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| NMFE UTILITY PROGRAM |
| |
+--------------------------------------------------------------------+
MEANING: The name of a computer program
CONTEXT: NONMEM support utility routine
USAGE:
nmfe74 controlfile reportfile [-background]
[-prsame] [-prcompile] [-prdefault] [-tprdefault]
[-trskip] [-nobuild]
[-maxlim=1] [-maxlim=2] [-maxlim=3]
[-rundir=directoryname] [-runpdir=directoryname]
[-parafile=filename]
[-parafprint=n]
[-nmexec=filename] [-xmloff]
[-licfile=filename]
[-locfile=filename]
[-simparon] [-flushtime>=0.0]
Default, if used in the run directory:
nmfe74 controlfile reportfile
-prsame (if possible; else -prcompile)
-rundir=run
-runpdir=temp_dir -nmexec=nonmem
-licfile=../license/nonmem.lic
Options may need to be in quotes, e.g.,
nmfe74 CONTROL5 REPORT5.res "-prsame"
The name of the command indicates the version of NONMEM, e.g. nmfe74
denotes NONMEM 7.4.0. The command will be shown generically as nmfe7
in this help file. For details specific to an earlier release than
NONMEM 7.4.0, see the help file for that release.
OPTIONS:
controlfile
Name of the input file containing the NM-TRAN control stream.
reportfile
Name of the output file into which NONMEM writes the results.
Also called "the standard results" file.
-prcompile,-prsame,-prdefault,-tprdefault
By default, nmfe7 copies the required PREDPP routines from the
nonmem ..\pr and ..\resource directories into a subfolder
temp_dir of the current directory and compiles the routines
there. (Some of these routines are needed even when $PRED is
used.) This is referred to as "pr recompilation". The resulting
object files are then linked with NONMEM, and the nonmem exe-
cutable is created. In a subsequent run, nmfe7 will skip the pr
recompilation if the same ADVAN/TRANS (or a $PRED) are used, and
the size of the problem (e.g., size of OMEGA and SIGMA) has not
changed.
-prcompile
Force pr recompilation, in case the run does not appear to exe-
cute properly when no pr recompilation occurs.
-prsame
Force the skipping of pr recompilation. Used when nmfe7 detects
a change in the previous run from the present run, but the user
is convinced there is no significant change. Uses the compiled
files from the previous run.
-prdefault
Do not recompile any routines other than FSUBS. Use the precom-
piled routines in ..\pr and ..\resource directories. May be used
if it is sufficient to use default values in sizes.f90 for the
various parameters (see ..\util\prsizes.f90 for the list of those
that are used.). Any NONMEM parameters that are not used (that
is, those not listed in prsizes.f90) will still be dynamically
sized.
-tprdefault
Tests if is okay to do -prdefault. If it is not okay, then it
will test if there are compiled pr routines in temp_dir direc-
tory,and if they are appropriate for the present model. If so,
it will not recompile those pr routines, and use those that are
already there. If not, it will perform a fresh PREDPP compile.
May be combined with either -prcompile or -prsame.
-tprdefault -prcompile
Tests if is okay to do -prdefault. If it is not okay, then it
will perform a fresh compile of the particular ..\pr routines,
even if there were appropriate ones in temp_dir already.
(-prcompile forces a compile regardless of whether it was neces-
sary).
-tprdefault -prsame
Tests if is okay to do -prdefault. If it is not okay, then it
will use those in temp_dir, assuming that they are appropriate
for the present problem.
-trskip
Requests that the NMTRAN step be skipped. The -trskip option is
useful if you wish to modify FSUBS.f90 created by a previous run,
and insert extra debug lines into FSUBS.f90, and prevent your
modified FSUBS.f90 from being over-written by NMTRAN (it will
still be compiled).
-trskip and any one of -prskip, -prnoskip, or -prstatic options
may be used together, or -trskip may be used by itself.
-nobuild
Prevents a new nonmem executable from being built, particularly
useful for a series of nonmem runs during boostrap procedures.
