Omission in NONMEM CD-ROM readme.doc
From: "Bachman, William (MYD)" bachmanw@iconus.com
Subject: [NMusers] Omission in NONMEM CD-ROM readme.doc
Date: 12/11/2003 1:28 PM
The following line in the readme.doc on the NONMEM distribution CD-ROM
omitted the compiler argument from the CDsetup.bat argument list.
The line:
"setup a c nmv df y link (or CDsetup d c nmv y link if you are installing
from the NONMEM CD-ROM and d is your CD-ROM drive)"
should instead read:
"setup a c nmv df y link (or CDsetup d c df nmv y link if you are installing
from the NONMEM CD-ROM and d is your CD-ROM drive)".
Additionally, an ASCII text version of the file is attached for those
without the capability to read a Word document.
William J. Bachman, Ph.D.
Manager, Pharmacometrics Research and Development
GloboMax
The Strategic Pharmaceutical Development Division of ICON plc
7250 Parkway Drive, Suite 430
Hanover, MD 21076
410-782-2212
bachmanw@iconus.com
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NONMEM Installation: Getting Started
Please note that the NONMEM Installation Guide, Guide III, provides a thorough description of the steps
required to install the NONMEM system. In particular, Appendices 3 through 5 contain detailed
installation information. When using the installation scripts, please be certain to designate the correct
Fortran compiler available on your system. The default compiler designation may not be correct for your
installation. Instructions for limited customization of NONMEM, PREDPP and NM-TRAN are provided
in Chapters III, IV and V. Additional information regarding installation and advanced features is given in
Chapter VII. After installing NONMEM, we recommend that a beginning user read the Introductory
Guide, Guide V.
Installation for Windows from floppy diskettes or CD-ROM
Previous installation of a Fortran compiler is required. Associated environmental variables must be set
before proceeding. Please see the documentation for your compiler. Supported compilers include
Compaq/Digital Visual Fortran versions 5.0 to 6.6b, GNU g77, Intel Fortran for Windows 7, Open
Watcom 1.0 and Microsoft Powerstation 4.0. The error message "out of environment space" is frequently
encountered with Windows 95 and 98 and is discussed in NONMEM Users Guide III (Installation)
Chapter VII Section 2.4.3.1. You might want to familiarize yourself with this chapter and with the
material in Chapter III in case any other difficulties arise.
To install NONMEM follow these steps:
1. Read Appendix 3 section 3.3 and Appendix 5 in NONMEM Users Guide Part III: NONMEM
Installation Guide.
2. Open a MS-DOS window by double-clicking the MS-DOS icon or
the Start=> Programs=>Command Prompt on Window-NT or
the Start=>Programs=>Accessories=>Command Prompt on Windows-2000.
The menu path may be different for other versions of Windows.
3. Insert disk #1 (Double Precision NONMEM and PREDPP) into the floppy drive or place the CD
in the CD drive.
4. Change to the appropriate floppy or CD-ROM drive by typing x: where x is the appropriate drive
letter.
5. At the command prompt, type the setup command and appropriate options. The setup command
is described in Appendix 5, Guide III. If the Compaq/Digital Visual Fortran compiler is used and
NONMEM is to be installed from the floppy drive labeled a: into the nmv directory on the c:
drive the command would be setup a c nmv df y link (or CDsetup d c nmv df y link if you are
installing from the NONMEM CD-ROM and d is your CD-ROM drive).
a is the floppy drive containing disk #1 (if installing from a CD specify the CD drive
label instead, e.g. "d")
c is the hard drive on which NONMEM will be installed
nmv is the directory on the hard drive into which NONMEM will be installed
df indicates that the Compaq/Digital Visual Fortran compiler is to be used
y selects default optimization
link is the linker command
For the GNU g77 compiler, the command is setup a c nmv g77 y link
For the Intel Fortran for Windows compiler, the command is setup a c nmv ifl y link
For the Open Watcom compiler the command is setup a c nmv wfl386 y link.
For the Microsoft Powerstation compiler the command is setup a c nmv fl32 y link.
