Introduction & motivation

When working on the command line such as in the Bash shell, applications support command line flags and parameters. Many programming languages offer support to conveniently deal with command line arguments out of the box, e.g., Python. However, quite a number of languages used in a scientific context, e.g., C/C++, Fortran, R, Matlab do not. Although those languages offer the necessary facilities, it is at best somewhat cumbersome to use them, and often the process is rather error prone.

Quite a number of libraries have been developed over the years that can be used to conveniently handle command line arguments. However, this complicates the deployment of the application since it will have to rely on the presence of these libraries.

ParameterWeaver has a different approach: it generates the necessary code to deal with the command line arguments of the application in the target language, so that these source files can be distributed along with those of the application. This implies that systems that don't have ParameterWeaver installed still can run that application.

Using ParameterWeaver is as simple as writing a definition file for the command line arguments, and executing the code generator via the command lnie. This can be conveniently integrated into a standard build process such as make.

ParameterWeaver currently supports the following target languages:

  • C/C++
  • Fortran 90
  • R

High-level overview & concepts

Parameter definition files

A parameter definition file is a CSV text file where each line defines a parameter. A parameter has a type, a name, a default values, and optionally, a description. To add documentation, comments can be added to the definition file. The types are specific to the target language, e.g., an integer would be denoted by int for C/C++, and by integer for Fortran 90. The supported types are documented for each implemented target language.

By way of illustration, a parameter definition file is given below for C as a target language, additional examples are shown in the target language specific sections:

int,numParticles,1000,number of particles in the system
double,temperature,273,system temperature in Kelvin
char*,intMethod,'newton',integration method to use

Note that this parameter definition file should be viewed as an integral part of the source code.

Code generation

ParameterWeaver will generate code to

  1. initialize the parameter variables to the default values as specified in the parameter definition file;
  2. parse the actual command line arguments at runtime to determine the user specified values, and
  3. print the values of the parameters to an output stream.

The implementation and features of the resulting code fragments are specific to the target language, and try to be as close as possible to the idioms of that language. Again, this is documented for each target language specifically. The nature and number of these code fragments varies from one target language to the other, again trying to match the language's idioms as closely as possible. For C/C++, a declaration file (.h) and a definition file (.c), while for Fortran 90 a single file (.f90 will be generated that contains both declarations and definitions.

Language specific documentation

C/C++ documentation

Data types

For C/C++, ParameterWeaver supports the following data types:

  1. int
  2. long
  3. float
  4. double
  5. bool
  6. char *

Example C program

Suppose we want to pass command line parameters to the following C program:

#include 
#include 
#include 
int main(int argc, char *argv[]) {
    FILE *fp;
    int i;
    if (strlen(out) > 0) {
        fp = fopen(out, "w");
    } else {
        fp = stdout;
    }
    if (verbose) {
        fprintf(fp, "# n = %d\n", n);
        fprintf(fp, "# alpha = %.16f\n", alpha);
        fprintf(fp, "# out = '%s'\n", out);
        fprintf(fp, "# verbose = %s\n", verbose);
    }
    for (i = 0; i < n; i++) {
        fprintf(fp, "%d\t%f\n", i, i*alpha);
    }
    if (fp != stdout) {
        fclose(fp);
    }
    return EXIT_SUCCESS;
}

We would like to set the number of iterations n, the factor alpha, the name of the file to write the output to out and the verbosity verbose at runtime, i.e., without modifying the source code of this program.

Moreover, the code to print the values of the variables is error prone, if we later add or remove a parameter, this part of the code has to be updated as well.

Defining the command line parameters in a parameter definition file to automatically generate the necessary code simplifies matters considerably.

Example parameter definition file

The following file defines four command line parameters named n, alpha, out and verbose. They are to be interpreted as int, double, char pointer and bool respectively, and if no values are passed via the command line, they will have the default values 10, 0.19, output.txt and false respectively. Note that a string default value is quoted. In this case, the columns in the file are separated by tab characters. The following is the contents of the parameter definition file param_defs.txt:

int n   10
double  alpha   0.19
char *  out 'output.txt'
bool    verbose false

This parameter definition file can be created in a text editor such as the one used to write C program, or from a Microsoft Excel worksheet by saving the latter as a CSV file.

As mentioned above, boolean values are also supported, however, the semantics is slightly different from other data types. The default value of a logical variable is always false, regardless of what is specified in the parameter definition file. As opposed to parameters of other types, a logical parameter acts like a flag, i.e., it is a command line options that doesn't take a value. Its absence is interpreted as false, its presence as true. Also note that using a parameter of type bool implies that the program will have to be complied as C99, rather than C89. All modern cmopiler fully support C99, so that should not be an issue. However, if your program needs to adhere strictly to the C89 standard, simply use a parameter of type int instead, with 0 interpreted as false, all other values as true. In that case, the option takes a value on the command line.