-maxlim=[1|2|3]
With maxlim=1, then LIM1, LIM3, LIM4, LIM13, and Lim15 (those
used during estimation, and therefore by workers in a paral-
lelization problem), will be set to the size needed to assure no
buffer files are used, and everything is stored in memory, for
the particular prolem. With -maxlim=2, then LIM1, LIM2, LIM3,
LIM4, LIM5, LIM6, LIM7, LIM8, LIM13, LIM15, and LIM16 are also
sized to what is needed to assure that buffer files are not
needed. With -maxlim=3, then MAXRECID will also be sized, to
MAXDREC, the largest number of records in any individual. With
maxlim=3, it is preferred to also use -tprdefault, or -prcompile,
but not -prdefault, as NMTRAN's optional resizing of the PREDPP
size parameter MAXRECID may conflict with the -prdefault option
-rundir=directoryname
Specifies a directory for the NONMEM run if it is different from
the present working directory. The directory must exist, and
must contain all necessary input files, such as the controlfile,
msf files, and data files.
-runpdir=directoryname
Specifies a directory for the compile if it is different from
temp_dir. This is useful if you are repeatedly going between two
or more problems, so that often they need to be pr recompiled,
and you want to save time. Specify a unique temporary directory
for the compilation for each problem.
-parafile=filename
Name of the "parallel file" (the parallelization profile) that
controls parallelization (distributed computing). Default file
name if not specified: parallel.pnm. For details on the content,
see the INTRODUCTION TO NONMEM 7. Versions prior to NONMEM 7.2
do not support parallel computing. |
-parafprint=n |
Sometimes the parallelization log files can become very large |
during the $EST and $COV steps. Each of these records have paraf- |
print options to control the print intervals. Or, you can con- |
trol the print iterations globally with the -parafprint option at |
the command line.
-locfile=filename
Name of a file to override the default file called "nmloc" or
"nmloc.bat". This is the location file, which gives the path for
compiler or MPI system. The nmfe7 script will display a state-
ment as to what path it uses. E.g., "Pathlist information for
compiler and MPI systems are located in nmpathlist.txt" where
nmpathlist.txt describes which verson of nmloc is being used.
-nmexec=filename
Specifies an alternate name for the NONMEM executable instead of
the default nonmem.exe (windows) or nonmem (Linux). Note that
when parallelization is used, this name must be specified in the
pnm file. Example:
nmfe7 controlfile reportfile -nmexec=nonmem2 -parafile=mpi2.pnm
Suppose mpi2.pnm is based on mpilinux_onecomputer.pnm, which con-
tains
1:mpirun -wdir "$PWD" -n 1 ./nonmem $*
2:-wdir "$PWD/wrk_mpi" -n 1 ./nonmem <control_stream> <licfile>
Then mpi2.pnm must be changed as follows:
1:mpirun -wdir "$PWD" -n 1 ./nonmem2 $*
2:-wdir "$PWD/wrk_mpi" -n 1 ./nonmem2 <control_stream> <licfile>
-background
If "-background" is present NONMEM does not poll the terminal for
ctrl characters (See below.)
-xmloff
Turns off production of the XML output file root.xml, where root
is the root name of the control stream file. This may speed up
fast computational problems such as $SIM on simple models and
small data sets. |
-simparon |
Turn on parallelization during simulation step. |
-flushtime>=0.0 |
File buffer contents are flushed to file not more frequently than |
flushtime seconds (1.0 second) is default. Floating number |
allowed.
DISCUSSION:
NMFE7.bat and NMFE7 are front-end tools for running NONMEM 7. Their
use is optional. NMFE7.BAT is a MS-DOS batch program. NMFE7 is a
UNIX C-shell script. Both are supplied on the NONMEM 7 distribution
medium.
They should be placed in a directory in the user's path. Both make
use of the support utilities nmlink7 and compile7, which are also sup-
plied on the NONMEM 7 distribution medium.
Both execute the following steps, stopping after any step in which
errors occur:
1) NM-TRAN processes the NM-TRAN control stream, which is found in a
file whose name is given as the first command-line argument.
