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gfortran work-around for PDx-Pop and NONMEM for Ubuntu

From: Bachman, William <William.Bachman>
Date: Mon, 1 Dec 2008 15:32:12 -0500

As of Ubuntu 8.10, g77 does not appear to be available in the Ubuntu
database. However, "gfortran" is available and can can be downloaded
and installed using "sudo apt-get install gfortran" from the Linux
command line. Versions of gfortran after version 4.1 are based on g95
but not a direct substitution for versions of g95 previously used with
NONMEM and PDx-Pop. I was able to find a workaround for my system that
hopefully will also work for others.

I downloaded gfortran and then "tricked" NONMEM and PDx-Pop into
thinking it was g95:

1. I created a symbolic link for gfortran to "g95":

sudo ln -s /usr/bin/gfortran /usr/bin/g95

2. I installed a fresh copy of NONMEM VI level 2.0 using the PDx-Pop 3.0
NMInstaller with the following settings:

- NONMEM VI Level 2.0
- /media/NONMEMVI2.0
- /home/bill/nm6g95 (not previously existing)
- GNU g95
- -O (not -O -fsloppy-char which would generate gfortran errors)
- New Install
- Intel

There were NUMEROUS Hollerith Warnings in the Installation Output window
and it seemed to take longer than usual but it eventually finished with
"End of Installation" in the window. I exited the NMInstaller and
returned to PDx-Pop.

3. I edited line 505 of the file /home/bill/pdxpop3/Go5pkg.pm by
removing "-fsloppy-char" from the line.
"nonmem -O -fsloppy-char" --> "nonmem -O "

4. In PDx-Pop, I used Tools > Edit Configuration, to change NonMemDir,
FortranFlag and Foptions to /home/bill/nm6g95, G95 and -O, respectively,
and saved the configuration and closed the configuration editor.
PDx-Pop then ran as expected with G95 (actually gfortran) including
NONMEM output in the Output Window.

Note: No changes to the source code other than those automatcally made
by the PDx-Pop NONMEM Installer are necessary. Previous posts regarding
the BLKDAT.f file recommended changing the second and third instances of
/dev/null to /dev/tty and JUNK for NONMEM. The values used by PDx-Pop
for NONMEM are /dev/stdout and /dev/null, respectively.



For those running and/or installing NONMEM from the Linux command prompt
on Ubuntu, the SETUP c-shell script included on the NONMEM distribution
CD-ROM can be used to install NONMEM after downloading gfortran. The
c-shell is not the default shell and may not have been installed by
Ubuntu. You can download and install the c-shell using "sudo apt-get
install csh". You don't have to use the c-shell to run SETUP or nmfe6,
but, they must be installed on your system for these scripts to work.

1. I created a symbolic link for gfortran to "g95":

sudo ln -s /usr/bin/gfortran /usr/bin/g95

2. Run setup from the /media/NONMEMVI2.0 directory with appropriate
arguments:
./SETUP /media/NONMEMVI2.0/ /home/bill/nm62gf g95 -O /usr/bin/ar Intel n

3. At Step. 5 of SETUP when it stops to allow modification of NONMEM
source files, I edited line 28 of BLKDAT.f as follows:
     1/'/dev/null','/dev/stdout','PRDERR','INTER','/dev/null'/
and then allowed the SETUP script to finish.

4. I tested the installation by changing to the /home/bill/nm62gf
directory and running CONTROL5:

bill
  
 WARNINGS AND ERRORS (IF ANY) FOR PROBLEM 1
             
 (WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.
             
 (WARNING 43) THE $PK BLOCK REQUESTS "CALL ONCE PER INDIVIDUAL RECORD",
BUT
 DATA ITEMS ARE USED IN THE $PK BLOCK. VALUES OF THESE DATA ITEMS
 SUBSEQUENT TO THOSE FROM THE FIRST EVENT RECORD WILL BE IGNORED. IF
THIS
 IS NOT APPROPRIATE, THE CALL DATA ITEM CAN BE USED TO OBTAIN ADDITIONAL
 CALLS, OR $PK'S CALLING PROTOCOL SHOULD BE CHANGED.
/usr/bin/ld: Warning: alignment 16 of symbol `cm41_' in
/home/bill/nm62gf/nm/BLKDAT.o is smaller than 32 in
/home/bill/nm62gf/nm/nonmem.a(INITL.o)
Starting nonmem execution ...

Note the alignment warning (that can be ignored) and lack of NONMEM
output to the console. However the run completed successfully and
correctly.


William J. Bachman, Ph.D.
Director, Pharmacometrics R&D
Icon Development Solutions
6031 University Blvd., Suite 300
Ellicott City, MD 21043
Office 215-616-8699
Cell 301-467-8635
William.Bachman

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Received on Mon Dec 01 2008 - 15:32:12 EST

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