Generating code

Generating the code fragments is now very easy. If appropriate, load the module (VIC3):

$ module load parameter-weaver

Next, we generate the code based on the parameter definition file:

$ weave -l C -d param_defs.txt

A number of type declarations and functions are generated, the declarations in the header file cl_params.h, the defintions in the source file cl_params.c.

  1. data structure: a type Params is defined as a typedef of a struct with the parameters as fields, e.g.,
    typedef struct {
        int n;
        double alpha;
        char *out;
        bool verbose;
    } Params;
        
  2. Initialization function: the default values of the command line parameters are assigned to the fields of the Params variable, the address of which is passed to the function
  3. Parsing: the options passed to the program via the command line are assigned to the appropriate fields of the Params variable. Moreover, the argv array containing the remaining command line arguments, the argc variable is set apprppriately.
  4. Dumper: a function is defined that takes three arguments: a file pointer, a prefix and the address of a Params variable. This function writes the values of the command line parameters to the file pointer, each on a separate line, preceeded by the specified prefix.
  5. Finalizer: a function that deallocates memory allocated in the initialization or the parsing functions to avoid memory leaks.

Using the code fragments

The declarations are simply included using preprocessor directives:

  #include "cl_params.h"

A variable to hold the parameters has to be defined and its values initialized:

  Params params;
  initCL(&params);

Next, the command line parameters are parsed and their values assigned:

  parseCL(&params, &argc, &argv);

The dumper can be called whenever the user likes, e.g.,

  dumpCL(stdout, "", &params);

The code for the program is thus modified as follows:

#include 
#include 
#include 
#include "cl_params.h"
int main(int argc, char *argv[]) {
    FILE *fp;
    int i;
    Params params;
    initCL(&params);
    parseCL(&params, &argc, &argv);
    if (strlen(params.out) > 0) {
        fp = fopen(params.out, "w");
    } else {
        fp = stdout;
    }
    if (params.verbose) {
        dumpCL(fp, "# ", &params);
    }
    for (i = 0; i < params.n; i++) {
        fprintf(fp, "%d\t%f\n", i, i*params.alpha);
    }
    if (fp != stdout) {
        fclose(fp);
    }
    finalizeCL(&params);
    return EXIT_SUCCESS;
}

Note that in this example, additional command line parameters are simply ignored. As mentioned before, they are available in the array argv, argv[0] will hold the programs name, subsequent elements up to argc - 1 contain the remaining command line parameters.

Fortran 90 documentation

Data types

For Fortran 90, ParameterWeaver supports the following data types:

  1. integer
  2. real
  3. double precision
  4. logical
  5. character(len=1024)

Example Fortran 90 program

Suppose we want to pass command line parameters to the following Fortran program:

program main
use iso_fortran_env
implicit none
integer :: unit_nr = 8, i, istat
if (len(trim(out)) > 0) then
    open(unit=unit_nr, file=trim(out), action="write")
else
    unit_nr = output_unit
end if
if (verbose) then
    write (unit_nr, "(A, I20)") "# n = ", n
    write (unit_nr, "(A, F24.15)") "# alpha = ", alpha
    write (unit_nr, "(A, '''', A, '''')") "# out = ", out
    write (unit_nr, "(A, L)") "# verbose = ", verbose
end if
do i = 1, n
    write (unit_nr, "(I3, F5.2)") i, i*alpha
end do
if (unit_nr /= output_unit) then
    close(unit=unit_nr)
end if
stop
end program main

We would like to set the number of iterations n, the factor alpha, the name of the file to write the output to out and the verbosity verbose at runtime, i.e., without modifying the source code of this program.

Moreover, the code to print the values of the variables is error prone, if we later add or remove a parameter, this part of the code has to be updated as well.

Defining the command line parameters in a parameter definition file to automatically generate the necessary code simplifies matters considerably.

Example parameter definition file

The following file defines four command line parameters named n, alpha, out and verbose. They are to be interpreted as integer, double precision, character(len=1024) pointer and logical respectively, and if no values are passed via the command line, they will have the default values 10, 0.19, output.txt and false respectively. Note that a string default value is quoted. In this case, the columns in the file are separated by tab characters. The following is the contents of the parameter definition file param_defs.txt:

integer n   10
double precision    alpha   0.19
character(len=1024) out 'output.txt'
logical verbose false

This parameter definition file can be created in a text editor such as the one used to write the Fortran program, or from a Microsoft Excel worksheet by saving the latter as a CSV file.

As mentioned above, logical values are also supported, however, the semantics is slightly different from other data types. The default value of a logical variable is always false, regardless of what is specified in the parameter definition file. As opposed to parameters of other types, a logical parameter acts like a flag, i.e., it is a command line options that doesn't take a value. Its absence is interpreted as false, its presence as true.