The corresponding commands if installing from the CD-ROM would be:
For the GNU g77 compiler, the command is CDsetup d c nmv g77 y link
For the Intel Fortran for Windows compiler, the command is CDsetup d c nmv ifl y link
For the Open Watcom compiler the command is CDsetup d c nmv wfl386 y link.
For the Microsoft Powerstation compiler the command is CDsetup d c nmv fl32 y link.
No changes should be necessary to the NONMEM source files during the installation if a default
installation is performed.
6. Test the NONMEM installation:
cd run
nmfe5 CONTROL5 REPORT5
Installation for Unix from UNIX tar diskettes
Read Appendix 3 sections 3.1 and 3.2 and Appendix 4 in NONMEM Users Guide Part III: NONMEM
Installation Guide.
Installation for Linux on a PC Unix from UNIX tar diskettes
Installation under Linux on a PC is very similar to installations for UNIX. The primary difference is
specifying the Intel floating point architecture.
1. Read Appendix 3 sections 3.1 and 3.2 and Appendix 4 in NONMEM Users Guide Part III:
NONMEM Installation Guide (floppy drive with Red Hat Linux is /dev/fd0).
2. The following assumes that the f77 compiler and dos2unix utility have been installed, the NONMEM
directories have been created under /opt, the full path name for the ar command is /usr/bin/ar, and that
the NONMEM files have been read from the distribution media as described in Appendix 3, section
3.1.
3. Make the setup script executable.
chmod +x SETUP
Run the setup command from the nmv directory. (Make certain that you are using a C shell.)
./SETUP /opt/nmv f77 -O /usr/bin/ar Intel
/opt/nmv is the main NONMEM directory
f77 is the compiler command
-O is the compiler option
/usr/bin/ar is the path and filename of the ar command
Intel specifies the Intel floating point architecture
4. Test the NONMEM installation.
cd run
./nmfe5 CONTROL5 REPORT5
Installing NONMEM from CD-ROM on Linux
The following installation was done on an Intel system running Red Hat Linux 7.2 and using the GNOME
desktop environment.
1. Log in as root and open a terminal emulation window.
2. Start a C-shell if not the default shell for root, "csh".
3. Create the NONMEM installation directory, "mkdir /opt/nmv".
4. Change to the NONMEM installation directory, "cd /opt/nmv".
5. Insert the NONMEM Installation CD-ROM into your CD-ROM drive. In the GNOME
environment, the CD will be auto-mounted.
6. Copy the tar files from /mnt/cdrom/Nonmem_V.1.1/UNIX to /opt/nmv.
7. Untar the disk1 files, "tar xvf disk1.tar".
8. Untar the disk3 files, "tar xvf disk3.tar".
9. Make a NONMEM help directory, "mkdir /opt/nmv/help".
10. Move the help tar file to the help directory, "mv help.tar help/help.tar.
11. Change to the help directory, "cd help".
12. Untar the help files, "tar xvf help.tar".
13. Change back to the install directory, "cd ..".
14. Run SETUP with the appropriate command line arguments, "./SETUP /opt/nmv g77 -O3
/usr/bin/ar Intel".
15. At Step 6. of SETUP (compiling the source files), edit /opt/nmv/nm/BLKDAT.f. Change the
second instance of "/dev/null" (the value for FNINT) to '/dev/stdout' if you will be using PDx-
Pop. If you will be using PDx-Pop, also edit /opt/nmv/BEGIN.f. Un-comment lines 13 and 14
("OPEN(6, "OUTPUT)" and "REWIND 6").
16. Allow SETUP to proceed to a successful termination.
17. Change to the run directory, "cd run".
18. Test the installation with the nmfe5 C-shell script "./nmfe5 CONTROL5 report5.txt". If
successful and you set up NONMEM for PDx-Pop, the file "OUTPUT" will contain the results of
the run. If successful and you set up NONMEM for running with nmfe5, the file "report5.txt"
will contain the results of the run.
Installation for UNIX from the NONMEM CD-ROM should be similar to the Linux installation.
nmconsult@globomaxnm.com
GloboMax LLC
7250 Parkway Drive, Suite 430
Hanover, MD 21076
Voice: (410) 782-2205
FAX: (410) 712-0737
22 October, 2003
_______________________________________________________