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¶
pymake can be used to compile MODFLOW 6 directly from the command line using
the Intel Fortran compiler ifort
from a subdirectory at the same level as
the src
subdirectory by specifying:
python -m pymake ../src/ ../bin/mf6 -mc --subdirs -fc ifort
To see help for running from command line, use the following statement.
python -m pymake -h
The help message identifies required positional arguments and optional arguments that can be provided to overide default values.
usage: __main__.py [-h] [-fc {ifort,mpiifort,gfortran,ftn,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] [--mb] [-mbd]
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,ftn,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-e, --expedite Only compile out of date source files.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, --makefile-dir 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)
--mb, --meson-build Use meson to build executable. (default is False)
-mbd, --mesonbuild-dir
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.
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 with the ifort
compiler
would be:
python -m pymake ../src/ ../bin/mf6 -mc --subdirs -fc ifort -ff='-O3'
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.