Generating code

Generating the code fragments is now very easy. If appropriate, load the module (VIC3):

$ module load parameter-weaver

Next, we generate the code based on the parameter definition file:

$ weave -l Fortran -d param_defs.txt

A number of type declarations and functions are generated in the module file cl_params.f90.

  1. data structure: a type params_type is defined as a structure with the parameters as fields, e.g.,
        type :: params_type
            integer :: n
            double precision :: alpha
            character(len=1024) :: out
            logical :: verbose
        end type params_type
        
  2. Initialization function: the default values of the command line parameters are assigned to the fields of the params_type variable
  3. Parsing: the options passed to the program via the command line are assigned to the appropriate fields of the params_type variable. Moreover, the next variable of type integer will hold the index of the next command line parameter, i.e., the first of the remaining command line parameters that was not handled by the parsing function.
  4. Dumper: a function is defined that takes three arguments: a unit number for output, a prefix and the params_type variable. This function writes the values of the command line parameters to the output stream associated with the unit number, each on a separate line, preceded by the specified prefix.

Using the code fragments

The module file is included by the use directive:

  use cl_parser

A variable to hold the parameters has to be defined and its values initialized:

  type(params_type) :: params
  call init_cl(params)

Next, the command line parameters are parsed and their values assigned:

    integer :: next
    call parse_cl(params, next)

The dumper can be called whenever the user likes, e.g.,

  call dump_cl(output_unit, "", params)

The code for the program is thus modified as follows:

program main
use cl_params
use iso_fortran_env
implicit none
type(params_type) :: params
integer :: unit_nr = 8, i, istat, next
call init_cl(params)
call parse_cl(params, next)
if (len(trim(params % out)) > 0) then
    open(unit=unit_nr, file=trim(params % out), action="write")
else
    unit_nr = output_unit
end if
if (params % verbose) then
    call dump_cl(unit_nr, "# ", params)
end if
do i = 1, params % n
    write (unit_nr, "(I3, F5.2)") i, i*params % alpha
end do
if (unit_nr /= output_unit) then
    close(unit=unit_nr)
end if
stop
end program main

Note that in this example, additional command line parameters are simply ignored. As mentioned before, they are available using the standard get_command_argument function, starting from the value of the variable next set by the call to parse_cl.

R documentation

Data types

For R, ParameterWeaver supports the following data types:

  1. integer
  2. double
  3. logical
  4. string

Example R script

Suppose we want to pass command line parameters to the following R script:

if (nchar(out) > 0) {
    conn <- file(out, 'w')
} else {
    conn = stdout()
}
if (verbose) {
    write(sprintf("# n = %d\n", n), conn)
    write(sprintf("# alpha = %.16f\n", alpha), conn)
    write(sprintf("# out = '%s'\n", out), conn)
    write(sprintf("# verbose = %s\n", verbose), conn)
}
for (i in 1:n) {
    write(sprintf("%d\t%f\n", i, i*alpha), conn)
}
if (conn != stdout()) {
    close(conn)
}

We would like to set the number of iterations n, the factor alpha, the name of the file to write the output to out and the verbosity verbose at runtime, i.e., without modifying the source code of this script.

Moreover, the code to print the values of the variables is error prone, if we later add or remove a parameter, this part of the code has to be updated as well.

Defining the command line parameters in a parameter definition file to automatically generate the necessary code simplifies matters considerably.

Example parameter definition file

The following file defines four command line parameters named n, alpha, out and verbose. They are to be interpreted as integer, double, string and logical respectively, and if no values are passed via the command line, they will have the default values 10, 0.19, output.txt and false respectively. Note that a string default value is quoted, just as it would be in R code. In this case, the columns in the file are separated by tab characters. The following is the contents of the parameter definition file param_defs.txt:

integer n   10
double  alpha   0.19
string  out 'output.txt'
logical verbose F

This parameter definition file can be created in a text editor such as the one used to write R scripts, or from a Microsoft Excel worksheet by saving the latter as a CSV file.

As mentioned above, logical values are also supported, however, the semantics is slightly different from other data types. The default value of a logical variable is always false, regardless of what is specified in the parameter definition file. As opposed to parameters of other types, a logical parameter acts like a flag, i.e., it is a command line options that doesn't take a value. Its absence is interpreted as false, its presence as true.

Generating code

Generating the code fragments is now very easy. If appropriate, load the module (VIC3):

$ module load parameter-weaver

Next, we generate the code based on the parameter definition file:

$ weave -l R -d param_defs.txt

Three code fragments are generated, all grouped in a single R file cl_params.r.

