nmmbt.txt file sequence of column headings
is more likely to be presented in a useful format when multiple runs are
combined.
The WFN extended control stream format supports the
use of $OMEGA parameter names when MU referencing is used. When the MU index is
the same as the corresponding ETA used for that MU then MU referencing can be
coded without counting ETA values e.g.
$THETA 10 ; POP_CL
$OMEGA 0.5 ; PPV_CL [this corresponds to eta(1)]
$PK
MU_1=LOG(POP_CL)
CL=EXP(MU_1+ETA(1))
Can be written:
$PK
MU_PPV_CL=LOG(POP_CL)
CL=EXP(MU_PPV_CL+PPV_CL)
Note: the use of parameter names for MU referencing
is optional. If you use the $OMEGA parameter name then WFN will replace it with
a suitable numeric value for NM-TRAN to process otherwise the code will not be
changed by WFN.
A bug has been fixed for reporting the estimation
method. Version 701 reported FOCE when it should have been FOCEI.
20 September
2009 Version 701/615
WFN Version 701 has had several changes to enable it
to work with the first release of NONMEM 7. It supports simple switching
between different sized versions of NONMEM. The first release of NONMEM 7
offers a regular size (reg) and a big size (big).
WFN supports switching to custom sized NONMEM installations.
Support is provided for NONMEM installations created
with Intel Visual Fortran (ivf), gfortran (gf) and g95 (g95)
compilers. Limited benchmarking indicates that the ivf
compiler is faster than gf. The g95 compiler is much
slower than ivf. The results from all 3 compilers appear
to be identical.
WFN Version 615 formats NONMEM VI output in the same
way as NONMEM 7 i.e. estimation method and time information are included in the
runname.smy and nmmbt.txt files.
A bug affecting the use of the INCLUDE abbreviated
code record has been fixed in Versions 701 and 615.
1 June 2009
Version 700/614
Version 700 is designed to work with NONMEM 7. Changes have been made to cope with modifications to the NONMEM 7 output listing.
Note that this version has been modified for use with NONMEM 7 and will not work with NONMEM VI or NONMEM V.
The default installation directory for WFN is
C:\nm7\wfn7
The default output for standard errors of OMEGA
and SIGMA is to report the relative standard error as OMEGA:se% and SIGMA:se%. This is
obtained by dividing the standard error by NONMEMs estimate of the variance of
OMEGA or SIGMA. An alternative output with an approximation to the relative
standard error of the sqrt(variance) of OMEGA and SIGMA can be obtained by setting the
environment variable nmraw
to include the characters SD e.g.
set nmraw=SD
http://www.mail-archive.com/nmusers@globomaxnm.com/msg00845.html
http://www.mail-archive.com/nmusers@globomaxnm.com/msg00847.html
Version 614 includes some minor bug fixes for use with NONMEM VI.
11 September 2007 Version 613/411
Bug fix for nmctl when used with 'i' option which failed to find SIGMA output
NMQ4WFN version 6.2.1 is compatible with NMQual 6.2.1
22 July 2007 Version 613/411
Bug fix for nmctl when used with 'i' option which failed to find SIGMA output
Compiler bug/feature workaround has been added.
The bug/feature did not add .exe extension to the NONMEM executable file when
there was a period character in the runname.
Documentation for nmbs revised to make it clear that IGNORE=@ cannot be used in control streams being run with nmbs.
16 July 2007 Version 612/410
wfntestver describes a utility for testing the performance of different installation versions of NONMEM.
NMQ4WFN version 6.2.0 is now compatible with NMQual 6.2.0
22 March 2007 Version 612/410
Bug fix for nmctl with more than 24 OMEGA parameters.
nmobj5.awk was missing from WFN611. It is now included for compatibility with NONMEM V.
11 February 2007 Version 611/409
Documentation added for use of NMQual 6 with WFN in wfnnmqual.htm
Documentation added for use of Xpose with WFN in wfnxpose.htm (thanks to Malin Rhodin for help with this)
Bug fix for nmbs when dropped data items contained the character 'C'.
[wfn.bat may need to be reinstalled - see Upgrading]. There are some changes to wfn.bat (WFN601 and WFN409) needed to support use of NMQual . If you want to use these features then you will need to recreate your wfn.bat based on the new wfn.txt file in %wfnhome%\bin.