With NONMEM 7.2 and higher, both lower and upper case may be used
for all user-defined and reserved words in the control stream. |
With NONMEM 7.3 and higher, & may be used at the end of any line |
of the control stream to indicate that the line is to be contin- |
ued, including control records as well as abbreviated code. |
Lines may be longer than 160 characters long. The maximum length |
is given by FSD in resource/SIZES.f90. (FSD=67000 with NONMEM |
7.3). This step is omitted if option -trskip is used.
2) NMLINK7 creates the file LINK.LNK (a list of object files to be
included in the NONMEM executable). With NONMEM 7, compile7 cre-
ates the file compile7.lnk (a list of PREDPP routines to be re-
compiled with the current array sizes) and a work directory
temp_dir is created. All files listed in compile7.lnk are copied
to temp_dir and compiled. They are then copied to the current run
directory. The recompilation of PREDPP routines can take a
noticeable amount of time. This step is skipped if option
-prsame or -prdefault is used.
(See $sizes.ctl).
3) If a file FSUBS.f90 of generated and/or user-supplied FORTRAN
code was created by NM-TRAN, it is compiled by the FORTRAN 90
compiler.
4) Utility program nonmem_mpi.exe is called to check if parallel
processing is requested, what transfer type is to be used, and
make sure the parallel file is syntactically okay. Either of two
sets of messages will appear at the console:
Exit status = 1
IN MPI
This indicates that parallel proccesing using the MPI method is
requested. MPI libraries will be included in the NONMEM exe-
cutable.
Exit status = 0
IN REGULAR/FILE TRANSFER
This indicates that no parallel processing was requested, or par-
allel processing uses the FPI (file transfer) method. No MPI
library is needed.
5) The NONMEM executable nonmem.exe (nonmem in UNIX) is created.
6) The NONMEM executable is run. It is passed an option -licfile,
which tells it where to find the NONMEM license file. Typically,
this is the file nonmem.lic in the sub-directory license of the
directory in which NONMEM was installed.
First, arrays are allocated dynamically, according to information
supplied by NM-TRAN in files FSIZES.
(See $sizes).
Processing may be performed as a single CPU process, or distruted
among multiple cores or nodes, as specified in the parallel file.
(See parallel).
The output file whose name is given as the second command-line
argument is created. During the run, NONMEM output can be found
in the file OUTPUT. When the run terminates, file OUTPUT is
copied to the output file and then removed.
While NONMEM 7 and higher is running, the following may be used if
"-backgound" was not present:
ctrl-J
Turn console iteration printing on/off during the Estimation
Step (Default is on).
ctrl-K
Stop the Estimation Step, which completes its output, and goes on
to next mode or estimation method.
ctrl-E
Exit program gracefully.
ctrl-T
Monitor the progress of each individual during an estimation by
toggling ctrl-T. Wait 15 seconds or more to observe a subject's
ID, and individual objective function value. It is also good to
test that the problem did not hang if a console output had not
been observed for a long while.
The signal program may be used in situations where NONMEM does not
respond to the ctrl key.
(See signal).
EXAMPLES OF USAGE:
nmfe7 CONTROL5 REPORT5.res
nmfe7 CONTROL5 REPORT5.res -background >& consout &
(Trailing & is used in UNIX to run the command in the background.)
Other files are created by nmfe7 and NONMEM:
FSUBS_MU.F90
Contains SUBROUTINE MUMODEL2. This subroutine contains only the
code that is needed to compute any MU parameters (MU_1, MU_2,
etc.) that were defined in $PK or $PRED abbreviated code. It is
also included in FSUBS.
FSUBS and FSUBS.f90
These are identical. They contain both the content of FSUBS as it
was in previous versions of NONMEM (generated subroutines PK,
PRED, MODEL, etc., plus any user-supplied code), and also subrou-
tine MUMODEL2. Note that user-supplied code must be in Fortran
90 format.
With NONMEM 7 and higher, additional output files are created, with
names controlfile.xxx, where xxx is ext, cov, etc.
(See additional_output_files).
(See raw_output_file).
REFERENCES: Guide III Section IV.1.0, V.7.0
REFERENCES: Guide Section Introduction_7
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