Appendix 3 - Shortcuts
This appendix contains shortcut installation procedures for users with MS-DOS, Microsoft Windows, and UNIX. This appendix lists the essential commands in the UNIX SETUP and MS-DOS CDSETUP6.BAT installation utilities. These utilities perform an install, oftentimes making it unnecessary to deal with any of the details contained in the chapters of this installation guide. This appendix also contains suggestions for reading NONMEM CD-ROM’s with UNIX, because such commands are not part of SETUP.
The commands presented in this chapter can be used by an installer who does not choose to, or cannot use, the installation utilities. Even if the utilities are used, it may be helpful to see a list of just the essential commands because SETUP and CDSETUP6.BAT contain many other commands. (The user may read the complete SETUP and CDSETUP6.BAT files from the distribution medium.) Chapter VII discusses the purpose of the commands in this appendix and the files and tools that they install. Appendix 4 describes how the UNIX SETUP utility is used, and describes briefly how NONMEM can be run after SETUP (or commands similar to those in Appendix 3) have been used to install NONMEM. Appendix 5 describes how the MS-DOS CDSETUP6.BAT utility is used, and describes briefly how NONMEM can be run after CDSETUP6.BAT (or commands similar to those in Appendix 3) have been used to install NONMEM.
These commands are suggested for reading the NONMEM distribution medium (CD-ROM). They may require modification for other versions of UNIX. Please consult a local systems administrator for further help if necessary. Although we suggest that the NONMEM VI directory be named /export/home/nmvi, any directory may be used. The full pathname of the NONMEM VI directory appears only in the instructions in this guide, not in the files that appear on the distribution medium.
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HOW TO READ UNIX TAR-FORMAT FILES IN MOST UNIX SYSTEMS |
The following commands create the NONMEM VI directory and the help and html subdirectories. They read the tar files nonmemvi.tar, help.tar and html.tar from the CD-ROM, and extract the contents into the appropriate directories.
mkdir /export/home/nmvi cd /export/home/nmvi mkdir help mkdir html cp /cdrom/cdrom0/nonmem~1.0/unix/* . tar xvf nonmemvi.tar mv help.tar help cd help tar xvf help.tar cd .. mv html.tar html cd html tar xvf html.tar cd ..
With Linux, the commands are the same, except that the CD may be located elsewhere, e.g.,
cp /media/NONMEM_6.1.0/UNIX/* .
These are the essential commands in SETUP (see Appendix 4). These commands can be used with most UNIX systems. Please refer to the main body of Guide III for a complete explanation of these commands.
The ar command is discussed in Chapter III Section 3.
At lines marked with ***, a file’s contents must be changed by the installer using an editor.
cd /export/home/nmvi mkdir nm mkdir pr mkdir tr mkdir tl mkdir util cp NMLINK6 util cp PRED1 util cp CONTROL1 util cp PK1 util cp ERROR1 util cp CONTROL2 util cp CONTROL3 util cp DATA3 util cp PHENO util cp THEO util cp THEOPP util cp CONTROL4 util cp CONTROL5 util cp CONTROL6 util cp CONTROL7 util cd util *** Make UNIX changes to sep.f - See Chapter III 1.2 f77 -o sep.exe sep.f >>& emsgs.txt cd ../nm cp ../NMD NMD ../util/sep.exe < NMD *** Make UNIX changes to BEGIN.f - See Chapter III 2.1 *** Make IEEE and UNIX changes to BLKDAT.f - See Chapter III 2.2 *** Make UNIX changes to FLU.f - See Chapter III 2.3 cd ../pr cp ../PPD1 PPD1 ../util/sep.exe < PPD1 cp ../PPD2 PPD2 ../util/sep.exe < PPD2 cd ../tr cp ../TRAN TRAN ../util/sep.exe < TRAN cd ../tl cp ../TRLD TRLD ../util/sep.exe < TRLD cd ../nm f77 -O -c *.f >>& emsgs.txt cd ../pr f77 -O -c *.f >>& emsgs.txt cd ../tr f77 -c *.f >>& emsgs.txt cd ../tl f77 -O -c *.f >>& emsgs.txt cd ../nm ar ruv nonmem.a *.o >>& emsgs.txt cd ../tr f77 -o nmtran.exe *.o >> emsgs.txt cd ../util cp ../NMLINK6 nmlink6.f *** Create the file path.for - See Chapter VII 2.1.1 f77 -o nmlink6.exe nmlink6.f >>& emsgs.txt cp ../NMFE6 nmfe6 chmod 755 nmfe6 *** Make changes to nmfe6 - See Chapter VII 2.2.1 cd .. mkdir run cp util/nmfe6 run cp util/CONTROL3 run cp util/CONTROL5 run cp util/DATA3 run cp util/THEOPP run cp SETUP util cp SETUP.TXT util cd help *** Include full path in nmhelp - see Chapter XI 1.3 chmod 755 nmhelp cd ..