30 November 2006 Version 600
This version is designed to work with NONMEM VI. A few minor changes have been made to cope with modifications to the NONMEM VI output listing.
Note that this version has been modified for use with NONMEM VI and will not work with NONMEM V.
The default installation directory for WFN is c:\nmvi\wfn6.
The code used by wfn.bat to convert long paths to 8 character format has been disabled. This code caused problems on some versions of Windows. It was there primarily to avoid some warnings when keeping NONMEM up to date with mknm.bat. mknm.bat is no longer included in this version because NMQual does a better job at creating a qualified NONMEM installation (although it does not currently support selective compilation when only some source files have changed which mknm.bat could do).
7 April 2006 Version 409
It is a common problem when running bootstraps that some runs fail with a variety of termination messages. The nmbssxs command can be used to count and summarize the success and failure of runs following the use of nmbs. Run nmbssxs in a directory containing one or more *.bs folders created by nmbs to obtain a summary of the results. A similar command nmrtsxs provides the same kind of information after using the nmrt command.
Improvements to documentation and commands for installing multiple NONMEM compilation versions.
nmone enhanced to find ID column and format numeric output as 'general'.
nmfe5 workalike command added. This is called similarly to the standard NONMEM nmfe5.bat but uses WFN to run NONMEM. If it placed in a directory on the system path e.g. C:\Windows then it can be used by programs such as NextLevelSolutions bootstrap.
Bug fix for converting long file name paths to 8 char paths.
Support for nmqual added. NMQual should be used by all NONMEM users to ensure their source code is up to date.
Note that there are two things to consider when
you use NMQual:
1. NMQual patches the source code to get a consistent
patch level and compiles a new installation of NONMEM
You can run the NMqual installation without using the
special NMqual front end that checks the integrity of
the installation every time you run it. Just use WFN and set NMHOME to the NMQual target directory e.g. C:\nmvqdf.
The df and ivf compilers create .obj files and you can use the NMQual generated output with WFN nmgo in the usual way.
The g77 compiler produces .o files so you need to change your NMQual config*.xml file as follows so that .obj files are produced:
Change from:
<instruction id='compile'>g77 -c -O *.for</instruction>
to
<instruction id='compile'>cmd /c "g77 -c
-O *.for && ren *.o
*.obj"</instruction>
Change from:
<instruction id='library'>ar
-r nonmem.lib *.o</instruction>
to
<instruction id='library'>ar -r nonmem.lib *.obj</instruction>
Change from:
<instruction id='nmtran'>g77 *.o -o nmtran.exe</instruction>
to
<instruction id='nmtran'>g77 *.obj -o
nmtran.exe</instruction>
Change from:
<suffix id='object'>o</suffix>
to
<suffix id='object'>obj</suffix>
Note: Change means you must change the original line. It is not sufficient just to add new lines.
You may also want to remove this line because it doesn't do anything useful as far as I can tell and will stop NMQUAL working if this variable is not defined in your environment.
<!--test class='environment' variable='CPU'/-->
2. NMQual runs NONMEM
and checks that the object code has not been changed since the installation.
I have tested NMQual with WFN and updated WFN to be
able to work with it. It requires you to use WFN version 409 or later and make
a change to an updated (see below) wfn.bat to allow it to run the NMQual version of NONMEM. I have tested NMQual
with df, g77 and ivf compilers.
In wfn.bat you need to specify the name of your nmqual target in wfn.bat. I suggest after 'set F77VER' you
should insert 'set NMQUALVER' with the name of your nmqual
target e.g.
set F77VER=df
set NMQUALVER=nmvqdf
The nmqual target is the name of the target directory
created after you run nmqual. If the target is c:\nmvqdf then the NMQual version needed by wfn.bat is nmvqdf.
Note that the target directory is NOT the directory used to install the nmqual files. It is created by NMqual
when you run the nmqual.p perl
script.
Support for Intel Visual Fortran (ivf) revised. Tested with Intel Visual Fortran Version 9.1
Support for GNU Gfortran added
[wfn.bat may need to be reinstalled - see Upgrading]. There are some changes to wfn.bat needed to support use of NMQual and the Intel and Gfortran compilers. If you want to use these features then you will need to recreate your wfn.bat based on the new wfn.txt file in %wfnhome%\bin.
23 November 2004 Version 408
Further work done on the documentation for the cts system.
