Getting Started#

Pymake can be used directly from the command line and within a python script. Examples of both use cases are given below.

Command Line Usage#

When pymake is installed, a mfpymake (or mfpymake.exe for Windows) program is installed. mfpymake can be used to compile MODFLOW 6 in the bin/ subdirectory directly from the command line using the Intel Fortran compiler from a subdirectory at the same level as the src subdirectory by specifying:

mfpymake src/ mf6 -mc --subdirs -fc ifort --appdir bin

MODFLOW 6 would be To see help for running from command line, use the following statement.

mfpymake -h

The help message identifies required positional arguments and optional arguments that can be provided to overide default values.

usage: mfpymake [-h] [-fc {ifort,mpiifort,gfortran,none}]
                [-cc {gcc,clang,clang++,icc,icl,mpiicc,g++,cl,none}]
                [-ar {ia32,ia32_intel64,intel64}] [-mc] [-dbl] [-dbg] [-e]
                [-dr] [-sd] [-ff FFLAGS] [-cf CFLAGS] [-sl {-lc,-lm}] [-mf]
                [-md] [-cs COMMONSRC] [-ef EXTRAFILES] [-exf EXCLUDEFILES]
                [-so] [-ad APPDIR] [-v] [--keep] [--zip ZIP] [--inplace]
                [--networkx] [--meson] [--mesondir]
                srcdir target

This is the pymake program for compiling fortran, c, and c++ source
files, such as the source files that come with MODFLOW. The program
works by building a directed acyclic graph of the module dependencies
and then compiling the source files in the proper order.

positional arguments:
  srcdir                Path source directory.
  target                Name of target to create. (can include path)

optional arguments:
  -h, --help            show this help message and exit
  -fc {ifort,mpiifort,gfortran,none}
                        Fortran compiler to use. (default is gfortran)
  -cc {gcc,clang,clang++,icc,icl,mpiicc,g++,cl,none}
                        C/C++ compiler to use. (default is gcc)
  -ar {ia32,ia32_intel64,intel64}, --arch {ia32,ia32_intel64,intel64}
                        Architecture to use for Intel and Microsoft compilers
                        on Windows. (default is intel64)
  -mc, --makeclean      Clean temporary object, module, and source files when
                        done. (default is False)
  -dbl, --double        Force double precision. (default is False)
  -dbg, --debug         Create debug version. (default is False)
  -e, --expedite        Only compile out of date source files. Clean must not
                        have been used on previous build. (default is False)
  -dr, --dryrun         Do not actually compile. Files will be deleted, if
                        --makeclean is used. Does not work yet for ifort.
                        (default is False)
  -sd, --subdirs        Include source files in srcdir subdirectories.
                        (default is None)
  -ff FFLAGS, --fflags FFLAGS
                        Additional Fortran compiler flags. Fortran compiler
                        flags should be enclosed in quotes and start with a
                        blank space or separated from the name (-ff or
                        --fflags) with a equal sign (-ff='-O3'). (default is
                        None)
  -cf CFLAGS, --cflags CFLAGS
                        Additional C/C++ compiler flags. C/C++ compiler flags
                        should be enclosed in quotes and start with a blank
                        space or separated from the name (-cf or --cflags)
                        with a equal sign (-cf='-O3'). (default is None)
  -sl {-lc,-lm}, --syslibs {-lc,-lm}
                        Linker system libraries. Linker libraries should be
                        enclosed in quotes and start with a blank space or
                        separated from the name (-sl or --syslibs) with a
                        equal sign (-sl='-libgcc'). (default is None)
  -mf, --makefile       Create a GNU make makefile. (default is False)
  -md, --makefiledir    GNU make makefile directory. (default is '.')
  -cs COMMONSRC, --commonsrc COMMONSRC
                        Additional directory with common source files.
                        (default is None)
  -ef EXTRAFILES, --extrafiles EXTRAFILES
                        List of extra source files to include in the
                        compilation. extrafiles can be either a list of files
                        or the name of a text file that contains a list of
                        files. (default is None)
  -exf EXCLUDEFILES, --excludefiles EXCLUDEFILES
                        List of extra source files to exclude from the
                        compilation. excludefiles can be either a list of
                        files or the name of a text file that contains a list
                        of files. (default is None)
  -so, --sharedobject   Create shared object or dll on Windows. (default is
                        False)
  -ad APPDIR, --appdir APPDIR
                        Target path that overides path defined target path
                        (default is None)
  -v, --verbose         Verbose output to terminal. (default is False)
  --keep                Keep existing executable. (default is False)
  --zip ZIP             Zip built executable. (default is False)
  --inplace             Source files in srcdir are used directly. (default is
                        False)
  --networkx            Use networkx package to build Directed Acyclic Graph
                        use to determine the order source files are compiled
                        in. (default is False)
  --meson               Use meson to build executable. (default is False)
  --mesondir            meson directory. (default is '.')

Note that the source directory should not contain any bad 
or duplicate source files as all source files in the source 
directory, the common source file directory (srcdir2), and 
the extra files (extrafiles) will be built and linked. 
Files can be excluded by using the excludefiles command 
line switch.

Examples:

Compile MODFLOW 6 from the root directory containing the 
source files in subdirectories in the src/ subdirectory:

$ mfpymake src/ mf6 --subdirs

Compile MODFLOW 6 in the bin subdirectory using the Intel 
Fortran compiler from the root directory containing the source 
files in subdirectories in the the src/ subdirectory:

$ mfpymake src/ mf6 --subdirs -fc ifort --appdir bin

Note that command line arguments for Fortran flags, C/C++ flags, and syslib libraries should be enclosed in quotes and start with a space prior to the first value (-ff ' -O3') or use an equal sign separating the command line argument and the values (-ff='-O3'). The command line argument to use an -O3 optimization level when compiling MODFLOW 6 in the bin/ subdirectory with the Intel Fortran compiler would be:

mfpymake ../src/ mf6 -mc --subdirs -fc ifort -ff='-O3' --appdir bin

From Python#

Script to compile MODFLOW 6#

When using the pymake object (Pymake()) only the positional arguments (srcdir, target) need to be specified in the script.

import pymake

pm = pymake.Pymake()
pm.srcdir = '../src'
pm.target = 'mf6'
pm.include_subdirs = True
pm.build()

It is suggested that optional variables required for successful compiling and linking be manually specified in the script to mininimize the potential for unsuccessful builds. For MODFLOW 6, subdirectories in the src subdirectory need to be included and ‘pm.include_subdirs = True’ has been specified in the script. Custom optimization levels and compiler flags could be specified to get consistent builds.

Non-default values for the optional arguments can specified as command line arguments. For example, MODFLOW 6 could be compiled using Intel compilers instead of the default GNU compilers with the script listed above by specifying:

python mymf6script.py -fc ifort -cc icc

Notes#

If gfortran is used to compile MODFLOW-based codes, the openspec.f and FILESPEC.inc (MT3DMS) files will automatically be changed to the following so that binary files are created properly using standard Fortran:

c -- created by pymake.py
CHARACTER*20 ACCESS,FORM,ACTION(2)
DATA ACCESS/'STREAM'/
DATA FORM/'UNFORMATTED'/
DATA (ACTION(I),I=1,2)/'READ','READWRITE'/
c -- end of include file

Use of STREAM access does not delete an existing unformatted file before opening it for writing. As a result, data from previous runs may exist in the file if the model is run for a shorter period of time. This does not apply to MODFLOW 6 simulations.

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