From: "Ramajogi" ramajogi@clinapps.com
Subject: [NMusers] Installation of NONMEM using NMQual.
Date: Mon, 24 Apr 2006 14:00:18 -0700
Hi All,
As of now we are installing NONMEM manually in the following way on Linux (1.1 Red Hat Linux ES V3.0)
1. Log in as root and open a terminal emulation window.
2. Type "csh" in terminal and press Enter. Create the NONMEM installation directory, "mkdir /opt/nmv".
3. Change to the NONMEM installation directory, "cd /opt/nmv".
4. Copy the tar files for NONMEM to /opt/nmv.
Note:-Unzip REDHAT\NONMEM.zip folder in FTP server. Copy tar files from NONMem\Nonmem_V.1.1\UNIX folder.
5. Type following command to untar disk1 file."tar xvf disk1.tar".
6. Type following command to untar disk3 file. "tar xvf disk3.tar".
7. Make a NONMEM help directory, "mkdir /opt/nmv/help".
8. Move the help tar file to the help, "mv help.tar help/help.tar".
9. Change to the help directory, "cd help". Untar the help, "tar xvf help.tar".
10. Change back to the NonMem install directory, "cd ..".
11. Run SETUP with the appropriate command line arguments,
"./SETUP /opt/nmv g77 -O3 /usr/bin/ar Intel".
12. At Step 6. of SETUP (compiling the source files), Find /opt/nmv/nm folder and
check file BEGIN.f. and open this file in Text editor. Un-comment lines 13 and 14 ("OPEN (6, "OUTPUT)"
and "REWIND 6").
13. Check file BLKDAT.f. in /opt/nmv/nm folder. And open this file in Text editor. Change the second
instance of "/dev/null" (the value for FNINT) to '/dev/stdout'.
14. Open CFILES.f from /opt/nmv/nm in a text editor and check that at line 46 code is written like "CLOSE(UN(28))". If not and is written
like "CLOSE(UN(28),STATUS=DELETED)" , then change code at line as "CLOSE (UN(28))"
15. Allow SETUP to proceed to a successful termination by typing "Y" at step 6.
16. Change to the run directory, "cd run".
17. 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.
But now, one of our clients wants to install NONMEM using NMQual. In that case, the changes in step 12 above is done by NMQual.
But the other changes in steps 13 and 14 are not done.
Now the Question is what is the need of installing NONMEM with NMQual?
If the changes mentioned in step 13 and 14 are not done, how it will effect the NONMEM execution.
Thanks in advance
Ramajogi
ramajogi@clinapps.com
www.clinapps.com
Installation of NONMEM using NMQual.
From: "Gastonguay, Marc" marcg@metrumrg.com
Subject: Re: [NMusers] Installation of NONMEM using NMQual.
Date: Mon, 24 Apr 2006 22:06:52 -0400
Dear Ramajogi,
I'll try to answer your general questions about NMQual and then the specific
questions about the code changes you are trying to implement.
NMQual is an open-source (GPL) tool to implement and track whatever NONMEM code
changes/install options a user wishes to make for a given installation. NMQual also
links each specific installation to a specific NONMEM run command and provides a mechanism
for ensuring installation code integrity at each run time. NMQual 4.1 is provided with
templates with typical code changes for all reported NONMEM V bug fixes and some of the
common setup options, compiler or operating system specific changes as well. I believe
that NMQual is the only publicly available tool that automates the processes of keeping
your NONMEM installation up to date and maintaining a record of all code changes. For
more information on how to use NMQual, please read the User Guide and see the FAQ on
the NMQual resources web site ( http://metruminstitute.org/downloads/nmqual/). You might
also be interested in attending the upcoming web-cast training sessions on NMQual
( http://metruminstitute.org/training.html).
A fee-based Professional Services Package with extended support is also available from Metrum
Research Group, LLC (nmqual-services@metrumrg.com).
The code changes you've identified in steps 13 and 14 are not part of the standard recommended code
changes for NONMEM installation on linux, but I think I've found the sources for these:
Your Step #13 is related to display of iteration results to the terminal and is not a required
installation step on linux. As Bill Bachman points out, this is a recommended code change if you
are running with the PDxPop interface. See:
http://www.cognigencorp.com/nonmem/nm/98dec112003.html
I can't find a reference in the NONMEM installation guides for your Step #14, but this change has been suggested by Nick
Holford so that NONMEM's INTER file is not deleted after completion of a run. See:
http://www.cognigencorp.com/nonmem/nm/98may192005.html
You can safely install NONMEM without implementing these changes, as is the default in the NMQual configuration and
changes (changes.linux.01.xml) files, but you can also modify the changes files to accommodate the additional changes.
For example, if you want to implement your Step # 14, you could create a new changes.*.xml file (call it changes.linux.02.xml)
by using changes.linux.01.xml as a template and inserting the following lines of code before the the last </changes>
sentinel in the xml code. (Make sure to refer to the new changes.linux.02.xml file in the setup configuration file):
<change>
<ref>From Nick Holford's nmusers post ( http://www.cognigencorp.com/nonmem/nm/98may192005.html)</ref>
<file>nm/CFILES.f</file>
<from>
CLOSE(UN(28),STATUS=DELETED)</from>
<to>
C ATTRIBUTION
C CLOSE(UN(28),STATUS=DELETED)
CLOSE(UN(28))</to>
</change>
One of the useful features of NMQual is that these changes will be tracked to a particular NONMEM installation and you
can re-use the configuration and changes files across multiple installations so that you don't have to do this manually
each time. NMQual can also be used to efficiently install NONMEM across a grid or cluster of computers.
I hope you'll find this useful.
Marc
-----------------------------
Marc R. Gastonguay, Ph.D.
marcg@metrumrg.com
www.metrumrg.com
NONMEM® is a registered trademark of the University of California and is licensed exclusively to GloboMax LLC.
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