Bug fix for cts.bat which was not working with the mksas option.
cts temporary files cleaned up.
nmbs keeps a log file if NM-TRAN finds an error which helps debugging.
nmbs bug when $INPUT line became greater than 80 char long has been fixed.
Bug with %nmctl% if not 4 chars long has been fixed (affected name of $TABLE file output)
Bug fixed in nm2wfn.bat used to convert standard NONMEM compilation versions to WFN named compilation versions.
ncabs now works and is more fully documented. A new command, ncasim, works like nmgosim but instead of doing a NONMEM analysis on the simulated data the analysis step uses nca.awk to do a non-compartmental analysis (AUC, cmax, tmax). nca.awk can be modified to perform any kind of analysis on the simulated data sets created by a NM-TRAN simulation control stream. The nature of the analysis will depend on how the user modifies nca.awk.
16 June 2004 Version 407
nmeigen displays the condition number and the extreme eigenvalues. This requires that $COV has the PRINT=E option and that the covariance step completes. A condition number over 1000 is a sign of overparameterization.
The cts procedures ctssplit.awk and mkctl.awk made more flexible.
Long file names in the NMHOME path will cause problems for WFN. A revised wfn.txt is provided that will automatically convert long file names used for WFNHOME, NMHOME and F77HOME variables into the 8 character short format. This will not work with Windows 98/ME but should work with Windows XP, Windows200*. If you want to take advantage of this feature you will need to replace your existing wfn.bat by saving wfn.txt as wfn.bat (see Upgrading). You will need to transfer all changes you have made to your original wfn.bat to the new version.
17 May 2004 Version 406
$THETA, $OMEGA, $SIGMA not recognized if $ was not first char of record. ntcs.awk has been fixed.
DIMTOK increased in LSIZES for s7t, 57t compilation versions
nmcg now refreshes the data descriptor file (*.dsc) if nmcg has been run previously
nmctl has an optional second argument ("i") which will use INTER.txt instead of the run listing file as the source to update parameter values.
Further work done on the documentation for the cts system.
25 November 2003 Version 405
nmgosim command provides a work around for NONMEM unreliable simulation and estimation steps in single problem.
Improved installation tools (wfninst
and wfnsetup) and documentation for named NONMEM compilation versions.
wfn.txt bug fixed to support ms compiler
Missing web files for index page added.
wfnlink.awk changed to support French version of output from DOS echo command
"F" is ignored if it used as a parameter name.
Bug fix in ntcs.awk to prevent name conflict problem if data item and parameter names are the same.
Case sensitivity of file names preserved if more than one TABLE file is requested.
Bug fix for nmfesf.bat for Win9x versions.
nmllp changed to recognize wider variety of parameter name syntax.
%wfnhome%\run directory and files now restored to WFN distribution file.
Log likelihood profiles can be created with the assistance of nmllp.
nmbs now allows comma separated values in $INPUT list of data items.
nmobj modified to let negative objective function values be sorted so that lowest OBJ appears first.
Various attempts to improve the web based documentation.
Bug in nmlink.awk fixed affecting users with NONMEM default locations for compiled files.
Source and binary directory structure revised.
GeoCities web site no longer supported.
nmac no longer fills up all disk space if there is a syntax error in the NM-TRAN autocovariate code.
wfn.bat unsets nmnice if OS is Win9x.
Support for Intel Fortran 7.0 compiler added (compiler code is ivf).
Bug with identical objective function values fixed when using nmobj.
More
bugs affecting nmac and nmcg removed.
15 Nov 2000 Version 217
Bugs
introduced in Version 209 affecting nmac removed.
14 Nov 2000 Version 216
Crossgraph
dsn files no longer overwrite existing files in run directory.
22 Oct 2000 Version 214
Minor bug fix for ntcs
translation of control stream.
1 Sept 2000 Version 212
Bug fixes for nmobj
and nmpe.
7 Aug 2000 Version 210
Improvements to nmctl
for making Bayesian prior control streams
25 Apr 2000 Version 203
Improvements to wfnsetup
and wfnpatch batch files for installing NONMEM.
12 Apr 2000 Version 202
Download file name
includes version.
14 Mar 2000
Information on
upgrading and re-installation of wfnauto.bat added to this page.
3 Mar 2000
Watcom
support for user defined subroutines (e.g. prior.for) fixed.
Send
comments and suggestions to Nick Holford
.
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