Copy the files
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/export/home/nmvi/util/nmfe6 |
to a directory in the NONMEM user’s path.
These are the essential commands in CDSETUP6.BAT (see Appendix 5). These commands can be used in an MS-DOS window running under Microsoft Windows (3.1, 95, NT, XP, Vista), or in MS-DOS 6.22 running alone (no windows). The df command for DIGITAL Visual Fortran 5.0 is shown. For Microsoft Powerstation Fortran 1.0 or 4.0, use
fl32 /Ox /Op
rather than
df /optimize:1 /fpe:0.
If g77 or g95 is used, see Chapter 7 for important differences.
If the hard drive is not c: and/or the CD-ROM drive is not d:, change every instance of c: and d: to the appropriate letters. Although we suggest that the NONMEM VI directory be named c:\nmvi, any directory may be used. The full pathname of the NONMEM VI directory appears only in the instructions in this guide, not in the files that appear on the distribution medium. Please refer to the main body of Guide III for a complete explanation of these commands.
If your compiler requires a command such
as
compile.bat
or f32env.bat
prior to using the compiler, be sure to type this command 1)
prior to installing NONMEM, and 2) each time
you open a new MS-DOS window to run NONMEM.
At lines marked with ***, a file’s contents must be changed by the installer using an editor.
cd c:\ mkdir nmvi cd nmvi mkdir nm mkdir pr mkdir tr mkdir tl mkdir util copy d:\NONMEM_6.1.0\CDsetup6.bat . copy d:\NONMEM_6.1.0\Disk_1\*.* . copy d:\NONMEM_6.1.0\Disk_3\*.* . copy nmutil util copy nmlink6 util copy pred1 util copy control1 util copy pk1 util copy error1 util copy control2 util copy control3 util copy data3 util copy pheno util copy theo util copy theopp util copy control4 util copy control5 util copy control6 util copy control7 util cd util copy ..\sep sep.for df sep.for cd ..\nm ..\util\sep < ..\nmd cd ..\pr ..\util\sep < ..\ppd1 ..\util\sep < ..\ppd2 cd ..\tr ..\util\sep < ..\tran cd ..\tl ..\util\sep < ..\trld cd ..\nm df /c /optimize:1 /fpe:0 *.for cd ..\pr df /c /optimize:1 /fpe:0 *.for cd ..\tr df /c *.for cd ..\tl df /c /optimize:1 /fpe:0 *.for cd ..\nm link /lib /out:nonmem.lib *.obj cd ..\tr df /Fenmtran *.obj cd ..\util copy ..\nmlink6 nmlink6.for *** Create the file path.for - See Chapter VII 2.1.1 df nmlink6.for copy ..\nmfe6.bat nmfe6.bat *** Make changes to nmfe6.bat - See Chapter VII 2.3.1 cd .. mkdir run copy util\nmfe6.bat run\nmfe6.bat copy control5 run copy control3 run copy data3 run copy theopp run copy cdsetup6.bat util copy setup.txt util mkdir html cd html copy d:\NONMEM_6.1.0\html\*.* cd .. mkdir guides cd guides copy d:\NONMEM_6.1.0\guides\*.* cd .. mkdir help cd help copy d:\NONMEM_6.1.0\help\*.* copy d:\NONMEM_6.1.0\Dos_tools\*.* install.exe cd ..
Copy the files
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c:\nmvi\util\nmfe6.bat |
to a directory in the NONMEM user’s path.
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