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Python package for compiling MODFLOW-based applications
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modflowpy/pymake
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Python package for building MODFLOW-based programs from source files.
This is a python package for compiling MODFLOW-based and other Fortran, C, andC++ programs. The package determines the build order using a directed acyclicgraph and then compiles the source files using GNU compilers (gcc,g++,gfortran), Clang compilers (clang,clang++), or the Intel compilers (ifort,icl,icc,mpiifort).
pymake can be run from the command line or it can be called from within python.By default, pymake sets the optimization level, Fortran flags, C/C++ flags, andlinker flags that are consistent with those used to compile MODFLOW-basedprograms released by the USGS.
Note that if gfortran is used to compile MODFLOW-based codes, theopenspec.fandFILESPEC.inc (MT3DMS) files will automatically be changed to thefollowing so that binary files are created properly using standard Fortran:
c -- created by pymake.pyCHARACTER*20 ACCESS,FORM,ACTION(2)DATA ACCESS/'STREAM'/DATA FORM/'UNFORMATTED'/DATA (ACTION(I),I=1,2)/'READ','READWRITE'/c -- end of include fileWhen pymake is installed, amfpymake (ormfpymake.exe for Windows) program is installed.mfpymake can be used tocompile MODFLOW 6 from source files located on your computer directly from the command line usingthe Intel Fortran compilerifort from the root directory containing thesrc subdirectory by specifying:
mfpymake src/ mf6 -mc --subdirs -fc ifortTo see help for running from command line, use the following statement.
mfpymake -hThe help message identifies required positional arguments and optional arguments that can be provided to overridedefault 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 targetThis is the pymake program for compiling fortran, c, and c++ sourcefiles, such as the source files that come with MODFLOW. The programworks by building a directed acyclic graph of the module dependenciesand then compiling the source files in the proper order.positional arguments: srcdir Path source directory. target Name of target to create. (can include path)options: -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 overrides 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 None) --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 --subdirsCompile 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 binNote that command line arguments for Fortran flags, C/C++ flags, and syslib libraries should be enclosed in quotes andstart with a space prior to the first value (-ff ' -O3') or use an equal sign separating the command line argument andthe values (-ff='-O3'). The command line argument to use an-O3 optimization level when compiling MODFLOW 6 withtheifort compiler would be:
mfpymake src/ mf6 -mc --subdirs -fc ifort -ff='-O3'When using the pymake object (Pymake()) only the positional arguments(srcdir,target) need to be specified in the script.
importpymakepm=pymake.Pymake()pm.srcdir='../src'pm.target='mf6'pm.include_subdirs=Truepm.build()
It is suggested that optional variables required for successful compiling and linking be manually specified in thescript to mininimize the potential for unsuccessful builds. For MODFLOW 6, subdirectories in thesrc subdirectory needto be included and 'pm.include_subdirs = True' has been specified in the script. Custom optimization levels andcompiler 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 becompiled using Intel compilers instead of the default GNU compilers with the script listed above by specifying:
python mymf6script.py -fc ifort -cc iccWhen pymake is installed, amake-program (ormake-program.exe for Windows) program is installed.make-program canbe used to build MODFLOW 6, MODFLOW-2005, MODFLOW-NWT, MODFLOW-USG, MODFLOW-LGR, MODFLOW-2000, MODPATH 6, MODPATH 7,GSFLOW, VS2DT, MT3DMS, MT3D-USGS, SEAWAT, and SUTRA. Utility programs CRT, Triangle, and GRIDGEN can alsobe built.make-program downloads the distribution file (requires an internet connection), unzips the file, sets thepymake settings required to build the program, and compiles the program from the source files. Optional pymake commandline arguments can be used to customize the build (-fc,-cc,--fflags, etc.). For example, MODFLOW 6 could bebuilt using intel compilers and anO3 optimization level by specifying:
make-program mf6 -fc=ifort --fflags='-O3'Seepymake Read the Docs for moreinformation.
To install pymake using pip type:
pip install mfpymakeTo install pymake using conda type:
conda install -c conda-forge mfpymakeTo install the latest pymake release directly from the git repository type:
pip install https://github.com/modflowpy/pymake/zipball/masterTo update your version of pymake with the latest development version from the git repository type:
pip install https://github.com/modflowpy/pymake/zipball/develop --upgradeAbout
Python package for compiling MODFLOW-based applications