  1. Initialization: the default values of the command line parameters are assigned to global variables with the names as specified in the parameter definition file.
  2. Parsing: the options passed to the program via the command line are assigned to the appropriate variables. Moreover, an array containing the remaining command line arguments is created as cl_params.
  3. Dumper: a function is defined that takes two arguments: a file connector and a prefix. This function writes the values of the command line parameters to the file connector, each on a separate line, preceded by the specified prefix.

Using the code fragments

The code fragments can be included into the R script by sourcing it:

  source("cl_parser.r")

The parameter initialization and parsing are executed at this point, the dumper can be called whenever the user likes, e.g.,

  dump_cl(stdout(), "")

The code for the script is thus modified as follows:

source('cl_params.r')
if (nchar(out) > 0) {
    conn <- file(out, 'w')
} else {
    conn = stdout()
}
if (verbose) {
    dump_cl(conn, "# ")
}
for (i in 1:n) {
    cat(paste(i, "\t", i*alpha), file = conn, sep = "\n")
}
if (conn != stdout()) {
    close(conn)
}

Note that in this example, additional command line parameters are simply ignored. As mentioned before, they are available in the vector cl_params if needed.

Octave documentation

Data types

For Octave, ParameterWeaver supports the following data types:

  1. double
  2. logical
  3. string

Example Octave script

Suppose we want to pass command line parameters to the following Octave script:

if (size(out) > 0)
    fid = fopen(out, "w");
else
    fid = stdout;
end
if (verbose)
    fprintf(fid, "# n = %.16f\n", prefix, params.n);
    fprintf(fid, "# alpha = %.16f\n", alpha);
    fprintf(fid, "# out = '%s'\n", out);
    fprintf(fid, "# verbose = %1d\n", verbose);
end
for i = 1:n
    fprintf(fid, "%d\t%f\n", i, i*alpha);
end
if (fid != stdout)
    fclose(fid);
end

We would like to set the number of iterations n, the factor alpha, the name of the file to write the output to out and the verbosity verbose at runtime, i.e., without modifying the source code of this script.

Moreover, the code to print the values of the variables is error prone, if we later add or remove a parameter, this part of the code has to be updated as well.

Defining the command line parameters in a parameter definition file to automatically generate the necessary code simplifies matters considerably.

Example parameter definition file

The following file defines four command line parameters named n, alpha, out and verbose. They are to be interpreted as double, double, string and logical respectively, and if no values are passed via the command line, they will have the default values 10, 0.19, output.txt and false respectively. Note that a string default value is quoted, just as it would be in Octave code. In this case, the columns in the file are separated by tab characters. The following is the contents of the parameter definition file param_defs.txt:

double  n   10
double  alpha   0.19
string  out 'output.txt'
logical verbose F

This parameter definition file can be created in a text editor such as the one used to write Octave scripts, or from a Microsoft Excel worksheet by saving the latter as a CSV file.

As mentioned above, logical values are also supported, however, the semantics is slightly different from other data types. The default value of a logical variable is always false, regardless of what is specified in the parameter definition file. As opposed to parameters of other types, a logical parameter acts like a flag, i.e., it is a command line options that doesn't take a value. Its absence is interpreted as false, its presence as true.

Generating code

Generating the code fragments is now very easy. If appropriate, load the module (VIC3):

$ module load parameter-weaver

Next, we generate the code based on the parameter definition file:

$ weave -l octave -d param_defs.txt

Three code fragments are generated, each in its own file, i.e., init_cl.m, parse_cl.m, and dump_cl.m.r.

  1. Initialization: the default values of the command line parameters are assigned to global variables with the names as specified in the parameter definition file.
  2. Parsing: the options passed to the program via the command line are assigned to the appropriate variables. Moreover, an array containing the remaining command line arguments is returned as the second value from parse_cl.
  3. Dumper: a function is defined that takes two arguments: a file connector and a prefix. This function writes the values of the command line parameters to the file connector, each on a separate line, preceded by the specified prefix.

Using the code fragments

The generated functions can be used by simply calling them from the main script. The code for the script is thus modified as follows:

params = init_cl();
params = parse_cl(params);
if (size(params.out) > 0)
    fid = fopen(params.out, "w");
else
    fid = stdout;
end
if (params.verbose)
    dump_cl(stdout, "# ", params);
end
for i = 1:params.n
    fprintf(fid, "%d\t%f\n", i, i*params.alpha);
end
if (fid != stdout)
    fclose(fid);
end

Note that in this example, additional command line parameters are simply ignored. As mentioned before, they are can be obtained as the second return value from the call to parse_cl.

Future work

The following features are plannen in future releases:

  • Additional target languages:
    • Matlab
    • Java
    Support for Perl and Python is not planned, since these language have facilities to deal with command line arguments in their respective standard libraries.
  • Configuration files are an alternative way to specify parameters for an application, so ParameterWeaver will also support this in a future release.

Contact & support

Bug reports and feature request can be sent to Geert Jan Bex.

System