WFN for UNIX/Linux

From: "Justin Wilkins" Subject:[NMusers] WFN for UNIX/Linux Date: Mon, 9 Jun 2003 12:03:23 +0200 Hi all, Has anyone converted Nick's fabulous Wings For NONMEM into UNIX-compatible shell script? Nick, would you have any objection if I had a crack? Best regards Justin

From: Nick Holford Subject:Re: [NMusers] WFN for UNIX/Linux Date:Tue, 10 Jun 2003 08:20:11 +1200 Justin, I have a limited version of WFN available for Unix type operating systems. It uses csh (tested with tcsh) instead of DOS batch files but the awk scripts are identical for the Windows and Unix. The fancier methods that come with WFN (nmbs, nmbs, nmac) are not currently translated for Unix. I would be delighted if you wanted to try the conversion. Nick *********************************************** This is the readme for the Unix Version of WFN: WFN for Unix Version 400u Nick Holford Last modified 23 July 2002 This is an early attempt at creating a WFN distribution for unix. It is assumed that you already have a working NONMEM installation on the unix platform. 1. Extract the zip file into a home directory for WFN e.g. ~/nmv/wfn. Be sure to extract with the -a option to create unix text files! E.g. assuming you have wfnunix400u.zip in ~/nmv : mkdir wfn cd wfn unzip -a ../wfnunix400u 2. Edit the wfn/bin/wfn csh script to point to your NONMEM installation (NMHOME) and your WFN installation (WFNHOME) e.g. setenv WFNHOME $NMHOME/wfn setenv NMHOME ~/nmv You also need to define a directory for the NONMEM source code and for the compiled binary files. The default NONMEM installation has the source and binaries in the same directory which makes it harder to manage different compilation versions with only minor source code differences. If you prefer the NONMEM default and do not plan to use alternate compilation versions then use this (it is important that NMOBJ is set to '.'): setenv NMOBJ . setenv NMSRCHOME $NMHOME setenv NMBINHOME $NMHOME A more flexible setting uses the NMOBJ variable to identify different compilation versions (see below). The NMOBJ value identifies the NONMEM compilation version. setenv NMSRCHOME $NMHOME/src setenv NMBINHOME $NMHOME/ver/$NMOBJ Some flexibility in the Fortran compiler you use can be achieved by defining the type (F77TYP) and executable name (F77EXE). F77TYP must be f77 or g77. If you know you are using the GNU g77 compiler then change F77TYP to g77 but this is not essential. setenv F77TYP f77 setenv F77EXE f77 Change the f77 compiler options to match those used when you compile NONMEM e.g. I use these with the compiler I have on the irix4d system at the University of Auckland: setenv NMFOPT '-O2 -n32 -mips4 -OPT:IEEE_a=3:ro=3:unroll_size=0:fast_sqrt=ON' If you don't know yet what to use then a safe default is: setenv NMFOPT -O2 Your local version of time should be specified using NMTIME. GNU time is suitable. You may need to use the -p option with time to get the correct output format e.g. setenv NMTIME '/usr/bin/time -p' NMTIME should return 3 lines of output (real, user, sys) e.g. try this test with NMTIME and the ls command: $NMTIME ls bin make run wfnreadme.txt wfnunix.zip real 0.003 user 0.000 sys 0.002 NMTIME is used to provide timing information on NONMEM runs. If you don't have a time that works like this then simply specify a null value for NMTIME and timing information will appear as zero in the WFN output. NMMAKE must be able to use a version of GNU make. This is essential for automatically keeping NONMEM compilation up to date e.g. setenv NMMAKE /usr/local/bin/make The other variables in wfn are the same as those described for the DOS version. See: http://wfn.sourceforge.net/wfninst.htm 3. Edit ~/.login to source the $WFNHOME/bin/wfn csh script and also add $WFNHOME/bin to the path so that your environment is set up for WFN e.g. add the following to your ~/.login: source ~nmv/wfn/bin/wfn std if ( "$path" !~ *$WFNHOME* ) set path=($path $WFNHOME/bin) The first argument for wfn (std in the example above) can be used to select different compilation versions (see below). Use 'wfn' instead of 'wfn std' if you prefer to use the default NONMEM installation.. 4. Now set up your WFN environment with this command: source ~/.login 5. Set executable permissions for the WFN shell scripts with: source $WFNHOME/chmod.lst You may wish to change the permissions in chmod.lst to reflect your local preferences. The $WFNHOME/bin commands need to be executable by all WFN users. The $WFNHOME/make commands by those wishing to recompile versions of NONMEM. 6. Code for 4 compilation versions is provided with WFN named std, s7x, 50x and 57x. See this page for more details: http://wfn.sourceforge.net/wfnnmver.htm If you wish to use different compilation version (highly recommended) you should copy files from your existing standard NONMEM installation using the $WFNHOME/make/nm2wfn shell script. **** Before using nm2wfn you must edit nm2wfn to set the OldHome variable to the location of your existing NONMEM installation e.g. set OldHome=~/nmv **** nm2wfn copies the NONMEM source and currently compiled files to the std compilation version directories. It makes the NSIZES, PSIZES, TSIZES, and LSIZES files writeable in order to support automated compilation of different versions of NONMEM that must change these files. A backup copy of the original versions of these files is created with the extension '.org'. 7. Check that your compilation is up to date by first generating "make" files with: $WFNHOME/make/genmake Make files are automatically generated using the names of files in the Fortran source code directories with the extension '.f'. They are created in the NONMEM source code directories under NMSRCHOME. ** Do not put other Fortran source code in the same directory as the NONMEM supplied source code. genmake assumes all the Fortran source code files are required for NONMEM compilation. Then check your current compilation with: $WFNHOME/make/mknm This uses the unix make utility to verify that your files are up to date. If necessary it will compile any files that are missing or older than the current source file. If there are errors they can be found in the $WFNHOME/make/make.log file. 8. Now qualify your installation with this example problem: cd $WFNHOME/run nmgo theopd See http://wfn.sourceforge.net/wfninst.htm for details of the expected output. 9. If you have successfully compiled the std version of NONMEM then you may wish to use this command to compile the 3 other versions (s7x, 50x and 57x): $WFNHOME/make/mkver 10. Other WFN commands available are nmobj nmmbt nmtbl You can find out about these commands by going to: http://wfn.sourceforge.net This is enough for basic NONMEM jobs. At some point I will port the more complex WFN commands like nmbs, nmrt, nmac. Note that executing $WFNHOME/bin/wfn once you are logged in will not change the environment variables. You cannot simply change your NONMEM compilation version by executing wfn like you can with the DOS version. The wfn script creates a wfn alias (see $WFNHOME/bin/wfn) which allows the command wfn to work as it does with the DOS version e.g. wfn std # selects the std compilation version or wfn s7x # selects the s7x compilation version Please send comments/suggestions to Nick Holford, n.holford@auckland.ac.nz _______________________________________________________